Package: SiPSiC 1.7.0

Daniel Davis

SiPSiC: Calculate Pathway Scores for Each Cell in scRNA-Seq Data

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.

Authors:Daniel Davis [aut, cre], Yotam Drier [aut]

SiPSiC_1.7.0.tar.gz
SiPSiC_1.7.0.zip(r-4.5)SiPSiC_1.7.0.zip(r-4.4)SiPSiC_1.7.0.zip(r-4.3)
SiPSiC_1.7.0.tgz(r-4.4-any)SiPSiC_1.7.0.tgz(r-4.3-any)
SiPSiC_1.7.0.tar.gz(r-4.5-noble)SiPSiC_1.7.0.tar.gz(r-4.4-noble)
SiPSiC_1.7.0.tgz(r-4.4-emscripten)SiPSiC_1.7.0.tgz(r-4.3-emscripten)
SiPSiC.pdf |SiPSiC.html✨
SiPSiC/json (API)
NEWS

# Install 'SiPSiC' in R:
install.packages('SiPSiC', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/danieldavis12/sipsic/issues

On BioConductor:SiPSiC-1.7.0(bioc 3.21)SiPSiC-1.6.0(bioc 3.20)

softwaredifferentialexpressiongenesetenrichmentbiomedicalinformaticscellbiologytranscriptomicsrnaseqsinglecelltranscriptionsequencingimmunooncologydataimport

5.26 score 6 stars 3 scripts 183 downloads 1 exports 29 dependencies

Last updated 3 months agofrom:688dfb8933. Checks:7 OK. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKJan 17 2025
R-4.5-winOKJan 17 2025
R-4.5-linuxOKJan 17 2025
R-4.4-winOKJan 17 2025
R-4.4-macOKJan 17 2025
R-4.3-winOKJan 17 2025
R-4.3-macOKJan 17 2025

Exports:getPathwayScores

Dependencies:abindaskpassBiobaseBiocGenericscrayoncurlDelayedArraygenericsGenomeInfoDbGenomeInfoDbDataGenomicRangeshttrIRangesjsonlitelatticeMatrixMatrixGenericsmatrixStatsmimeopensslR6S4ArraysS4VectorsSingleCellExperimentSparseArraySummarizedExperimentsysUCSC.utilsXVector

SiPSiC - Infer Biological Pathway Activity from Single-Cell RNA-Seq Data

Rendered fromSiPSiC.Rmdusingknitr::rmarkdownon Jan 17 2025.

Last update: 2023-12-11
Started: 2023-01-09