Package: sciNOME 0.99.0

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_0.99.0.tar.gz
sciNOME_0.99.0.zip(r-4.7)sciNOME_0.99.0.zip(r-4.6)sciNOME_0.99.0.zip(r-4.5)
sciNOME_0.99.0.tgz(r-4.6-any)sciNOME_0.99.0.tgz(r-4.5-any)
sciNOME_0.99.0.tar.gz(r-4.7-any)sciNOME_0.99.0.tar.gz(r-4.6-any)
sciNOME_0.99.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
sciNOME/json (API)
NEWS

# 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

4.34 score 23 exports 113 dependencies

Last updated from:890d8da44f. Checks:8 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE188
linux-devel-x86_64NOTE243
source / vignettesOK309
linux-release-x86_64NOTE257
macos-release-arm64NOTE171
macos-oldrel-arm64NOTE177
windows-develNOTE178
windows-releaseNOTE173
windows-oldrelNOTE196
wasm-releaseOK168

Exports:AddMetaData_RNAAggregate_epiRegionsBuild_RNAObjectCreateRNAObjectExtract_epiDataIntegrate_MultiOmicsPlotDimRed_EpiPlotDimRed_RNAPlotLandscape_EpiPlotOmicsMatrixPlotOmicsScatterPlotPseudo_RNAPlotQC_RNAPlotVolcano_EpiPlotVolcano_RNAProcessQC_RNAQC_epiDataReduce_epiDimsRun_DiffanalysisRunClustering_RNARunDEA_RNARunDimReduction_RNARunPseudotime_RNA

Dependencies:abindbackportsBHBiobaseBiocGenericsBiocManagerbootbroomcarcarDatacliclustercodetoolscolorspacecorrplotcowplotcpp11data.tableDerivdigestdoBydoParalleldplyrdqrngfarverFNNforeachforecastFormulafracdiffgenericsGenomicRangesggplot2ggpubrggrepelggridgesggsciggsignifgluegridBasegridExtragtableigraphimputeIRangesirlbaisobanditeratorslabelinglatticelifecyclelme4lmtestmagrittrMASSMatrixMatrixModelsmgcvmicrobenchmarkminqamodelrnlmenloptrNMFnnetnumDerivpatchworkpbapplypbkrtestpillarpkgconfigplyrpolynomprincurvepurrrquantregR6rbibutilsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppProgressRdpackreformulasregistryreshape2rlangrngtoolsRSpectrarstatixRtsneS4VectorsS7scalesSeqinfositmoSparseMstringistringrsurvivaltibbletidyrtidyselecttimeDateurcautf8uwotvctrsviridisLitewithrzoo

Epigenetic Data Processing and Analysis using sciNOME

Shitao Zhou

Rendered fromEpi_Analysis.Rmdusingknitr::rmarkdownon Jun 14 2026.

Last update: 2026-05-14
Started: 2026-05-13

Multi-Omics Integration in sciNOME

Shitao Zhou

Rendered fromMultiOmics_Integration.Rmdusingknitr::rmarkdownon Jun 14 2026.

Last update: 2026-05-14
Started: 2026-05-13

Single-Cell RNA Analysis Pipeline in sciNOME

Shitao Zhou

Rendered fromRNA_Analysis.Rmdusingknitr::rmarkdownon Jun 14 2026.

Last update: 2026-05-14
Started: 2026-05-13

Visualization Gallery in sciNOME

Shitao Zhou

Rendered fromPlot.Rmdusingknitr::rmarkdownon Jun 14 2026.

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