NADIA - Missing Value-Aware Differential Abundance Analysis of DIA Proteomics Data
Provides an end-to-end workflow for differential abundance analysis of protein quantification data, with particular attention to missing values in data-independent acquisition (DIA) proteomics. Quantification reports exported from Spectronaut, DIA-NN and Proteome Discoverer for TMT and label-free experiments (DDA/DIA) are converted into a common data structure, normalised, optionally batch-corrected, imputed and analysed using limma or limpa. The package includes individual and two-stage imputation strategies that treat values assumed to be missing at random and missing not at random separately. Data-driven functions evaluate and rank normalisation and imputation workflows using simulated missingness or spike-in datasets with known ground truth, allowing method selection to be justified for each dataset. Results can be explored through interactive Highcharts visualisations, static ggplot2 and ComplexHeatmap figures, and sortable tables.
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softwareproteomicsmassspectrometrydifferentialexpressionnormalizationqualitycontrolbatcheffect
6.12 score 51 scripts 46 downloadsepiwraps - epiwraps: Wrappers for plotting and dealing with epigenomics data
A set of wrappers to facilitate working with epigenomics data. Includes in particular wrappers for producing multitrack single-regions plots, enrichment heatmaps, bigwig generation, normalization, etc. The focus was put on a simple yet flexible interface.
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epigeneticssequencingnormalizationvisualization
5.83 score 210 scripts
prolfqua - Proteomics Label Free Quantification
The prolfqua package integrates essential steps of the mass spectrometry based label free quantification data analysis workflow: quality control, data normalization, protein aggregation, modeling, hypothesis testing and sample size estimation. We use prolfqua to : develop highly customizable, visually appealing, and interactive data analysis reports in pdf or HTML format; to visualize and model simple experimental designs with a single explanatory variable and complex experiments with multiple factors; to benchmark data acquisition, data preprocessing or data modeling methods. We developed and improved the package by applying the "Eating your own dog food" principle, when analysing dozens of proteomics datasets.
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massspectrometryproteomicsmetabolomicsnormalizationpreprocessingqualitycontrol
5.77 score 1 stars 81 scriptsmesa - Methylation Enrichment Sequencing Analysis
A package for the analysis of methylation enrichment sequencing data (e.g. MBD-seq or MEDIP-seq). This allows for the window-based evaluation of methylation levels (using the 'qsea' package), including functions for determining differentially methylated regions. Many functions are provided for tidyverse style modification of the qseaSet objects originally defined in 'qsea'.
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sequencingdnamethylationcpgislandpreprocessingnormalizationqualitycontrolvisualizationcopynumbervariationdifferentialmethylationcoveragechipseqchiponchip
5.28 score 14 scriptsGeneTrackR - Genomic Track Visualization and Haplotype Analysis
Provides tools to read, validate, query, transform, write, and visualize gene annotations, genomic signal tracks, and variant tracks using a shared genomic coordinate framework. Supports GenePred, GTF, GFF3, and BED annotations; bedGraph, wig, and bigWig signals; VCF variants; integrated locus visualization; haplotype construction; phenotype association; linkage disequilibrium; haplotype refinement; and variant-effect analysis. The package interoperates with GenomicRanges objects and uses a pure-R signal I/O layer so core workflows do not require a compiled extension.
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softwaregenomeannotationvariantannotationcoveragesequencingvisualization
5.08 score 20 scriptsMagellanNTK - Configurable Shiny data-analysis workflows
MagellanNTK (Magellan Navigation ToolKit) is a collection of Shiny modules which provide the basis for a generic workflow manager for data processing tools with several steps. It works in combination with any package which implements data processing pipelines compliant with MagellanNTK such as Prostar2.
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softwareguishinyappsworkflowstep
4.95 score 42 scripts
PhiSpace - Continuous cell state annotation for single-cell and spatial omics data
Continuous phenotyping of bulk, single-cell and spatial omics data using partial least squares regression. The methods are described in Mao et al. (2025) <doi:10.1186/s13059-025-03755-8> and Mao et al. (2026) <doi:10.1016/j.crmeth.2026.101483>.
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softwaresinglecellspatialsequencingtranscriptomicsgeneexpressioncellbiologyclassificationregressiondimensionreductionclustering
4.87 score 62 scriptsSpatialData.plot - SpatialData visualization
Visualization suit for 'spatialdataR'. Current functionality includes handling of multiscale 'images', visualizing 'labels', 'points', and 'shapes'. For the latter, POINT, POLYGON, and MULTIPOLYGON geometries are supported. For all but 'images', there is support to pass information from annotation 'tables' as aesthetics (e.g., 'colData' or 'assay' data).
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spatialsinglecellvisualizationinfrastructureimmunooncologygeneexpressiontranscriptomics
4.81 score 26 scriptsOmicsLake - OmicsLake: Versioned, On-Disk Omics Data Management for Bioconductor
A lightweight framework for versioned, on-disk omics data management using DuckDB, Arrow, and Parquet. It provides read/write-style functions, snapshots, and version-aware dataset lineage for tracked or explicitly annotated workflows. Adapters preserve supported Bioconductor containers, including SummarizedExperiment and MultiAssayExperiment, while retaining queryable tabular components.
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infrastructuredataimportdatarepresentation
4.69 score 41 scriptsstrainspy - Strain Level Microbiome Wide Association Studies
Fits statistical models to detect microbial strains associated with a phenotype. For small sample sizes, models can be fitted using empirical Bayes maximum a posteriori (MAP) priors to improve detection power. Supports various experimental design scenarios, including repeated measures.
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softwaremicrobiomemetagenomicsmicrobialstraindifferentialexpressionregressionexperimentaldesignsequencing
4.66 score 46 scripts
GenomicDataStream - Read Genomic Data Files (VCF, BCF, BGEN, PGEN, BED, H5AD) into R/Rcpp in Chunks
Read genomic data files (i.e. VCF, BCF, BGEN, PGEN, BED, H5AD, DelayedArray) into R/Rcpp in chunks for analysis with Armadillo / Eigen / Rcpp libraries. Modern datasets are often too big to fit into memory, and many analyses operate on a small chunk features at a time. GenomicDataStream provides interfaces at both the C++ and R levels for out-of-core analysis.
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dataimportinfrastructureopenblaszlibcurlcpp
4.65 scoreSPAROscore - A package to compute gene signature scores from transcriptomics data
SPAROscore is a gene signature scoring method designed to be robust across diverse gene expression datasets. SPAROscore adapts to varying levels of sparsity, allowing signature scores to be efficiently computed across bulk, single-cell, and spatial transcriptomic datasets. The resulting scores quantify the relative expression of a gene signature compared with the background expression of each sample/cell/domain, making the scores straightforward to interpret biologically. Internally, SPAROscore ranks genes within each column and computes the Spearman footrule distance between the observed ranks of the signature genes and a background gene expression rank estimated from the geometric mean expression of the sample, cell, or spatial domain.
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geneexpressionsinglecellspatialtranscriptomicsgenesetenrichmentpathwayssoftware
4.52 score
CMEnt - Characterization of Methylation using positional ENTanglement
CMEnt implements a correlation-based method for identifying Differentially Methylated Regions (DMRs) from genomic seeds, commonly Differentially Methylated Positions (DMPs). The package expands regions around significant seeds considering both statistical significance and biological relevance of methylation changes. It supports array-based (450K, EPIC, EPICv2) and NGS methylation data through tabix-indexed files, provides DMR interaction analysis via motif similarity, and includes comprehensive visualization tools including circos plots and beta value heatmaps.
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dnamethylationdifferentialmethylationepigeneticsstatisticalmethodworkflowstepannotationmethylationarraymotifannotation
4.49 score 13 scriptsgDRplots - 'gDRplots'
gDRplots provides static visualization functions and dedicated helpers for the gDR drug response platform. Designed for high-throughput screening (HTS), pharmacogenomics, and chemical genomics research, it enables comprehensive analysis of single-agent, co-dilution, and drug combination cell viability assays. The package supports quality control (plate layouts, control mapping), data normalization inspection, dose-response curves, distribution boxplots, drug synergy heatmaps with overlaid isobolograms, and combination index plots. Additionally, it integrates with PRISM and DepMap datasets to generate volcano plots and correlation scatter plots for molecular feature associations.
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softwarevisualizationqualitycontrolnormalizationcellbasedassayspharmacogenomicsmicrotitreplateassay
4.49 score 26 scripts
SpaMTP - Spatial Metabolomics and Multi-Omics Analysis
Provides analysis, annotation, visualisation, and multi-omic integration methods for spatial metabolomics data. SpaMTP interoperates with Cardinal and SpatialExperiment containers, with optional Seurat conversion; supports indexed accurate-mass annotation using versioned RaMP resources; and implements spatial feature analysis, pathway enrichment, pathway-network visualisation, and alignment with spatial transcriptomics data.
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massspectrometryimagingmassspectrometrymetabolomicsspatialtranscriptomicsalignment
4.45 score 20 scriptsscMAGeCK - Identify genes associated with multiple expression phenotypes in single-cell CRISPR screening data
scMAGeCK is a computational model to identify genes associated with multiple expression phenotypes from CRISPR screening coupled with single-cell RNA sequencing data (e.g. CROP-seq, Perturb-seq). It provides two complementary modules: a rank-based test (scMAGeCK-RRA) that links a perturbation to a single marker or gene signature, and a linear-regression test (scMAGeCK-LR) that estimates the effect of each perturbation on the expression of all genes. The package also estimates single-cell perturbation-response scores to capture heterogeneous perturbation effects across individual cells.
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crisprsinglecellrnaseqsequencingpooledscreenstranscriptomicsgeneexpressionregressioncpp
4.43 score 68 scripts
lantern - Ancestry-Specific Rare Variant Association Analysis
Ancestry-specific rare variant burden testing for admixed populations. Splits genotype dosages by local ancestry (as inferred by 'RFMix') into per-ancestry dosages, using either phased haplotypes or unphased genotypes with shrinkage toward global ancestry, and writes them to 'SeqArray' GDS files. Ancestry-stratified gene-level tests are then run with the 'SMMAT' framework of Chen et al. (2019) <doi:10.1016/j.ajhg.2018.12.012> as implemented in 'GMMAT', and the per-ancestry p-values are combined with the Cauchy combination test of Liu and Xie (2020) <doi:10.1080/01621459.2018.1554485>.
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softwaregeneticsgenomewideassociationsnpvariantannotation
4.41 score 13 scriptssciNOME - Region-Centric Integration for Single-Cell Multi-Omics
Provides an end-to-end pipeline for processing RNA, DNA methylation, and chromatin accessibility data at the single-cell level. It features ultra-fast data aggregation, quality control, dimensionality reduction, and multi-omics integration based on genomic regions. Additionally, it offers extensive publication-ready visualization tools for downstream analysis.
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softwaresinglecellepigeneticstranscriptomicsdnamethylationdifferentialexpressiondimensionreductionclusteringqualitycontrol
4.41 scorePscanR - Motif Enrichment Analysis of Regulatory DNA Sequences
R implementation of the 'Pscan' algorithm for motif enrichment analysis in regulatory DNA sequences, based on Zambelli et al. (2009) <doi:10.1093/nar/gkp464>. 'PscanR' scans a set of DNA sequences (e.g., promoters) from co-regulated or co-expressed genes, using transcription factor binding motifs from databases such as JASPAR. It identifies significantly enriched motifs, providing thus hints on which transcription factors could be common regulators of the genes studied, together with the location of their candidate binding sites in the sequences.
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sequencematchingtranscriptiongeneregulationmotifannotation
4.30 score 7 scriptsKODAMA - Knowledge Discovery by Accuracy Maximization
Knowledge Discovery by Accuracy Maximization using KNN or SIMPLS followed by latent-space LDA. The portable source package vendors the MIT-licensed CPU implementation from the standalone 'kodama-cpp' library. Optional developer builds can link the same public interface to NVIDIA CUDA or Apple Metal backends. Reusable nearest-neighbor graphs, graph-aware visualization, preprocessing, and adapters for common single-cell containers are provided.
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softwareclassificationclusteringdimensionreductiongpupreprocessingvisualizationsinglecellspatialcpp
4.24 score 497 downloadsIntegratedLearner - Integrated Multi-Omics Learning for Survival and Other Outcomes
Provides a unified interface for multi-omics prediction using early and late fusion for continuous, binary, multiclass, and survival outcomes. It supports both MultiAssayExperiment and PCL-style inputs, performs input validation and feature/sample harmonization across layers, and provides model fitting, prediction, plotting, and variable-importance utilities.
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softwareclassificationsurvivalmicrobiomeopenjdk
4.22 score 11 scriptsmgcca - Generalized Canonical Correlation Analysis with Missing Individuals
Implements Generalized Canonical Correlation Analysis (GCCA) with missing individuals (whole missing rows; van de Velden and Bijmolt, 2006) for multi-block omics integration. The package operates directly on HDF5 matrices via the BigDataStatMeth C++ API to scale computations; R functions are thin wrappers around the C++ core.
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statisticalmethoddimensionreductionprincipalcomponentgeneexpressiontranscriptomicsepigeneticsmetabolomicsopenblascurlopensslcppopenmp
4.20 score 6 scriptspdactrace - Stage-Aware PDAC Atlas and Prospectively Frozen Tissue-to-Serum Biomarker Audit Framework
pdactrace implements a transparent, deterministic claim-audit framework for stage-aware pancreatic ductal adenocarcinoma (PDAC) tissue-to-blood biomarker evidence. It integrates per-stage trajectory matching across bulk RNA-seq, tissue proteomics, single-cell origin, serum proteomics, and pancreatitis context, with explicit anchor-enrichment evaluation against a curated external reference set. The framework comprises a 12-template competitive trajectory catalog, a 3-axis + 2-gate reference score, an Evidence Math layer, TRACE-D tissue-to-serum directional evidence concordance, claim-tier classification, and weight-robustness and Pareto support audits. A prespecification layer supports freezing candidate scores, directions and a decision rule under a content hash before outcome labels are opened, with a distinct inconclusive terminal state when a frozen gate fails. Scope is deliberately PDAC-specific: the bundled atlas, the anchor reference set and every validated claim are PDAC, and no result is claimed for any other disease. Separately, no supervised classifier is trained or shipped, because validated non-circular early-detection ground truth is unavailable in PDAC.
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softwarebiomedicalinformaticsclassificationtranscriptomicsproteomicsgeneexpressiondifferentialexpressionsinglecellvisualizationannotation
4.20 scoresbivar - Test for Spatial Bivariate Association Across Omics Types
Sbivar implements a suite of tests for Spatial BIVARiate association across omics modalities, with possibly disjoint coordinate sets. Implemented tests are generalized additive models (GAMs), modified t-test, bivariate Moran's I and Gaussian processes (GPs). Both single images and replicated experiments can be analysed.
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transcriptomicsspatialproteomicsmetabolomicsopenblascpp
4.18 score 4 scripts
tTEscanR - A user-friendly integrative R package for quantifying and visualizing translation efficiency from sequencing data in diverse biological systems
Translation elongation is dependent on codon-anticodon interactions, with suitable nucleotide pairing being essential for efficient translation. To quantify this relationship, we previously developed a computational pipeline (GitHub - wgao688/sc_tRNA_mRNA) that uses mRNA codon usage relative to tRNA anticodon availability as a proxy for theoretical translation efficiency (tTE). Here, we introduce tTEscanR, a powerful and user-friendly R-based package that extends this approach to quantify translation efficiency from both bulk and single-cell sequencing data. tTEscanR is a versatile tool for exploring translation efficiency in diverse cellular processes, disease mechanisms, and therapeutic development. It also features an advanced visualization module to generate high-quality plots, enhancing result interpretation and communication.
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softwareepitranscriptomicstranscriptomicsgeneexpressiongeneregulationsequencingsinglecellcellbasedassays
4.15 score 6 scriptsremart - Reimplementation of the 'biomaRt' Package Using Modern Ensembl APIs
This package aims to offer a drop-in replacement to biomaRt using the same interface but the more modern and better maintained APIs provided by Ensembl. It provides an easy solution for compatibility with minimal changes for existing projects and packages. New projects may prefer to use another approach which is not constrained by the need for backward compatibility with biomaRt.
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annotationdataimport
4.13 score 4 scriptsfaissR - FAISS-Backed Nearest Neighbours, kNN Models, and k-Means
Native nearest-neighbour search, k-nearest neighbour prediction, and k-means helpers for large dimensionality reduction workflows in high-throughput biological data analysis, including single-cell, flow cytometry, imaging, and mass spectrometry applications. Functional native builds require the FAISS C++ library, including CPU-only indexes, and can optionally use FAISS GPU indexes with NVIDIA cuVS integration or direct RAPIDS cuVS/CUDA indexes on NVIDIA machines. CPU-only systems do not need NVIDIA libraries, but NVIDIA CUDA/cuVS libraries are mandatory when a GPU-enabled build is explicitly requested. Unsupported WebAssembly and Bioconductor staging platforms may build diagnostic-only stubs that report the unavailable native functionality. Supervised kNN models use knn(Xtrain, Ytrain) and predict(), or knn(Xtrain, Ytrain, Xtest) for immediate prediction. Class probabilities are returned through predict(type = "prob") for kNN classification models.
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softwareinfrastructuregpusinglecellflowcytometrymassspectrometryimagingmassspectrometryproteomicsclusteringdimensionreductionclassificationfunctionalpredictionopenblasfortrancppopenmp
4.11 score
BamScaleR - Bioconductor-Friendly Multithreaded BAM Processing
Multithreaded sequential BAM processing built on top of the ompBAM C++ engine. BamScaleR provides user-friendly BAM read and scan interfaces designed for compatibility with existing Bioconductor workflows.
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softwaredataimportsequencingcoveragealignmentqualitycontrolzlibcppopenmp
4.08 score
bppg - Bipartite peptide-protein graphs
This package contains functionality to create and characterize bipartite graphs that model the relationship between peptides and proteins in bottom-up proteomics. With these graphs, protein ratios (fold change between two sample groups) are calculated from the respective measured peptide ratios. The main aim is to make use of quantitative information contained in shared peptides and making it possible to quantify proteins without shared peptides. Further, the package offers general analysis of peptide and protein relationships using bipartite graphs and visualization for these graphs.
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proteomicsgraphandnetworkmassspectrometrymultiplecomparisonvisualization
4.08 score 1 scriptsreglScatterplotR - Interactive WebGL Scatterplots for Biological Data Exploration
Lightweight 'htmlwidgets' interface to the JavaScript 'regl-scatterplot' library, rendering millions of two-dimensional points in the browser via WebGL. Designed for exploratory visualisation of single-cell, spatial transcriptomics and other high-dimensional biological data. Features include synchronised pan/zoom across multiple plots, categorical and continuous colour mapping, lasso selection, range and category filtering, PNG/SVG/PDF export, and Shiny integration. The widget works in the 'RStudio' Viewer, standalone HTML files, Shiny applications and Jupyter notebooks running the 'IRkernel'.
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softwarevisualizationsinglecellspatialgeneexpressiontranscriptomicsdimensionreductionshinyapps
4.08 score 15 scriptsfastPLS - Fast Partial Least Squares for High-Dimensional Data
Fast implementations of partial least squares models for high-dimensional regression and classification. The package provides compiled implementations of PLS-SVD, SIMPLS, OPLS and kernel PLS, together with truncated singular value decomposition backends, discriminant classifiers, cross-validation utilities and optional CUDA or Apple Metal acceleration when the required system libraries are available. Compact latent prediction and memory-aware numerical routes support analyses with large predictor or multivariate-response matrices.
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softwaredimensionreductionclassificationregressiongenepredictiongeneexpressionmetabolomicssinglecellgpuopenblascpp
4.04 score 5 scripts 198 downloadsmethylTFR - Quantification of DNA Methylation Signatures in TFBS
methylTFR is an extensive R package designed specifically for analyzing DNA methylation signatures within transcription factor binding sites (TFBS) across diverse genomic annotations. It enhances methylation analysis by calculating a bias-corrected 'deviation' in methylation levels, leveraging GC bias distribution and frequency data. This package offers a variety of functions that facilitate the motif activity exhibiting diverse methylation patterns across distinct samples or cells.
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softwarednamethylationsinglecellstatisticalmethodgeneregulationepigeneticstranscriptionsequencingwholegenomedifferentialmethylationmotifannotationmotifdiscoverycoverage
3.90 score 7 scripts
QuickBLAST - High-Performance Sequence Alignment using BLAST and Apache Arrow
A BLAST Wrapper to call BLAST directly from R (interoperable and without Sys.call()) coupled with Apache Arrow's columnar format with parquet, IPC and csv file support.
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softwarealignmentsequencematchingsequencingdataimportlibunwindcppopenmp
3.90 score 3 scriptsGDSAnnotator - Whole-genome variant annotation data manipulation using GDS files
Fast and memory-efficient manipulation of whole-genome variant annotation data stored in Genomic Data Structure (GDS) files. The annotated GDS (aGDS) format introduced by FAVOR stores the FAVOR annotations of the variants together with the genotypes in one SeqArray GDS file. This package generalizes the format to annotation GDS files of any source, with or without genotypes. Annotation resources and annotator outputs, including FAVOR, gnomAD, Ensembl VEP and SnpEff, are converted into compact SeqArray-compatible GDS files with random access. Variants can be given as chr-pos-ref-alt strings, data frames, GRanges objects, VCF files or objects, or SeqArray GDS files. They are annotated by querying the annotation files, and the annotations can be written back into a genotype GDS file. Summary statistics of the variants and their annotations are computed in a single pass over a file and rendered as a VEP/SnpEff-like report. The package is intended for large-scale whole-genome sequencing studies.
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infrastructuredatarepresentationdataimportsequencingwholegenomegeneticsannotationvariantannotationgenomeannotationgenomicvariation
3.88 score
PACE - Proximity-Associated Changes in Expression for Spatial Transcriptomics
PACE (Proximity-Associated Changes in Expression) is a hierarchical empirical Bayes framework that quantifies how a cell's gene expression changes with proximity to specific neighbouring cell types in imaging-based spatial transcriptomics such as Xenium and CosMx. It fits negative binomial mixed models with partial pooling across cell types, corrects for transcript contamination between adjacent cells with a per-cell ambient term, and decomposes expression variance into cell-type identity, spatial cell state, contamination, and residual components. Input and output follow SpatialExperiment conventions.
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spatialtranscriptomicsgeneexpressionsinglecellregressionbayesiandifferentialexpressionsoftwarecpp
3.85 score 5 scripts 10 downloadsDgeaHeatmap - Implementation of Functions to Analyze Nanostring and Other Data for DGE and to Generate Heatmaps
Package for data extraction from Nanostring GeoMx DSP data, also works for other data. Simple functions for Differential Expression Analysis. User-friendly and highly customizable functions for heatmap generation.
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clusteringdifferentialexpressionsoftware
3.85 score 1 starscellpaintr - Perturbation Analysis for Cell Painting Data
This package load cell painting data into R and preprocess feature to make them ready for machine learning. We use random forest to predict cell perturbations from CellProfiler features. We summarize the results in a volcano plot.
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singlecellsoftwareclassificationfeatureextractionpreprocessingvisualization
3.85 score 1 stars 2 scriptsMsBackendParquet - Apache Parquet-based Mass Spectrometry Data Backend
Mass spectrometry (MS) data backend for the Spectra Bioconductor package that stores and retrieves spectra and peak data from on-disk Apache Parquet datasets. Spectra metadata together with m/z and intensity values are stored in a columnar Parquet format that supports compression, dictionary encoding and Hive-style partitioning. Datasets are written with the Apache Arrow R bindings and queried with DuckDB. Spectra variables are held in a bounded in-memory index so that filtering and metadata access are fast while peak data remains on disk.
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infrastructuremassspectrometrymetabolomicsproteomicsdataimport
3.82 score 11 scriptsscProkaR - Microbial Single-Cell RNA-Seq Analysis for Bacterial Systems
scProkaR provides a SingleCellExperiment-centred workflow for microbial single-cell RNA sequencing data. It standardises bacterial input objects from count matrices, 10x Genomics directories or Seurat objects, and computes prokaryote-specific quality-control metrics such as ribosomal RNA fraction. It performs batch integration with several backends and scores the resulting embeddings with scIB-inspired benchmarking metrics. It also supports pseudobulk differential expression with edgeR and Time Aware Trajectory Analysis (TATA), a time-informed trajectory abstraction for perturbation time courses.
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softwaresinglecellrnaseqtranscriptomicsgeneexpressiondifferentialexpressionclusteringgraphandnetworkqualitycontrolmultiplecomparisonnormalizationbatcheffectdimensionreductiontimecoursemicrobiomesequencingvisualization
3.78 scoreexposomeSC - Single-Cell Exposome-Wide Association Studies with Cross-Omic Network Inference
A framework for cell-type-specific exposome-wide association studies (sc-ExWAS) that bridges donor-level environmental exposures with single-cell resolution gene expression. The package extends SingleCellExperiment to store exposure measurements alongside transcriptomic data, and implements donor-level raw-count pseudobulk inference to avoid cellular pseudoreplication (Squair et al. 2021 <doi:10.1038/s41467-021-25960-2>). The default workflow uses robust edgeR quasi-likelihood models, exposure-independent expression-support filtering, complete-transcriptome offsets, design-rank diagnostics, and global multiplicity correction. Additional modules support dose-response modelling, exposure mixtures, cross-cohort synthesis, and cell-level gene-protein coupling. Exploratory decomposition and mediation utilities report model-based associations; they do not by themselves identify causal effects.
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singlecellgeneexpressiondifferentialexpressiontranscriptomicscellbiologystatisticalmethodnetworknetworkinferenceregression
3.78 scoreloopQTL - Anchor-Restricted Loop QTL Mapping from Hi-C
Maps chromatin loop QTLs by testing whether genotype at a loop's anchors associates with the loop's contact strength across samples. Reads .hic files via strawr, builds an exact-coordinate consensus loop set, normalizes contact strength across samples via band-wise quantile normalization in the style of BNBC (implemented on top of preprocessCore), and runs anchor-restricted SNP-by-loop regressions with MatrixEQTL. Intra-chromosomal loops only; no FDR or lead-SNP selection (left to the user).
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softwaredna3dstructureepigeneticshicquantitativetraillocussnp
3.78 scorefastEmbedR - Native UMAP and Interpolation-Based t-SNE Embeddings
A native float32 UMAP implementation and a configurable interpolation-based t-SNE implementation for embeddings from data matrices or precomputed nearest-neighbor indices and distances. One-call workflows use package-native CPU HNSW and Apple Metal exact or IVF-Flat search. Optional CUDA support links directly to FAISS GPU and the RAPIDS cuVS C API while retaining nearest-neighbor results on the device. Preprocessing, graph or affinity construction, fixed-reference transform, and layout optimization use native code with explicit CPU, Metal, and CUDA backend reporting. UMAP exposes neighborhood, metric, graph mode, backend, seed, and preprocessing controls, while optimizer controls such as epochs, minimum distance, spread, learning rate, repulsion, and negative sampling follow a recorded release policy rather than a general-purpose sweep API. Optional graph utilities support downstream Louvain, Leiden, and Walktrap community detection.
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softwareinfrastructurepreprocessingdimensionreductionvisualizationclusteringsinglecellflowcytometrygeneexpressiongpucpp
3.78 scorespbtest3 - Test Single Package Builder
What the package does (one paragraph).
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softwaredataimportbiologicalquestion
3.78 score 2 scriptsMOTL - Multi-omics matrix factorization with transfer learning
A transfer learning algorithm for multi-omics matrix factorization called 'MOTL' (Multi-Omics Transfer Learning). 'MOTL' is a Bayesian transfer learning method, based on 'MOFA'. 'MOTL' infers latent factor values for a multi-omics target dataset, consisting of a small number of samples, by incorporating latent factor values already inferred with a 'MOFA' factorization of a large, heterogeneous, learning dataset.
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dimensionreductionfeatureextractionbayesiannormalization
3.70 score
orthoRibbon - Ribbon-Diagram Visualization of Orthologous Genes Across Species
OrthoRibbon is a visualization toolkit for displaying orthologous gene relationships across species using ribbon-based diagrams. It enables intuitive comparison of conserved genes and genomic correspondence between chromosomes or genomic regions. The package supports flexible input formats and produces publication-quality figures for comparative genomics and evolutionary analysis.
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visualizationannotationcomparativegenomics
3.65 scoreGeneSCARAB - Gene Set Circular Analysis for Rhythms Ascertainment in Bioprocesses
GeneSCARAB includes a range of features designed to enable a robust and comprehensive analysis of the circular distributions of biomolecules (genes, proteins, metabolites, ...) associated with bioprocesses in any species. It is specifically designed for circadian omics studies and facilitates data organization, statistical analysis, and the visualization of results. It works with the output of standard rhythm detection software, such as CircaCompare, MetaCycle or RAIN.
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geneticsmultiplecomparisonproteomicssoftwaresystemsbiologytimecoursetranscriptomicsstatisticalmethod
3.65 score
ggwas - Modern 'ggplot2' Visualizations for Genome-Wide Association Studies
Create publication-ready visualizations for genome-wide association studies. Provides 21 plot types including Manhattan, value Manhattan, QQ, Miami, locus zoom, PheWAS, colocalization, fine-mapping, genetic correlation, SNP density, and density-signal comparison plots. Reads PLINK, REGENIE, GCTA, and GEMMA formats natively. All plot functions return 'ggplot2' objects for full customization. Smart downsampling handles datasets with 10 million+ variants.
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visualizationgenomewideassociationannotationdataimportsoftware
3.60 score 7 scriptsTweedieverse - Differential Analysis of Omics Data Based on the Tweedie Distribution
A toolkit for differential analysis of omics data. Implements a CPLM-based statistical workflow built on the Tweedie distribution. Unlike traditional single-omics tools, Tweedieverse is technology-agnostic and can be applied to both count and continuous measurements arising from diverse high-throughput technologies (e.g. transcript abundances from bulk and single-cell RNA-Seq studies in the form of UMI counts or non-UMI counts, microbiome taxonomic and functional profiles in the form of counts or relative abundances, and compound abundance levels or peak intensities from metabolomics and other mass spectrometry-based experiments, among others). The software includes multiple customization options such as the inclusion of random effects and multiple covariates along with several data exploration capabilities and visualization modules in a unified estimation umbrella.
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differentialexpressionsoftwarevisualizationcellbasedassaysatacseqmicrobiomemassspectrometrysinglecellmetabolomicsmetagenomicsworkflowstepmultiplecomparisonnormalizationregressionrnaseq
3.60 score
RAMEN - Regional Association of Methylome variability with the Exposome and geNome
RAMEN is an R package which goal is to identify Variable Methylated Loci (VML) in microarray DNA methylation data and then, using genome and exposome data, identify which individual genetic (G) or environmental (E) or joint (G+E or GxE) model better explains the VML variability. This package provides estimates of genetic and environmental contribution for each VML, allowing researchers to gain insights into the complex interplay between genetics, environment and DNA methylation.
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dnamethylationgenomewideassociationepigeneticsregressionsnpmicroarraymethylationarraygeneticvariability
3.60 score 3 scripts
MRManalyzeR - Process and Analyse Targeted LC-MS Lipidomics and Metabolomics Data
Reproducible post-acquisition processing of targeted LC-MS/MS lipidomics and metabolomics results exported from Waters TargetLynx or from Skyline, or supplied as a plain sample-by-analyte matrix. Reads the quantitative result tables, integrates them with sample and feature metadata, and applies configurable signal filtering (SNR, LOD or LOQ), blank filtering, batch correction, normalisation, internal-standard and volume adjustment of vendor-reported concentrations, and missing-value imputation. Each step is an exported function acting on a struct DatasetExperiment; a complete workflow can additionally be driven from a single YAML configuration via runMRManalyzeR(), which also renders self-contained HTML data-quality and statistical reports. Chromatographic peak detection, peak integration and calibration-curve fitting from raw mass-spectrometry data are outside its scope.
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metabolomicslipidomicsmassspectrometryqualitycontrolnormalizationbatcheffectvisualizationworkflowstep
3.48 score 5 scriptsdmsa - Directional Methylation Set Analysis
Aligns probe-level methylation effects to their predicted effect on gene expression and, for system-level analysis, to each gene's curated polarity with respect to the system's activation tone (e.g. NR3C1 opposes HPA-axis activation). Pools the aligned coefficients with fixed-sign or expected-sign estimators and reports coverage and activation/brake balance per set. Ships the Project Alpha gene-system map, a gene-to-system polarity table carrying a stated source and review flag on every row, and a curated system > module > gene > probe selection cascade whose module labels carry literature-audited evidence tiers and citations; genes without a polarity entry must be specified by the user.
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dnamethylationdifferentialmethylationmethylationarraygenesetenrichmentgeneexpressionepigeneticsmicroarraycoveragestatisticalmethodmultiplecomparisonregressionsoftware
3.48 scorecpgdirectionData - Data Layers for the cpgdirection Package (ExperimentHub)
ExperimentHub companion to the cpgdirection package. Serves the eight data layers too large to ship inside a Bioconductor software package: the three tissue catalogue lookup tables (blood, nasal epithelium, solid tissue; hg19), the SMR causal-direction table, the EPIC v2 hg19 probe positions, the brain SMR directions, the genome-wide saliva bridge scores, and the multi-source EPIC v2 probe-to-gene annotation (five cross-validated annotation tracks with per-track support flags). Each resource is a serialized data.frame retrieved from ExperimentHub on first use and cached locally thereafter. The cpgdirection package consumes these resources transparently; direct use is possible through the accessors documented here.
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experimentdataexperimenthubhomo_sapiens_datamicroarraydatamethylationarraydatatissuemicroarraydatatissuegenome
3.48 score 1 dependentscellchatr - Fast Ligand-Receptor Interaction Screening for Single-Cell Data Using Rust
Fast identification of over-expressed genes and ligand-receptor interactions in single-cell RNA-seq data, the pre-processing steps of cell-cell communication analysis tools such as CellChat. Works directly on SummarizedExperiment and SingleCellExperiment objects and accepts any ligand-receptor table (for example the CellChatDB interaction table). The per-gene, per-cell-group Wilcoxon rank-sum tests are implemented in Rust via extendr and run in parallel with Rayon.
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singlecellgeneexpressiontranscriptomicsdifferentialexpressionnetworksoftwarerustcargo
3.40 scoremyoRDNA - Tools for Calculating for rDNA in Muscle Sequencing Data
Functions for working with rDNA data generated from sequencing experiments. The package includes functions to calculate the relative rDNA copy number from coverage data, as well as functions to calculate the absolute rDNA copy number using methylation data.
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softwarednamethylationepigeneticscopynumbervariationsequencingcoverage
3.40 scorewoven - Weighted Omics View Embedding via Nystrom for Incomplete Multi-Omics Data
Supervised multi-omics integration for block-missing ("ragged") data. WOVEN learns a shared latent space across V omics modalities using only fully-observed anchor subjects, then projects block-missing subjects via Nystrom extension without feature-level imputation. Supervision enters through a label-augmented cross-covariance (analogous to DIABLO), and projection matrices can optionally be ridge-regularized and univariately feature-screened for high-dimensional modalities. Designed for comparative effectiveness research where intersection-only methods introduce selection bias.
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softwarestatisticalmethodmultiplecomparisongeneexpressiontranscriptomicsproteomicsmetabolomicsdimensionreductionclusteringclassificationsequencing
3.40 score 3 scripts
MsExperimentStash - Save and restore MsExperiment objects in interoperable file formats
The serialization mechanism of R allows to save and load R data objects in a binary format, that can however not be read by other programming languages or software. The MsExperimentStash package implements the serialization methods from the MsStash package for MsExperiment objects. Data can be stashed in a variety of file formats and types, including HDF5 and JSON-based formats defined by the Bioconductor *alabaster* package. The package provides also functionality to read a full MS experiment, including MS data and experimental metadata information, from the MetaboLights repository.
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infrastructuremassspectrometrymetabolomicsdataimportproteomics
3.40 scoreepiPortrait - Replicate-Aware Epigenomic Domain Profiling
Provides methods for replicate-aware quantitative phenotyping and comparison of epigenomic domains from normalized continuous signal tracks and per-sample native peak/domain calls (histone-mark ChIP-seq / CUT&Tag as the primary use case; also applicable to ATAC-seq-derived domains). It characterizes each shared genomic domain by integrated signal magnitude (Intensity), sample-specific native peak breadth geometry, and continuous within-domain signal architecture (SignalDispersion). Replicate-level evidence is retained and aggregated with specified support rules, enabling condition-specific classification of Intensity-Super, Breadth-Super, Dual-Super, Typical, or Uncertain domain states without using the consensus-domain width as the breadth caller. The package further supports condition transitions, continuous domain-width remodeling, signal quality control, genome-aware domain annotation with a three-level export (per-domain summary, per-domain-gene pair, and raw relationship detail), optional BEDPE contact evidence, expression-aware candidate-gene prioritization, differential domain analysis on continuous BigWig signal using limma, and result visualization.
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chipseqatacseqepigeneticscoveragenormalizationdifferentialexpressiongenomeannotationqualitycontrolvisualizationprincipalcomponent
3.40 scoresaintexpress - Pure R Implementation of SAINTexpress
A pure R implementation of the SAINTexpress scoring engines for affinity purification-mass spectrometry data, covering both the spectral-count and intensity models, together with validation of SAINT input tables. The output mirrors the native SAINTexpress 'list.txt' format, so protein-protein interactions can be scored without external binaries. The underlying method is described in Teo et al. (2014) <doi:10.1016/j.jprot.2013.10.023>.
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massspectrometryproteomicssoftware
3.40 score 2 scriptsClinicalVariantR - Clinical Variant Interpretation Using ACMG/AMP Germline Criteria
ClinicalVariantR is an interactive Shiny platform for evidence-based germline variant classification under ACMG/AMP 2015 guidelines. It accepts VEP-, SnpEff-, or ANNOVAR-annotated VCF files and applies automated plus curator-guided ACMG criteria. The package supports streaming analysis of large call sets and exports structured per-criterion evidence with reproducibility metadata for clinical review.
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softwarevariantannotationgeneticssequencingvisualizationguiclassification
3.40 scoreWithinHostExperiment - Within-Host Pathogen Variant QC, Diversity, and Bottleneck
Provides a SummarizedExperiment-based container and workflow functions for analysing intra-host single nucleotide variants (iSNV) from pathogen deep sequencing data. Supports replicate-aware quality control with full provenance tracking, multi-caller import harmonisation, within-host diversity quantification, and standardised export to transmission bottleneck estimation tools. Designed as infrastructure that bridges upstream variant callers (iVar, LoFreq, Freebayes) with downstream analysis packages through a common data object with uncertainty-preserving QC.
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geneticsvariantannotationsequencinggenomicvariationqualitycontrolvariantdetectiondataimportlongread
3.30 scoreGSE142512 - 450K and EPIC Methylation ExperimentHub Data from GEO
Provides ExperimentHub access to processed DNA methylation resources derived from GEO accession GSE142512. The resources contain Illumina HumanMethylation450 and Infinium MethylationEPIC data represented as RangedSummarizedExperiment objects with beta, M, and CN assays, hg19 genomic ranges, and sample phenotype metadata.
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experimentdataexperimenthubgeohomo_sapiens_datamethylationarraydatamicroarraydatatissue
3.30 score 4 scriptsMiCARA - Microbiome Confounder-Adjusted Robust Analysis
Provides a comprehensive framework for multi-cohort microbiome differential abundance and residual correlation analysis. It integrates confounder-adjusted linear models with centered log-ratio transformed taxonomic and functional pathway profiles. The package features robust preprocessing, automated covariate handling, multiple-testing correction, and quality control diagnostics for multi-omics data. Interactive visualization tools are included to facilitate downstream interpretation of cross-domain interaction networks.
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microbiomedifferentialexpressionsoftwaremetagenomicsnetworkinferencepathwaysnetworkpreprocessingqualitycontrol
3.30 scoreperturbMatch - Match Transcriptomics Signatures to Single-Gene Perturbation References
Matches a query transcriptomics signature against a reference database of single-gene perturbation signatures, ranking the perturbations whose expression response most resembles the query and so nominating the regulators most likely to drive the observed change. Query signatures derived from a differential expression result are scored using cosine, GSEA and signed-Jaccard similarity metrics. Reference databases are supplied as HDF5-backed SummarizedExperiment objects for memory-efficient handling of large perturbation collections, and helper functions rank and visualise the best-matching regulators.
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generegulationtranscriptomicstranscriptiongenesetenrichmentgenetargetgeneexpressiondifferentialexpression
3.30 score 4 scriptsECLIPSE - ECLIPSE: Enhanced CLonotypic Inference via Prediction of Single-cell Expression
This package is used for the analysis of single-cell T cell receptor sequencing data (scTCR-seq). ECLIPSE maps chain pairings across a sample to predict the true clonotype of each cell, unlike other methods which only consider the chains that are sequenced in each cell. Seurat objects and Cell Ranger vdj/multi contig files are required as inputs.
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softwaregeneexpressionbiomedicalinformaticsimmunooncologytranscriptomicsclassificationsinglecellannotationsequencing
3.30 score 5 scriptsSwitchClass - Label-Switch Classification for Baseline- and Perturbation-Aligned Features
Quantifies baseline-aligned and perturbation-aligned molecular features across biological perturbations using a label-switch classification framework. Provides a unified workflow for identifying changes in molecular-feature alignment in longitudinal or comparative omics datasets. Includes tools for classification, visualization, dimension reduction, and pathway enrichment.
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softwareclassificationfeatureextractiongeneexpressionproteomicstranscriptomicssinglecellpathways
3.30 score
bHIVE - B-cell Hybrid Immune Variant Engine
The bHIVE package implements an Artificial Immune Network (AI-Net) algorithm for clustering and classification tasks. Inspired by biological immune systems, it employs clonal selection, mutation, and network suppression to analyze and model datasets. This package provides flexible functionality, including affinity metrics, mutation strategies, and hyperparameter tuning.
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softwareclusteringclassificationnetworkopenblascpp
3.30 score 8 scriptsmethylTFRAnnotationHg38 - methylTFR Annotations for hg38
Precomputed transcription factor binding sites, motif GC frequency tables and a genome-wide GC distribution for use with the methylTFR package. Binding sites are genome-wide motif matches extended to the footprint window methylTFR reads across; the GC tables record how each motif's sites distribute over genome-wide GC quintiles, which is what allows a deviation score to be corrected for sequence composition. The data are hosted on AnnotationHub and retrieved on first use; this package provides the accessors and the documentation.
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annotationdataannotationhubfunctionalannotationsequenceannotationhomo_sapiens
3.29 score 13 scriptsTweedSpot - Self-Adaptive Spatial Tweedie Models for Spatially Variable Gene Detection
TweedSpot detects spatially variable genes (SVGs) in spatially resolved transcriptomics data using self-adaptive Tweedie generalized additive models with nonparametric spatial smoothing. The method models raw counts directly, avoiding the bias introduced by log-transformation, adapts a gene-specific Tweedie index parameter to the mean-variance relationship of each gene, and offers an optional two-part formulation to accommodate excess zeros. Inputs and outputs use the SpatialExperiment infrastructure for interoperability with the Bioconductor ecosystem.
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softwaretranscriptomicsgeneexpressionriboseqspatialregressionstatisticalmethoddifferentialexpression
3.18 scoreconsensusRegions - Consensus Regions from Replicated ChIP-seq and ATAC-seq Experiments
Merges the evidence carried by replicated ChIP-seq, ATAC-seq or CUT&RUN experiments into a single set of consensus regions. When several replicates agree on a position their p-values are combined, so that a peak too weak to survive on its own can still be retained. Fisher, Stouffer, Lancaster and rank-product combinations are available; the weighted ones accept per-replicate weights taken from FRiP scores, library sizes, or the peak sets themselves when no alignment file is at hand. Input can be anything from a full narrowPeak to a bare BED3: scores are rank-transformed when p-values are missing, and a weighted k-of-n presence rule takes over when even the score is absent. The threshold on the combined significance can be calibrated against a permutation null rather than fixed a priori. Quality control plots and export to SummarizedExperiment are included.
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chipseqatacseqpeakdetectionepigeneticssequencingqualitycontrolmultiplecomparisonsoftware
3.18 score 3 scriptsCanvasXpressBio - CanvasXpress Visualizations for Bioconductor Data Structures
Bridges the CanvasXpress interactive visualization library to core Bioconductor data structures. Provides a generic to render a SummarizedExperiment, and any class that extends it such as SingleCellExperiment or DESeqDataSet, as an interactive CanvasXpress heatmap that carries its row and column annotations, together with a volcano helper for differential-expression result tables. Charts are reproducible CanvasXpress widgets usable in R, R Markdown and Shiny.
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softwarevisualizationgeneexpressiondifferentialexpressionrnaseqsinglecelltranscriptomics
3.18 score 6 scriptsmethylTFRAnnotationMm10 - methylTFR Annotations for mm10
Precomputed transcription factor binding sites, motif GC frequency tables and a genome-wide GC distribution for use with the methylTFR package. Binding sites are genome-wide motif matches extended to the footprint window methylTFR reads across; the GC tables record how each motif's sites distribute over genome-wide GC quintiles, which is what allows a deviation score to be corrected for sequence composition. The data are hosted on AnnotationHub and retrieved on first use; this package provides the accessors and the documentation.
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annotationdataannotationhubfunctionalannotationsequenceannotationmus_musculus
3.18 score 3 scriptsGO.ddb - Tidy Interface to GO Semantic SQL via DuckDB
Provides a tidyverse-oriented user interface to Gene Ontology data via the Semantic SQL representation, accessed through DuckDB. Replaces the GO.db + AnnotationDbi::select nexus with lazy tibble-based operations for term lookup, ancestor/descendant traversal, and gene-GO annotation queries. The Semantic SQL resource is managed by the ontoProc2 package via BiocFileCache.
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annotationgoontology
3.18 score 2 scriptsCDEnrich - Enrichment Analysis for Cell Death Pathways
Provides a curated collection of gene sets for major cell death modalities, together with tools for over-representation analysis, gene set enrichment analysis, single-sample gene set enrichment analysis, differential pathway analysis, and visualization.
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genesetenrichmentpathwaysgeneexpressiondifferentialexpressioncellbiology
3.18 scoreTxDb.Gmax.JGI.Gmv4 - Transcripts Annotation Database for Soybean
TxDb.Gmax.JGI.Gmv4 provides transcript, exon, and CDS annotations for soybean (Glycine max Wm82.a4.v1). It is a Bioconductor TxDb object built from the official JGI/Phytozome GFF3 annotation and is available via AnnotationHub (retrievable with AnnotationHub()); after loading you can use GenomicFeatures accessors (genes(), transcripts(), exonsBy(), cdsBy()) to extract gene models identified by JGI/Phytozome locus IDs.
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annotationdatatxdbglycine_maxsequenceannotationannotationhub
3.18 scoreTxDb.Athaliana.Ensembl.TAIR10 - Transcripts Annotation Database for Arabidopsis thaliana
TxDb.Athaliana.Ensembl.TAIR10 provides transcript, exon, CDS, and gene annotations for Arabidopsis thaliana based on the TAIR10 reference genome and Ensembl Plants release 63. The TxDb object is built from the Ensembl Plants GFF3 annotation and can be queried using GenomicFeatures accessors such as genes(), transcripts(), exonsBy(), and cdsBy().
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annotationdatatxdbarabidopsis_thalianasequenceannotationannotationhub
3.18 scorePlantTxDbHub - Transcript Database Hub for Plant Genomes
Provides TxDb (transcript database) annotations for plant species. The SQLite files are hosted on Zenodo (or other permanent URLs) and are downloaded on demand via the `downloadPlantTxDbs()` function. The list of available species and their download URLs is maintained in a curated CSV file (inst/extdata/metadata.csv), allowing users and contributors to easily add new databases without modifying R code.
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annotationdatatxdbarabidopsis_thalianaoryza_sativaglycine_maxsequenceannotation
3.18 scoregeneticumap - Evolutionary Algorithm for UMAP-based Clustering Pipeline Parameter Optimization for Single-Cell RNA-Seq Data
The geneticumap package searches for single-cell clustering parameters by treating the Seurat preprocessing and clustering workflow as an optimization problem. The UMAP-based clustering pipeline parameters for single-cell RNA-seq data (like resolution, number of PCs, or neighbor counts) evolve using an evolutionary algorithm to systematically search for an optimal set of parameters for a given dataset. The most appropriate configuration is objectively identified by the Calinski-Harabasz index. The package is developed at the [Institute of Medical Systems Biology of Ulm University](https://sysbio.uni-ulm.de).
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geneexpressionsinglecelltranscriptomicsclusteringdimensionreductionpreprocessing
3.00 score
HaploBreedR - High-Resolution Functional Haplotype Discovery and Genomic Selection
An end-to-end quantitative genomics and molecular breeding suite for crops. Identifies superior functional haplotypes from coding variants under false discovery rate control and conducts haplotype-guided genomic selection, analytical cross usefulness prediction, and linkage-aware pyramiding optimization.
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softwaregeneticsgenomewideassociationsnpgenomeassemblynetworkprincipalcomponentnetworkenrichmentgofunctionalgenomicsfunctionalpredictiongeneprediction
3.00 scorepath2path - Directional Pathway-by-Pathway Interaction Maps from Genome-Scale Perturb-Seq
Builds a directional pathway-by-pathway interaction map from genome-scale Perturb-seq differential-expression statistics by two stacked runs of preranked gene set enrichment analysis: once per perturbation over genes, then once per readout pathway over perturbations. Entry (j,k) of the resulting matrix measures whether perturbations targeting pathway j's members produce a coordinated transcriptional response in pathway k. The package includes target exclusion, effective-size filters, overlap masking, Stage 2 p-values with false-discovery-rate control, and a whole-pipeline permutation calibration with generalized-Pareto tail estimation.
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softwaregenesetenrichmentpathwayscrisprsinglecelldifferentialexpressiontranscriptomicsnetworkinferencegeneexpressiongenetargetkeggwholegenome
3.00 scoreMRCCC - Bayesian Mendelian Randomization for Causal Cell-Cell Communication
Implements MR-CCC, a Bayesian Mendelian randomization framework for inferring causal ligand-receptor signalling between cell types from population-scale single-cell expression and genotype data. For each ligand-receptor-pathway triplet, cis-eQTL genotypes instrument ligand expression in the sender cell type and receptor expression in the receiver cell type, and a working model with a ligand-by-receptor interaction is fitted to downstream pathway activity by a blocked Gibbs sampler. A spike-and-slab prior on the causal block yields a posterior inclusion probability that serves as the communication score, and the retained draws support credible intervals, sign probabilities, the receptor level at which the ligand effect reverses sign, and Bayesian false discovery rate control across many triplets.
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softwarestatisticalmethodbayesiangeneexpressionsinglecellgeneticssystemsbiologygeneregulationopenblascpp
3.00 scorecircaTime - Unified Inference of Circadian Phase from Bulk and Pseudobulk Transcriptomes
Provides a single SummarizedExperiment-based interface to published circadian phase (time-of-sample-collection) inference methods for bulk and donor-level pseudobulk transcriptomes, along with a shared cross-validation benchmarking harness, cross-dataset transfer testing, and a calibrated uncertainty layer: bootstrap and Bayesian confidence intervals validated for real coverage, a fixed or dynamically-selected clock-gene quality flag, and consensus phase estimation across every bundled engine. Does not implement a new phase-inference algorithm; unifies existing published methods that are otherwise scattered across incompatible standalone implementations.
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softwaregeneexpressiontranscriptomicssequencingmicroarraytimecoursepreprocessing
3.00 score 5 scriptsscDonorAudit - Audit Donor Influence in Single-Cell Pseudobulk Analyses
Audits sample and donor design for two-condition single-cell pseudobulk differential expression analyses. Fits an edgeR quasi-likelihood model to each cell type and repeats the analysis after omitting each donor. Links planned donor omissions to design checks, fit outcomes and observed gene-effect changes. Provides descriptive summaries of donor-deletion sensitivity together with the coverage of valid effects.
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singlecellrnaseqgeneexpressiondifferentialexpressionqualitycontrolsoftware
3.00 scorePscanRBackgrounds - Precomputed Promoter Backgrounds for PscanR
Provides ExperimentHub metadata and documentation for the promoter-background score distributions used by PscanR transcription factor binding motif enrichment analyses. Each of the 105 backgrounds is a separate ExperimentHub resource, covering the JASPAR 2020, 2022 and 2024 CORE collections, seven genome assemblies of five organisms, and five promoter windows. The files are hosted on Zenodo, one record per JASPAR release, and archived together in a version-specific Zenodo record.
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experimenthubgenomehomo_sapiens_datamus_musculus_datadrosophila_melanogaster_datasaccharomyces_cerevisiae_dataarabidopsis_thaliana_data
3.00 scorehcocena - Horizontal Integration and Analysis of Multiple Transcriptomics Datasets
Tools for the joint analysis of multiple transcriptomics datasets using a network-based integration approach. The package provides an S4 object model based on MultiAssayExperiment for reproducible analysis of single-layer and multi-layer studies. It includes workflows for clustering, module visualization, functional annotation, upstream inference, and longitudinal follow-up while retaining compatibility helpers for legacy hCoCena objects.
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softwareclusteringgeneexpressionkeggnetworknetworkinferencetranscriptomicsworkflowstep
3.00 score
OmniCorr - Multi-omics Integration and Visualization Framework
OmniCorr is an R package for correlation-based integration and visualization of multi-omics datasets, including transcriptomics, metatranscriptomics, metagenomics, metaproteomics, and associated sample metadata. The package computes pairwise correlations between independently processed omics layers and provides flexible tools for organizing and visualizing cross-omics associations using aligned heatmaps and optional network-style visualizations. OmniCorr is designed to complement existing preprocessing and network inference workflows rather than replace them.
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dimensionreductionfeatureextractionmetabolomicsmetagenomicsmicrobiomenetworkinferencepreprocessingproteomicstranscriptomicssoftware
3.00 scoreselexprepR - Preprocessing Public HT-SELEX Sequencing Data
Provides reproducible preprocessing for high-throughput SELEX sequencing data. Supports primer inference, extraction of random regions, sparse sequence counting across rounds, quality control, and provenance manifests. Public-study discovery and checksum-aware ENA FASTQ download planning are included for reproducible data acquisition.
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softwaredataimportpreprocessingqualitycontrolsequencing
3.00 score 3 scriptspanpathAudit - Audit Sequence Preservation in GFA Traversals
Audits source FASTA sequences against named paths and coordinate-aware walks in GFA files. It reports exact recovery, divergence coordinates, digests, and optional base-level statistics. Graph topology is not validated.
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alignmentdataimportgenomeassemblygeneticssequencingzlibcpp
3.00 scorescGenePanel - Multi-panel visualization for single cell expression data
scGenePanel creates coordinated, gene-centric multi-panel visualizations for single-cell RNA-seq data stored in Seurat or SingleCellExperiment objects. It combines group-stratified UMAP embeddings, cell-type-specific expression distributions, and quantitative cell-frequency and expression summaries in a single figure. An accompanying Shiny application supports interactive exploration using the same workflow.
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softwaregeneexpressionsinglecellvisualizationdimensionreductiontranscriptomics
3.00 score 2 scripts
RhyME - Beta Regression Cosinor Models for Circadian Methylation Analysis
Fits cosinor-based beta regression models for detecting circadian rhythmicity in DNA methylation array data using Template Model Builder (TMB) for efficient likelihood optimization. Supports fixed-effects (cross-sectional) and mixed-effects (repeated measures) designs with configurable period and adjustment covariates. Implements empirical Bayes shrinkage of the beta distribution precision parameter across CpG sites, analogous to limma's moderated variance, to improve genome-wide inference. Provides amplitude, phase, and MESOR estimation on both logit-link and response scales.
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epigeneticsdnamethylationtimecourseregressiondifferentialmethylationsoftwarecppopenmp
3.00 scoremdclust - Maximum Diversity Clustering
Standalone implementation of the maximum diversity clustering algorithm (Algorithm 2) from Korsunsky et al. (2019), Nature Methods. Soft spherical k-means with a batch-diversity penalty.
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softwareclusteringdimensionreductionquartoopenblascpp
3.00 score 5 scriptsloopcityData - Experimental Data for the loopcity Package
Provides Hi-C loop calls and chromatin interaction data used in examples and vignettes for the loopcity package. Includes GM12878 Hi-C loop calls at 10 kb resolution (Rao et al. 2014, GSE63525), shipped directly as GInteractions objects. K562 Hi-C contact matrices and CTCF and H3K27ac ChIP-seq signal tracks from Bond et al. 2023 (GSE214123, GSE213908) are hosted on ExperimentHub and retrieved on demand.
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experimenthubexperimentdatahomo_sapiens_datasequencingdata
3.00 score 7 scriptsTxParq.Hs.gencode.v49 - Parquet-based representation of GENCODE gene models v49 for Homo sapiens
This is a parquet-based representation of GENCODE gene models v49 for Homo sapiens. Parquet is chosen to reduce footprint, to support tidyverse-oriented operations natively, and to provide opportunities for cloud-backed annotation services. Community contributions to functionality and architecture are welcome.
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infrastructure
3.00 score 5 scriptspostexportKinetics - Kinetic Model Comparison for Post-Export RNA Conversion
Compartment-resolved four-state kinetic modelling of nuclear and cytoplasmic, unprocessed and processed RNA. Implements a constrained nested-model comparison between a null model without a post-export conversion rate and a full model with a non-negative post-export conversion rate, using trapezoidal interval balances, propagated and regularised measurement covariance, whitened non-negative least squares and a replicate-level generative bootstrap with an add-one p-value. Also provides simulation with the manuscript simulator and assay-noise models, diagnostic comparison of sampling designs with the manuscript benchmark, multiple-testing adjustment, exploratory candidate ranking, tidy result tables and plots. The post-export conversion rate is a phenomenological parameter and does not identify a specific molecular mechanism.
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softwaretranscriptomicsrnaseqalternativesplicingtimecoursestatisticalmethodmultiplecomparisonvisualization
2.70 scorecrossarrayEWAS - Design-Aware Region and Block Detection for Cross-Array Longitudinal EWAS
Estimation and region-calling routines for epigenome-wide association studies that combine Illumina HumanMethylation450 and MethylationEPIC samples and follow subjects over more than one visit. Probe-level effects are fitted within subject, so subject identity, array type and chip are absorbed rather than modelled; adjacent probes are grouped by within-subject co-methylation; regions are obtained by total-variation denoising with a distance-decaying penalty, which places boundaries where the effect track jumps instead of thresholding a smooth curve; and long-range blocks are called from a three-state hidden semi-Markov model whose transition probabilities decay with genomic distance. Selection stability and permutation nulls resample subjects, not samples, so a subject's visit series is never split.
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dnamethylationdifferentialmethylationepigeneticsmethylationarrayregressionsoftware
2.70 scorehmagmaR - Incorporation of chromatin interaction and epigenetic profiles to predict risk genes
Combines chromatin interaction (e.g. PLAC-seq/Hi-C) data with regulatory region annotations (e.g. promoters, enhancers, H3K27ac) to link non-coding GWAS SNPs to their putative target genes, producing MAGMA-compatible gene annotation files for downstream gene-level association testing.
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softwareepigeneticschipseqgeneregulationsnpgenomeannotationfunctionalgenomicsgenetargethic
2.70 scoreGENCODEHub - GENCODE AnnotationHub
Provides access through AnnotationHub to genomic annotation resources derived from GENCODE releases. The release 50 collection represents every feature type in the human GRCh38.p14 GTF. Feature-specific GRanges objects retain the imported identifiers and attributes, while a TxDb resource supports gene, transcript, exon, and coding-sequence queries.
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annotationdataannotationhubgenomicsequencehomo_sapienspackagetypesequenceannotationtxdb
2.70 score 4 scriptsperturbMatchData - Reference Perturbation Signatures from GEO RNA-seq Experiments
Provides the reference perturbation expression signatures used by the perturbMatch package, which ranks the single-gene perturbations whose expression response most resembles a query signature. Each reference signature summarises the differential expression observed after a single-gene perturbation (knockdown, knockout or overexpression) in a human RNA-seq experiment deposited in the Gene Expression Omnibus. Signatures are summarised either by the characteristic direction method or by limma, each with and without surrogate variable analysis batch correction, giving four datasets served as HDF5-backed SummarizedExperiment objects.
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experimenthubexperimentdataexpressiondatarnaseqdatasequencingdatahomo_sapiens_datageo
2.70 scoredrugannotR - Coordinate-Level Pharmacological Annotation of Genomic Regions
Maps genomic regions to gene features and then to traceable drug-gene relationships. The package preserves genomic coordinates, relationship categories, evidence scope, and source provenance. It deliberately reports coordinate-level pharmacological relevance rather than predicting treatment response, efficacy, toxicity, or dose.
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annotationdatarepresentationdataimportgenetargetgenomeannotationpharmacogeneticspharmacogenomicsvariantannotation
2.70 score
PTMsToPathwaysData - ExperimentHub Data for PTMsToPathways
Companion data package for PTMsToPathways that registers large post-translational modification data resources and intermediate processed data for vignettes in ExperimentHub.
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experimenthubcancerdatamassspectrometrydata
2.70 scorescOverlay - Multilayer plots for single-cell data
scOverlay provides publication-grade plotting helpers to display a foreground feature (gene expression or metadata) on top of a contextual background (clusters, cell types, samples, or a solid colour) in the same reduced dimension panel, each with independent colour scales (via ggnewscale). It integrates with SingleCellExperiment / SummarizedExperiment, supports flexible subsetting of foreground cells, multiple assays (e.g. counts, logcounts), and grid arrangements by user-defined grouping columns.
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softwarevisualizationsinglecelltranscriptomicsgeneexpressiondatarepresentation
2.70 score 3 scriptsPACMOSData - ExperimentHub Data for PACMOS
Large reference datasets used by the PACMOS package for multi-omics and MOFA analysis of lung neuroendocrine neoplasms and MESOMICS data.
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experimentdatahomo_sapiens_datacancerdatasequencingdataexperimenthub
2.70 scoreinferRecom - Homologous Recombination Detection in Family Pedigrees
This package implements a pedigree-based algorithm to detect homologous recombination. Additional functions are supplied to detect runs of homozygosity and to phase haplotypes at informative SNPs.
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geneticssnpgenomeannotationsequencingcoverage
2.70 scorespbtest5 - Test Single Package Builder
What the package does? (one paragraph).
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softwaredataimportbiologicalquestion
2.70 scoreProtein2Tissue - An R package for tissue expression analysis and gene set enrichment
Protein2Tissue provides a comprehensive framework for analysing tissue-specific gene and protein expression patterns. The package allows users to map genes or proteins to their predominant tissue types, perform tissue-based enrichment analysis on gene sets, and explore expression profiles across a wide range of human tissues. Reference expression data is derived from publicly available databases the Human Protein Atlas (https://www.proteinatlas.org).
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proteomicstranscriptomicsgenesetenrichmentnetwork
2.48 score 3 scriptsConvergeR - Whitfield Convergence Score and Seurat Metadata Association
Calculates the convergence score defined by Whitfield et al. 2026 (doi: 10.1158/0008-5472.CAN-25-4403). It allows visualization of this score alongside qualitative and quantitative Seurat object metadata via barplots and density curves, and runs appropriate statistical tests for associations.
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softwaresinglecelltranscriptomicsgeneexpression
2.00 score