Package: genomicInstability 1.19.0

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:Mariano Alvarez [aut, cre], Pasquale Laise [aut], DarwinHealth [cph]

genomicInstability_1.19.0.tar.gz
genomicInstability_1.19.0.zip(r-4.7)genomicInstability_1.19.0.zip(r-4.6)genomicInstability_1.19.0.zip(r-4.5)
genomicInstability_1.19.0.tgz(r-4.6-any)genomicInstability_1.19.0.tgz(r-4.5-any)
genomicInstability_1.19.0.tar.gz(r-4.7-any)genomicInstability_1.19.0.tar.gz(r-4.6-any)
genomicInstability_1.19.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
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

Datasets:
  • 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-1.19.0(bioc 3.24)genomicInstability-1.18.0(bioc 3.23)

systemsbiologygeneexpressionsinglecell

4.38 score 5 stars 12 scripts 330 downloads 5 exports 88 dependencies

Last updated from:190734f548. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING179
linux-devel-x86_64NOTE334
source / vignettesOK258
linux-release-x86_64NOTE331
macos-release-arm64NOTE401
macos-oldrel-arm64NOTE207
windows-develNOTE292
windows-releaseNOTE429
windows-oldrelNOTE381
wasm-releaseOK143

Exports:generateChromosomeGeneSetgenomicInstabilityScoregiDensityPlotgiLikelihoodinferCNV

Dependencies:abindaskpassbackportsbase64encBiobaseBiocGenericsbslibcachemcheckmateclicpp11crosstalkcurldata.tableDelayedArraydigestdplyrevaluatefarverfastmapfontawesomefsgenericsGenomicRangesggplot2gluegtablehighrhtmltoolshtmlwidgetshttrIRangesisobandjquerylibjsonlitekernlabknitrlabelinglaterlatticelazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimemixtoolsnlmeopensslotelpillarpkgconfigplotlypromisespurrrR6rappdirsRColorBrewerRcpprlangrmarkdownS4ArraysS4VectorsS7sassscalessegmentedSeqinfoSparseArraystringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselecttinytexutf8vctrsviridisLitewithrxfunXVectoryaml

Using genomicInstability

Rendered fromgenomicInstability.Rnwusingutils::Sweaveon May 30 2026.

Last update: 2021-03-05
Started: 2021-02-26