SiPSiC

This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see SiPSiC.

Calculate Pathway Scores for Each Cell in scRNA-Seq Data

Bioconductor version: 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")):

Installation

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


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
BiocManager::install("SiPSiC")

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

Documentation

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

browseVignettes("SiPSiC")

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

Reference Manual PDF

NEWS Text

LICENSE Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews BiomedicalInformatics, CellBiology, DataImport, DifferentialExpression, GeneSetEnrichment, ImmunoOncology, RNASeq, Sequencing, SingleCell, Software, Transcription, Transcriptomics

Version 1.4.3

In Bioconductor since BioC 3.17 (R-4.3) (1.5 years)

License file LICENSE

Depends Matrix, SingleCellExperiment

Imports

System Requirements

URL https://www.genome.org/cgi/doi/10.1101/gr.278431.123

Bug Reports https://github.com/DanielDavis12/SiPSiC/issues

Suggests knitr, rmarkdown, BiocStyle

Linking To

Enhances

Depends On Me

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Build Report Build Report

Package Archives

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

Source Package SiPSiC_1.4.3.tar.gz

Windows Binary (x86_64) SiPSiC_1.4.3.zip

macOS Binary (x86_64) SiPSiC_1.4.3.tgz

macOS Binary (arm64) SiPSiC_1.4.3.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

Old Source Packages for BioC 3.19 Source Archive