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✨
DESCRIPTION |NEWS
card.svg |card.png
genomicInstability/json (API)

# 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)

systemsbiology geneexpression singlecell

4.38 score 5 stars 12 scripts 5 exports 88 dependencies

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

Target	Result	Time
bioc-checks	WARNING	215
linux-devel-x86_64	NOTE	483
source / vignettes	OK	273
linux-release-x86_64	NOTE	473
macos-release-arm64	NOTE	263
macos-oldrel-arm64	NOTE	244
windows-devel	NOTE	285
windows-release	NOTE	461
windows-oldrel	NOTE	307
wasm-release	OK	164

Exports:generateChromosomeGeneSet genomicInstabilityScore giDensityPlot giLikelihood inferCNV

Dependencies:abind askpass backports base64enc Biobase BiocGenerics bslib cachem checkmate cli cpp11 crosstalk curl data.table DelayedArray digest dplyr evaluate farver fastmap fontawesome fs generics GenomicRanges ggplot2 glue gtable highr htmltools htmlwidgets httr IRanges isoband jquerylib jsonlite kernlab knitr labeling later lattice lazyeval lifecycle magrittr MASS Matrix MatrixGenerics matrixStats memoise mime mixtools nlme openssl otel pillar pkgconfig plotly promises purrr R6 rappdirs RColorBrewer Rcpp rlang rmarkdown S4Arrays S4Vectors S7 sass scales segmented Seqinfo SparseArray stringi stringr SummarizedExperiment survival sys tibble tidyr tidyselect tinytex utf8 vctrs viridisLite withr xfun XVector yaml

Using genomicInstability

Overview of genomicInstability | Installation of genomicInstability package | Use-case example for the analysis of HNSC and normal cells | Session Information

Rendered fromgenomicInstability.Rnwusingutils::Sweave

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

Citation

Development and contributors

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