Package: genomicInstability 1.11.0

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_1.11.0.tar.gz
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genomicInstability_1.11.0.tgz(r-4.4-any)genomicInstability_1.11.0.tgz(r-4.3-any)
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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-1.11.0(bioc 3.20)genomicInstability-1.10.0(bioc 3.19)

bioconductor-package

5 exports 0.49 score 94 dependencies

Last updated 2 months agofrom:6dfde846dd

Exports:generateChromosomeGeneSet genomicInstabilityScore giDensityPlot giLikelihood inferCNV

Dependencies:abind askpass backports base64enc Biobase BiocGenerics bslib cachem checkmate cli colorspace cpp11 crayon crosstalk curl data.table DelayedArray digest dplyr evaluate fansi farver fastmap fontawesome fs generics GenomeInfoDb GenomeInfoDbData 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 mgcv mime mixtools munsell nlme openssl pillar pkgconfig plotly promises purrr R6 rappdirs RColorBrewer Rcpp rlang rmarkdown S4Arrays S4Vectors sass scales segmented SparseArray stringi stringr SummarizedExperiment survival sys tibble tidyr tidyselect tinytex UCSC.utils utf8 vctrs viridisLite withr xfun XVector yaml zlibbioc

Using genomicInstability

Rendered fromgenomicInstability.Rnwusingutils::Sweaveon Jun 13 2024.

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