Package: SwarnSeq 0.99.5

Samarendra Das

SwarnSeq: Differential Expression and Differential Zero Inflation analysis

This R package performs differential expression and differential zero inflation analysis of single-cell RNA-seq (scRNA-seq) UMI counts data through adjusting cell capture efficiency.

Authors:Samarendra Das [aut, cre], Satyajit Chhatoi [aut], Indian Council of Agricultural Research [fnd], Science and Engineering Research Board [fnd]

SwarnSeq_0.99.5.tar.gz
SwarnSeq_0.99.5.zip(r-4.7-any)SwarnSeq_0.99.5.zip(r-4.6-any)SwarnSeq_0.99.5.zip(r-4.5-any)
SwarnSeq_0.99.5.tgz(r-4.6-any)SwarnSeq_0.99.5.tgz(r-4.5-any)
SwarnSeq_0.99.5.tar.gz(r-4.7-any)SwarnSeq_0.99.5.tar.gz(r-4.6-any)
SwarnSeq_0.99.5.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
SwarnSeq/json (API)

# Install 'SwarnSeq' in R:

install.packages('SwarnSeq', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/nifmd-bbf/swarnseq/issues

Datasets:

SpikeInData - Spike-in counts data for the SwarnSeqToyData.
SwarnSeqToyData - A test scRNA-seq Real Dataset for SwarnSeq

On BioConductor:SwarnSeq-0.99.5(bioc 3.24)

software singlecell rnaseq differentialexpression geneexpression statisticalmethod

4.18 score 1 stars 5 scripts 216 downloads 6 exports 23 dependencies

Last updated from:651b42d4ae. Checks:8 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	164
linux-devel	NOTE	359
source / vignettes	OK	202
linux-release	NOTE	270
macos-release	NOTE	234
macos-oldrel	NOTE	182
windows-devel	NOTE	229
windows-release	NOTE	232
windows-oldrel	NOTE	254
wasm-release	OK	112

Exports:capEff extAdjNormData swarnAdjLrt swarnClassDe swarnTopTags swarnUnadjLrt

Dependencies:abind Biobase BiocGenerics DelayedArray edgeR generics GenomicRanges IRanges lattice limma locfit MASS Matrix MatrixGenerics matrixStats S4Arrays S4Vectors Seqinfo SingleCellExperiment SparseArray statmod SummarizedExperiment XVector

SwarnSeq

Rendered fromSwarnSeq.Rmdusingknitr::rmarkdown

Last update: 2026-07-22
Started: 2025-08-25

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Cell Capture Efficiency Estimating Function	capEff
Two-Factor Normalized Counts Matrix Splitting Function	extAdjNormData
Spike-in counts data for the SwarnSeqToyData.	SpikeInData
Differential gene expression analysis for single-cell data	swarnAdjLrt
ScRNA-seq Influential Gene Classification Function	swarnClassDe
A test scRNA-seq Real Dataset for SwarnSeq	SwarnSeqToyData
Most Statistically Significant Gene Filtering Function	swarnTopTags
Differential gene expression analysis for single-cell data without Capture Efficiency Correction	swarnUnadjLrt