SiPSiC

This is the released version of SiPSiC; for the devel version, see SiPSiC.

Calculate Pathway Scores for Each Cell in scRNA-Seq Data

Bioconductor version: Release (3.20)

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	1.6.0
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
Imports Me
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	SiPSiC_1.6.0.tar.gz
Windows Binary (x86_64)	SiPSiC_1.6.0.zip
macOS Binary (x86_64)	SiPSiC_1.6.0.tgz
macOS Binary (arm64)	SiPSiC_1.6.0.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