Package: genomicInstability 1.13.0
Mariano Alvarez
genomicInstability: Genomic Instability estimation for scRNA-Seq
This package contain functions to run genomic instability analysis (GIA) from scRNA-Seq data. GIA estimates the association between gene expression and genomic location of the coding genes. It uses the aREA algorithm to quantify the enrichment of sets of contiguous genes (loci-blocks) on the gene expression profiles and estimates the Genomic Instability Score (GIS) for each analyzed cell.
Authors:
genomicInstability_1.13.0.tar.gz
genomicInstability_1.13.0.zip(r-4.5)genomicInstability_1.13.0.zip(r-4.4)genomicInstability_1.13.0.zip(r-4.3)
genomicInstability_1.13.0.tgz(r-4.4-any)genomicInstability_1.13.0.tgz(r-4.3-any)
genomicInstability_1.13.0.tar.gz(r-4.5-noble)genomicInstability_1.13.0.tar.gz(r-4.4-noble)
genomicInstability_1.13.0.tgz(r-4.4-emscripten)genomicInstability_1.13.0.tgz(r-4.3-emscripten)
genomicInstability.pdf |genomicInstability.html✨
genomicInstability/json (API)
NEWS
| # Install 'genomicInstability' in R: |
| install.packages('genomicInstability', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/darwinhealth/genomicinstability/issues
- geneLength - Average length of human and mouse known genes
- geneLength - Average length of human and mouse known genes
- genePosition - Chromosomal coordinate of human and mouse known genes
- genePosition - Chromosomal coordinate of human and mouse known genes
On BioConductor:genomicInstability-1.13.0(bioc 3.21)genomicInstability-1.12.0(bioc 3.20)
systemsbiologygeneexpressionsinglecell
Last updated 2 months agofrom:a8d038857c. Checks:OK: 1 NOTE: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 29 2024 |
| R-4.5-win | NOTE | Nov 29 2024 |
| R-4.5-linux | NOTE | Dec 29 2024 |
| R-4.4-win | NOTE | Nov 29 2024 |
| R-4.4-mac | NOTE | Dec 29 2024 |
| R-4.3-win | NOTE | Nov 29 2024 |
| R-4.3-mac | NOTE | Dec 29 2024 |
Exports:generateChromosomeGeneSetgenomicInstabilityScoregiDensityPlotgiLikelihoodinferCNV
Dependencies:abindaskpassbackportsbase64encBiobaseBiocGenericsbslibcachemcheckmateclicolorspacecpp11crayoncrosstalkcurldata.tableDelayedArraydigestdplyrevaluatefansifarverfastmapfontawesomefsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegtablehighrhtmltoolshtmlwidgetshttrIRangesisobandjquerylibjsonlitekernlabknitrlabelinglaterlatticelazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemixtoolsmunsellnlmeopensslpillarpkgconfigplotlypromisespurrrR6rappdirsRColorBrewerRcpprlangrmarkdownS4ArraysS4VectorssassscalessegmentedSparseArraystringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselecttinytexUCSC.utilsutf8vctrsviridisLitewithrxfunXVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Average length of human and mouse known genes | geneLength |
| Chromosomal coordinate of human and mouse known genes | genePosition |
| Topological gene sets | generateChromosomeGeneSet |
| Genomic Instability Analysis | genomicInstabilityScore |
| Genomic instability plot | giDensityPlot |
| Genomic instability likelihood | giLikelihood |
| Inference of CNV from expression data | inferCNV |
| Plot chromosome map | plot.inferCNV |
