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 (3.24)
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("SiPSiC")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | 1.13.0 |
| In Bioconductor since | BioC 3.17 (R-4.3) (3.5 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 | GSABenchmark |
| 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_1.13.0.tar.gz |
| Windows Binary (x86_64) | SiPSiC_1.13.0.zip |
| macOS Binary (big-sur-x86_64) | SiPSiC_1.13.0.tgz |
| macOS Binary (sonoma-arm64) | SiPSiC_1.13.0.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 |