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

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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

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-1.13.0(bioc 3.21)genomicInstability-1.12.0(bioc 3.20)

systemsbiologygeneexpressionsinglecell

4.00 score 5 stars 3 scripts 228 downloads 5 exports 93 dependencies

Last updated 4 months agofrom:a8d038857c. Checks:1 OK, 7 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKFeb 27 2025
R-4.5-winNOTEFeb 27 2025
R-4.5-macNOTEFeb 27 2025
R-4.5-linuxNOTEFeb 27 2025
R-4.4-winNOTEFeb 27 2025
R-4.4-macNOTEFeb 27 2025
R-4.3-winNOTEFeb 27 2025
R-4.3-macNOTEFeb 27 2025

Exports:generateChromosomeGeneSetgenomicInstabilityScoregiDensityPlotgiLikelihoodinferCNV

Dependencies:abindaskpassbackportsbase64encBiobaseBiocGenericsbslibcachemcheckmateclicolorspacecpp11crayoncrosstalkcurldata.tableDelayedArraydigestdplyrevaluatefansifarverfastmapfontawesomefsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegtablehighrhtmltoolshtmlwidgetshttrIRangesisobandjquerylibjsonlitekernlabknitrlabelinglaterlatticelazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemixtoolsmunsellnlmeopensslpillarpkgconfigplotlypromisespurrrR6rappdirsRColorBrewerRcpprlangrmarkdownS4ArraysS4VectorssassscalessegmentedSparseArraystringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselecttinytexUCSC.utilsutf8vctrsviridisLitewithrxfunXVectoryaml

Using genomicInstability

Rendered fromgenomicInstability.Rnwusingutils::Sweaveon Feb 27 2025.

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