Introduction | Installation | Code Example | SiPSiC's Algorithm | 1. Pathway data extraction | 2. Score normalization | 3. Normalized gene rankings calculation | 4. Gene weighing | 5. Pathway scoring | Session Information
Package: SiPSiC 1.13.0
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:
SiPSiC_1.13.0.tar.gz
SiPSiC_1.13.0.zip(r-4.7)SiPSiC_1.13.0.zip(r-4.6)SiPSiC_1.13.0.zip(r-4.5)
SiPSiC_1.13.0.tgz(r-4.6-any)SiPSiC_1.13.0.tgz(r-4.5-any)
SiPSiC_1.13.0.tar.gz(r-4.7-any)SiPSiC_1.13.0.tar.gz(r-4.6-any)
SiPSiC_1.13.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
SiPSiC/json (API)
| # Install 'SiPSiC' in R: |
| install.packages('SiPSiC', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/danieldavis12/sipsic/issues
On BioConductor:SiPSiC-1.13.0(bioc 3.24)SiPSiC-1.12.0(bioc 3.23)
softwaredifferentialexpressiongenesetenrichmentbiomedicalinformaticscellbiologytranscriptomicsrnaseqsinglecelltranscriptionsequencingimmunooncologydataimport
Last updated from:ee7c0723f8. Checks:1 NOTE, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 142 | ||
| linux-devel-x86_64 | OK | 249 | ||
| source / vignettes | OK | 219 | ||
| linux-release-x86_64 | OK | 278 | ||
| macos-release-arm64 | OK | 151 | ||
| macos-oldrel-arm64 | OK | 139 | ||
| windows-devel | OK | 198 | ||
| windows-release | OK | 173 | ||
| windows-oldrel | OK | 173 | ||
| wasm-release | OK | 109 |
Exports:getPathwayScores
Dependencies:abindBiobaseBiocGenericsDelayedArraygenericsGenomicRangesIRangeslatticeMatrixMatrixGenericsmatrixStatsS4ArraysS4VectorsSeqinfoSingleCellExperimentSparseArraySummarizedExperimentXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Calculate Pathway Scores for Each Cell in scRNA-Seq Data | SiPSiC-package SiPSiC |
| Calculate Pathway Scores for all Cells in a scRNA-Seq Data | getPathwayScores |
| Gene counts normalization | normalizeCountsForGene |
