epiwraps - 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
5.72 score 208 scriptsDuckDBDataFrame - DuckDB-Backed DataFrame and Table Structures
Provides DuckDB-backed implementations of core tabular data structures including DuckDBTable, DuckDBDataFrame, and DuckDBColumn. These classes extend Bioconductor's S4Vectors framework to enable efficient, out-of-memory operations on large tabular datasets using DuckDB's analytical database engine. The package includes SQL function discovery, connection management, and support for list columns and embeddings stored in ARRAY[] columns.
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dataimportdatarepresentationinfrastructuresoftware
5.31 score 4 dependentsspatialdataR - Representation of Python's spatialdata in R
R interface to Python/scverse's 'spatialdata' framework for unified spatial omics data handling. Adheres to OME-NGFF standards, providing lazy, on-disk representations for multiscale images and labels (ZarrArray), as well as points and shapes (DuckDB-backed tables). Includes handling of coordinate transformation systems and spatial utilities for cropping, masking, and querying. Integrates tabular annotations as 'SingleCellExperiment's (via 'anndataR'), enabling interoperable spatial omics workflows across R and Python.
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dataimportdatarepresentationinfrastructureimmunooncologygeneexpressiontranscriptomicssinglecellspatial
4.93 score 12 scriptsDuckDBArray - DuckDB-Backed DelayedArray Implementation
Provides DuckDB-backed implementations of DelayedArray and DelayedMatrix classes for efficient, out-of-memory operations on large array and matrix datasets. The package includes DuckDBArray, DuckDBArraySeed, and DuckDBMatrix classes with optimized matrixStats methods. Supports sparse arrays, grid partitioning, and parallel processing for scalable genomic data analysis.
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dataimportdatarepresentationinfrastructuresoftware
4.91 score 1 dependentsMultiAssaySpatialExperiment - Multi-Assay Experiment with Spatial Context
Extends MultiAssayExperiment with spatial context elements (images, labels, points, shapes) for integrative analysis of spatially resolved multi-omics data. Supports coercion to and from SpatialExperiment and SpatialFeatureExperiment.
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infrastructuredatarepresentation
4.69 score 1 dependentsDuckDBGRanges - DuckDB-Backed GenomicRanges Implementation
Provides DuckDB-backed implementations of GenomicRanges data structures for efficient, out-of-memory operations on large genomic interval datasets. The package includes DuckDBGRanges and DuckDBGRangesList classes with optimized range operations including restrict, flank, shift, findOverlaps, and distance calculations. Ideal for variant analysis, scATAC-seq peak analysis, and other genomic workflows requiring memory-efficient range operations on large datasets.
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dataimportdatarepresentationinfrastructuresequencingsoftware
4.69 score 1 dependentsSPAROscore - 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
4.46 score 17 scriptstTEscanR - An advanced R-based package to quantify and visualize translation efficiency from sequencing data
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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softwareepitranscriptomicstranscriptomicsgeneexpressiongeneregulationsequencingsinglecell
4.34 score 1 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
4.34 scorescMAGeCK - 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
4.32 score 52 scriptsBiocDuckDB - Bioconductor DuckDB Integration and High-Level I/O
Integration package providing high-level Parquet I/O functions and optimized methods for single-cell analysis workflows using DuckDB-backed data structures. Includes readParquet and writeParquet functions for seamless serialization of SummarizedExperiment, SingleCellExperiment, MultiAssayExperiment, and MultiAssaySpatialExperiment objects, plus SQL-optimized implementations of scran and scuttle methods for variance modeling, marker detection, QC metrics, and normalization. This package brings together DuckDBDataFrame, DuckDBArray, DuckDBGRanges, and DuckDBSpatial (optional) for complete Bioconductor integration.
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dataimportdatarepresentationinfrastructurernaseqsequencingsinglecellsoftware
4.30 scorepepitope - Extract, QC and Screen Peptide Epitopes
Supports T cell receptor neoantigen co-culture screen analysis from peptide library design to sequencing quality control and differential abundance testing. The package annotates somatic variants and RNA fusions, extracts mutant and reference peptide context, prepares barcoded minigene construct tables, counts sample and construct barcodes from sequencing data, and identifies immunogenic epitopes in dropout screens.
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dnaseqvariantannotationimmunooncologyzlibcpp
4.26 score 4 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.
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softwaredimensionreductionclassificationregressiongeneexpressionmetabolomicssinglecellgpuopenblascpp
4.23 score 21 scripts 189 downloadsIntegratedLearner - Integrated Multi-Omics Learning for Survival and Other Outcomes
Provides a unified interface for multi-omics prediction using early, late, and intermediate 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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softwareclassificationsurvivalmicrobiome
4.19 score 11 scriptssbivar - 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
4.13 score 4 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
4.13 score 15 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
4.08 scoreDuckDBSpatial - DuckDB-Backed Spatial Data Structures
Provides DuckDB-backed implementations of spatial data structures for efficient out-of-memory operations on large spatial datasets. The package includes 68 sf-compatible spatial methods (st_intersects, st_contains, st_within, etc.) and GeoParquet 1.0 I/O support via writeGeoParquet(). Ideal for spatial analysis, genomic interval analysis, and integration with BiocDuckDB for MultiAssaySpatialExperiment workflows requiring memory-efficient operations on large datasets.
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dataimportdatarepresentationinfrastructuresoftware
4.04 score
pepVet - Evaluate Proteolytic Digests for Proteomics Workflows
Simulates proteolytic digestion, scores the resulting peptides for LC-MS/MS suitability, compares candidate enzymes, and reports digest quality at the protein level. Supports 40 cleaver-compatible enzyme rules, workflow presets, peptide mass and pI calculations, sequence-local cleavage-efficiency annotations, and proteome-aware uniqueness scoring. Evaluates multi-FASTA files in batches with per-protein triage and proteome-level summaries. Exports peptide lists for Skyline and generic downstream tools and prints styled console reports.
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proteomicsmassspectrometryqualitycontrol
4.03 score 12 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
4.02 scorecellpaintr - 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
3.88 score 2 scriptsLIPIDIFy - Comprehensive Lipidomics Data Analysis with Interactive Visualization
Provides a comprehensive toolkit for end-to-end lipidomics data analysis, including missing value imputation, batch effect correction, normalization, differential abundance analysis using limma and edgeR, gene set enrichment analysis, and extensive visualization capabilities. Lipid names are automatically classified by class, subclass, and fatty-acid saturation. Features both an interactive Shiny interface for bench biologists and fully scriptable R functions for bioinformaticians. Supports flexible custom lipid classification schemes and user-defined enrichment sets.
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lipidomicsmassspectrometrynormalizationpreprocessingdifferentialexpressiongenesetenrichmentvisualizationshinyappsmultiplecomparisonbatcheffectqualitycontroldataimport
3.78 score 4 scriptsgeneslator - Geneslator, a tool for accurate gene name conversion
Geneslator is a comprehensive R package that performs gene identifier conversion and ortholog mapping. The tool integrates multiple cross-organism databases (NCBI, Ensembl, UniProt, GO, KEGG, Reactome, Wikipathways) and organism-specific resources within a single, coherent framework. Geneslator currently supports the following organisms: human, mouse, rat, yeast, worm, fly, zebrafish and arabidopsis.
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orgdborganismdbannotationdatahomo_sapiensmus_musculusrattus_norvegicuscaenorhabditis_eleganssaccharomyces_cerevisiaedrosophila_melanogasterdanio_rerioarabidopsis_thalianaorganismzebrafishpackagetype
3.78 score 9 scriptsspbtest3 - 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
3.74 scoreGPlinksR - Building Gene-Peak Network for ATAC-RNA Integration
GPlinksR constructs gene-peak regulatory networks for ATAC-RNA integration by combining enhancer-based, promoter-based, and proximity (closest-gene) mappings. The package accepts direct peak and gene vectors as well as container-based inputs through a wrapper for common Bioconductor object classes. Enhancer-gene links are obtained from the PEREGRINE enhancer-gene datasets provided by AnnoQ, while promoter and gene coordinates are retrieved from EnsDb.Hsapiens.v86.
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geneexpressionnetworksequencingtranscriptomics
3.70 score 2 scriptsSimiCviz - Visualization Tools for Gene Regulatory Network Analysis
Visualization and export utilities for SimiC and SimiCPipeline outputs. The package focuses on importing SimiC-style results (e.g., weights, AUC metrics) from pickle/CSV files, processing and generating publication-ready plots (networks, heatmaps, distributions) and tables saved into a reproducible, ordered directory hierarchy.
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softwarevisualizationgeneregulationnetworkinferencenetworksinglecell
3.60 score 1 stars 5 scripts
TiDEomics - Time-course Differential Expression analysis of omics data
TiDEomics provides tools for time-course omics data analysis, focusing on differential expression across multiple experimental groups (>2 conditions). The package implements workflows for quality control, data processing, and analysis of temporal patterns, enabling integrated analysis of all groups in addition to pairwise comparisons. It supports datasets with missing values, including mass spectrometry-based proteomics, and operates on SummarizedExperiment objects to ensure compatibility with the Bioconductor ecosystem.
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softwaregeneexpressiondifferentialexpressionproteomicstranscriptomicstimecoursemultiplecomparisonpathwaysvisualizationmassspectrometryqualitycontrol
3.60 score 6 scriptsSpectraStash - Serialize and restore Spectra 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 SpectraStash package implements the serialization methods from the MsStash package for Spectra objects and its MsBackend classes. A variety of different file formats and types, including HDF5 and JSON-based formats defined by the Bioconductor *alabaster* package are supported. The file type can be defined and configured through a second argument `param` of the save/read methods.
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infrastructuremassspectrometrymetabolomicsdataimportproteomics
3.48 scoreMsBackendMetabolomicsWorkbench - Retrieve Mass Spectrometry Data from Metabolomics Workbench
Metabolomics Workbench is one of the main public repositories for storage of metabolomics experiments. The MsBackendMetabolomicsWorkbench package provides functionality to retrieve and represent mass spectrometry (MS) data from Metabolomics Workbench. Data files are downloaded and cached locally avoiding repetitive downloads. MS data from metabolomics experiments can thus be directly and seamlessly integrated into R-based analysis workflows with the Spectra and MsBackendMetabolomicsWorkbench package.
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infrastructuremassspectrometrymetabolomicsdataimportproteomics
3.48 scoreClinicalVariantR - ACMG/AMP Germline Variant Interpretation from Annotated VCF Files
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, applies automated and curator-guided ACMG criteria, supports streaming analysis of large call sets, and exports structured per-criterion evidence with reproducibility metadata.
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softwarevariantannotationgeneticssequencingclassificationvisualizationgui
3.48 scoregdscloud - Cloud Storage Access for GDS Files
Provides read-only access to GDS (Genomic Data Structure) files stored on cloud storage services including Amazon S3, Google Cloud Storage (GCS), and Azure Blob Storage, as well as any HTTP/HTTPS URL. Extends the 'gdsfmt' package to transparently open GDS files from cloud URLs (http://, https://, s3://, gs://, az://) using efficient block caching and HTTP Range requests via libcurl.
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infrastructuredataimportcurlopensslcpp
3.48 score
grayleafspotr - Quantitative Analysis of Gray Leaf Spot Colonies from Plate Images
Quantitative phenotyping of gray leaf spot (Cercospora zeae-maydis) fungal colonies grown on petri dishes. The package segments colonies from time-lapse plate photographs using a bundled SmallUNet deep-learning model, extracts morphometric and texture features (area, eccentricity, crack coverage, radial profile), and provides tidy result objects together with template ggplot2 visualisations. Python dependencies are managed automatically through basilisk; no manual environment setup is required.
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softwarepreprocessingvisualizationclassificationfeatureextraction
3.48 score 1 stars 7 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. The package requires the FAISS C++ library for all builds, 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. 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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softwareinfrastructuregpusinglecellflowcytometrymassspectrometryimagingmassspectrometryproteomicsclusteringdimensionreductionclassificationfortrancppopenmp
3.40 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
3.40 score 8 scriptsMRManalyzeR - 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, normalisation, internal-standard and volume adjustment of vendor-reported concentrations, missing-value imputation and batch correction. Each step is an exported function acting on a struct DatasetExperiment; a complete workflow can additionally be driven from a single YAML configuration via run_MRManalyzeR(), 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
3.30 scorepolyICSFlow - Identifying the Frequency of Polyfunctional Antigen-Specific T cells in ICS Flow Cytometry Data
polyICSFlow systematically identifies all cytokine combinations detected in an intracellular cytokine staining (ICS) flow cytometry assay and quantifies polyfunctional antigen-specific responses to single or multiple antigens. The package also offers versatile plotting options for efficient data exploration and visualization of cytokine co-expression profiles.
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flowcytometryimmunologysoftwaresinglecell
3.30 scorescCertify - Explainable Confidence Scoring for Single-Cell Annotations
scCertify provides an explainable framework for assessing the confidence of cell-type annotations in single-cell RNA sequencing data. Confidence scores are computed using marker enrichment, neighborhood agreement, entropy-based uncertainty estimation, and ontology-aware label matching to support transparent interpretation of annotation quality.
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softwaresinglecellrnaseqgeneexpressionsequencing
3.18 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 via label-augmented cross-covariance (analogous to DIABLO) with optional sparse projection matrices (PMD). Designed for comparative effectiveness research where intersection-only methods introduce selection bias.
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softwarestatisticalmethodmultiplecomparisongeneexpressiontranscriptomicsproteomicsmetabolomicsdimensionreductionclusteringclassificationsequencing
3.18 score 3 scriptsmdclust - 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 2 scriptsmultipletR - Adaptive Detection of Human-Mouse Multiplets in PDX Single-Cell Data
Detects human-mouse multiplets in patient-derived xenograft (PDX) single-cell RNA-seq data using an adaptive threshold method that does not assume a fixed species proportion. Takes a 10x CellRanger GEM classification file and returns the data with added multiplet classifications, with optional diagnostic plots and helpers to annotate a Seurat or SingleCellExperiment object with multiplet classifications or remove multiplets from it.
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singlecellrnaseqpreprocessingqualitycontroltranscriptomics
3.00 scorervarsim - Variant Simulator with HGVS Notation
Simulates all possible single nucleotide variants (SNVs) across MANE Select transcripts including coding sequence (CDS), untranslated regions (UTRs), and canonical splice sites. Outputs variants in HGVS notation. Provides a comprehensive HGVS toolkit: parsing, syntactic and semantic validation, normalization (3' shifting, common affix trimming), format conversion (HGVS <-> VCF <-> SPDI), transcription mapping (genomic <-> coding), translation to protein consequence, backtranslation from protein to coding variants, variant extraction from sequence alignment, and liftover between genome assemblies.
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geneticsvariantannotationsnpsequencingtranscriptionvariantdetectionalignmentnormalizationsequencematching
3.00 scoreloopcityData - 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 scriptsPlantTxDbHub - 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_maxsequenceannotationannotationhub
3.00 scoreTxParq.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 scriptsDgeaHeatmap - 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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bayesianclusteringdifferentialexpressiongeneexpressionnormalizationprincipalcomponentrnaseqregressionsequencingsoftwaretranscriptionalternativesplicingbatcheffectbiomedicalinformaticscellbiologycheminformaticsdataimportdifferentialsplicingepigeneticsexonarrayfunctionalgenomicsgenesetenrichmentgeneticsimmunooncologymetabolomicsmicrornaarraymicroarraymultiplecomparisononechannelpreprocessingproprietaryplatformsproteomicsqualitycontrolsystemsbiologytimecoursetwochannelmrnamicroarray
2.85 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
2.70 scoreGSE142512 - GSE142512 DNA Methylation ExperimentHub Data
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
2.70 scoreGSE280465 - GSE280465 EPICv2 Methylation ExperimentHub Data
Provides ExperimentHub access to a processed DNA methylation resource derived from GEO accession GSE280465. The resource contains adult Illumina Infinium MethylationEPIC version 2 data from 163 samples across four tissue types, represented as a RangedSummarizedExperiment with beta, M, and CN assays, hg38 genomic ranges, and sample phenotype metadata.
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experimentdataexperimenthubgeohomo_sapiens_datamethylationarraydatamicroarraydatatissue
2.70 scorePTMsToPathwaysData - 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 scoreCySA - Interactive Cluster Selector for Cytometry Data
Provides an interactive Shiny application for selecting and visualizing clusters from flow cytometry data stored in SingleCellExperiment objects.
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singlecellflowcytometryclusteringvisualizationshinyapps
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 scoreMetaPathNet - KEGG-Based Metabolic and Signaling Network Analysis for Systems Biology
Provides tools to construct KEGG-based metabolic and signaling networks as edge lists for single-organism or cross-species analyses. The package supports identifier mapping, shortest-path and topology analyses, community detection, permutation testing, pathway over-representation analysis, and node annotation for host-microbiome studies. It also provides network visualisation in R and Cytoscape and supports extension of KEGG-based networks through additional reaction resources and user-defined reactions.
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networkpathwayskeggsystemsbiologyclassificationmicrobiome
2.48 scoreGO.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
2.00 score 2 scripts