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SiPSiC

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")):

Installation

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


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

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
Imports
System Requirements
URL https://doi.org/10.1101/2023.03.27.534310
Bug Reports https://github.com/DanielDavis12/SiPSiC/issues
See More
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_1.3.2.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