Package: sciNOME 0.99.4

Shitao Zhou

sciNOME: 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.

Authors:Shitao Zhou [aut, cre], Medinfo Lab [fnd]

sciNOME_0.99.4.tar.gz
sciNOME_0.99.4.zip(r-4.7-any)sciNOME_0.99.4.zip(r-4.6-any)sciNOME_0.99.4.zip(r-4.5-any)
sciNOME_0.99.4.tgz(r-4.6-any)sciNOME_0.99.4.tgz(r-4.5-any)
sciNOME_0.99.4.tar.gz(r-4.7-any)sciNOME_0.99.4.tar.gz(r-4.6-any)
sciNOME_0.99.4.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
sciNOME/json (API)

# Install 'sciNOME' in R:
install.packages('sciNOME', repos = c('https://biocstaging.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/medinfo-lab/scinome/issues

On CRAN:

Conda:

softwaresinglecellepigeneticstranscriptomicsdnamethylationdifferentialexpressiondimensionreductionclusteringqualitycontrol

4.38 score 23 exports 112 dependencies

Last updated from:af1b85c1ee. Checks:8 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE168
linux-develNOTE220
source / vignettesOK277
linux-releaseNOTE230
macos-releaseNOTE202
macos-oldrelNOTE171
windows-develNOTE178
windows-releaseNOTE197
windows-oldrelNOTE143
wasm-releaseOK140

Exports:AddMetaData_RNAAggregate_epiRegionsBuild_RNAObjectCreateRNAObjectExtract_epiDataIntegrate_MultiOmicsPlotDimRed_EpiPlotDimRed_RNAPlotLandscape_EpiPlotOmicsMatrixPlotOmicsScatterPlotPseudo_RNAPlotQC_RNAPlotVolcano_EpiPlotVolcano_RNAProcessQC_RNAQC_epiDataReduce_epiDimsRun_DiffanalysisRunClustering_RNARunDEA_RNARunDimReduction_RNARunPseudotime_RNA

Dependencies:abindbackportsBHBiobaseBiocGenericsBiocManagerbootbroomcarcarDatacliclustercodetoolscolorspacecorrplotcowplotcpp11data.tableDerivdigestdoBydoParalleldplyrdqrngfarverFNNforeachforecastFormulafracdiffgenericsGenomicRangesggplot2ggpubrggrepelggridgesggsciggsignifgluegridBasegridExtragtableigraphimputeIRangesirlbaisobanditeratorslabelinglatticelifecyclelme4lmtestmagrittrMASSMatrixMatrixModelsmgcvminqamodelrnlmenloptrNMFnnetnumDerivpatchworkpbapplypbkrtestpillarpkgconfigplyrpolynomprincurvepurrrquantregR6rbibutilsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppProgressRdpackreformulasregistryreshape2rlangrngtoolsRSpectrarstatixRtsneS4VectorsS7scalesSeqinfositmoSparseMstringistringrsurvivaltibbletidyrtidyselecttimeDateurcautf8uwotvctrsviridisLitewithrzoo

Epigenetic Data Processing and Analysis using sciNOME
Introduction | 1. Setup and Mock Data Generation | 2. Data Aggregation | 3. Extracting specific Metrics and Quality Control | 4. Dimensionality Reduction | 5. Differential Epigenetic Analysis | Session Information
Rendered fromEpi_Analysis.Rmdusingknitr::rmarkdown

Last update: 2026-08-23
Started: 2026-05-13

Multi-Omics Integration in sciNOME
Introduction | 1. Prepare Mock Multi-Omics Data | 1.1 Global Metadata | 1.2 Region Dictionary | 1.3 Simulate Omics Matrices | 2. Multi-Omics Integration | Mode A: Tri-Omics Integration (RNA + CpG + GpC) | Mode B: Dual Integration (RNA + CpG) | Mode C: Epigenetics Only Integration (CpG + GpC) | Session Information
Rendered fromMultiOmics_Integration.Rmdusingknitr::rmarkdown

Last update: 2026-08-23
Started: 2026-05-13

Single-Cell RNA Analysis Pipeline in sciNOME
Introduction | 1. Data Preparation | 2. Object Construction and QC | 3. Dimensionality Reduction | 4. Unsupervised Clustering | 5. Differential Expression Analysis (DEA) | 6. Trajectory Inference (Pseudotime) | Session Information
Rendered fromRNA_Analysis.Rmdusingknitr::rmarkdown

Last update: 2026-08-23
Started: 2026-05-13

Visualization Gallery in sciNOME
Introduction | 1. Single-Cell RNA Visualization | 1.1 Quality Control Plot | 1.2 Dimensionality Reduction Plot | 1.3 Volcano Plot for DEA | 1.4 Trajectory & Pseudotime Plot | 2. Epigenetic Visualization | 2.1 Epigenetic Landscape (Ridge Plot) | 2.2 Dimensionality Reduction for Epigenetics | 2.3 Epigenetic Volcano Plot | 3. Multi-Omics Integration Plots | 3.1 Omics Correlation Matrix | 3.2 Pairwise Scatter Plots | Session Information
Rendered fromPlot.Rmdusingknitr::rmarkdown

Last update: 2026-08-23
Started: 2026-05-14