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 (3.21)
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] (ORCID:
Maintainer: Daniel Davis <DanielDavis000 at gmail.com>
citation("SiPSiC")):
Installation
To install this package, start R (version "4.5") 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | BiomedicalInformatics, CellBiology, DataImport, DifferentialExpression, GeneSetEnrichment, ImmunoOncology, RNASeq, Sequencing, SingleCell, Software, Transcription, Transcriptomics |
| Version | 1.7.0 |
| 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 |
See More
| 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_1.7.0.tar.gz |
| Windows Binary (x86_64) | SiPSiC_1.7.0.zip (64-bit only) |
| macOS Binary (x86_64) | SiPSiC_1.7.0.tgz |
| macOS Binary (arm64) | SiPSiC_1.7.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/SiPSiC |
| Source Repository (Developer Access) | git clone [email protected]:packages/SiPSiC |
| Bioc Package Browser | https://code.bioconductor.org/browse/SiPSiC/ |
| Package Short Url | https://bioconductor.org/packages/SiPSiC/ |
| Package Downloads Report | Download Stats |