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This is the development version of SiPSiC; for the stable release version, see SiPSiC.

Calculate Pathway Scores for Each Cell in scRNA-Seq Data

Bioconductor version: Development (3.19)

Infer biological pathway activity of cells from single-cell RNA-sequencing data by calculating a pathway score for each cell (pathway genes are specified by the user). It is recommended to have the data in Transcripts-Per-Million (TPM) or Counts-Per-Million (CPM) units for best results. Scores may change when adding cells to or removing cells off the data. SiPSiC stands for Single Pathway analysis in Single Cells.

Author: Daniel Davis [aut, cre] , Yotam Drier [aut]

Maintainer: Daniel Davis <DanielDavis000 at gmail.com>

Citation (from within R, enter citation("SiPSiC")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

Infer Biological Pathway Activity from Single-Cell RNA-Seq Data HTML R Script
Reference Manual PDF


biocViews BiomedicalInformatics, CellBiology, DataImport, DifferentialExpression, GeneSetEnrichment, ImmunoOncology, RNASeq, Sequencing, SingleCell, Software, Transcription, Transcriptomics
Version 1.3.2
In Bioconductor since BioC 3.17 (R-4.3) (1 year)
License file LICENSE
Depends Matrix, SingleCellExperiment
System Requirements
URL https://doi.org/10.1101/2023.03.27.534310
Bug Reports https://github.com/DanielDavis12/SiPSiC/issues
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Suggests knitr, rmarkdown, BiocStyle
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package SiPSiC_1.3.2.tar.gz
Windows Binary SiPSiC_1.3.2.zip
macOS Binary (x86_64) SiPSiC_1.3.2.tgz
macOS Binary (arm64) SiPSiC_1.3.2.tgz
Source Repository git clone https://git.bioconductor.org/packages/SiPSiC
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/SiPSiC
Bioc Package Browser https://code.bioconductor.org/browse/SiPSiC/
Package Short Url https://bioconductor.org/packages/SiPSiC/
Package Downloads Report Download Stats