Package: consICA 2.11.0

Petr V. Nazarov

consICA: consensus Independent Component Analysis

consICA implements a data-driven deconvolution method – consensus independent component analysis (ICA) to decompose heterogeneous omics data and extract features suitable for patient diagnostics and prognostics. The method separates biologically relevant transcriptional signals from technical effects and provides information about the cellular composition and biological processes. The implementation of parallel computing in the package ensures efficient analysis of modern multicore systems.

Authors:Petr V. Nazarov [aut, cre], Tony Kaoma [aut], Maryna Chepeleva [aut]

consICA_2.11.0.tar.gz
consICA_2.11.0.zip(r-4.7)consICA_2.11.0.zip(r-4.6)consICA_2.11.0.zip(r-4.5)
consICA_2.11.0.tgz(r-4.6-any)consICA_2.11.0.tgz(r-4.5-any)
consICA_2.11.0.tar.gz(r-4.7-any)consICA_2.11.0.tar.gz(r-4.6-any)
consICA_2.11.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
consICA/json (API)

# Install 'consICA' in R:

install.packages('consICA', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/biomod-lih/consica/issues

Datasets:

samples_data - Samples of gene expression

On BioConductor:consICA-2.11.0(bioc 3.24)consICA-2.10.0(bioc 3.23)

technology statisticalmethod sequencing rnaseq transcriptomics classification featureextraction

4.70 score 5 scripts 13 exports 77 dependencies

Last updated from:6e95b58cc9. Checks:8 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	241
linux-devel-x86_64	NOTE	423
source / vignettes	OK	367
linux-release-x86_64	NOTE	394
macos-release-arm64	NOTE	263
macos-oldrel-arm64	NOTE	209
windows-devel	NOTE	365
windows-release	NOTE	354
windows-oldrel	NOTE	379
wasm-release	OK	236

Exports:anovaIC consICA estimateVarianceExplained getFeatures getGO is.consICA oneICA overlapGO plotICVarianceExplained saveReport setOrientation sortDataFrame survivalAnalysis

Dependencies:abind AnnotationDbi askpass BH Biobase BiocGenerics BiocParallel Biostrings bit bit64 blob cachem cli codetools cpp11 crayon curl DBI DelayedArray farver fastICA fastmap formatR futile.logger futile.options generics GenomicRanges ggplot2 glue GO.db graph gtable httr IRanges isoband jsonlite KEGGREST labeling lambda.r lattice lifecycle Matrix MatrixGenerics matrixStats memoise mime openssl org.Hs.eg.db pheatmap pkgconfig png R6 RColorBrewer Rcpp RcppArmadillo RcppParallel Rfast rlang RSQLite S4Arrays S4Vectors S7 scales Seqinfo sm snow SparseArray SparseM SummarizedExperiment survival sys topGO vctrs viridisLite withr XVector zigg

The consICa package: User’s manual

Rendered fromConsICA.Rmdusingknitr::rmarkdown

Last update: 2023-09-18
Started: 2022-04-01

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
ANOVA test for independent component across factors	anovaIC
Calculate consensus Independent Component Analysis	consICA
Enrichment analysis of GO-terms based on Ensembl IDs	enrichGO
Estimate the variance explained by the model	estimateVarianceExplained
Get features from consICA deconvolution result	getFeatures
Assigns IC signatures to Gene Ontologies	getGO
Is the object is consensus ICA compliant?	is.consICA
Runs 'fastICA'	oneICA
Similarity of two gene ontologies lists	overlapGO
Barplot variance explained by each IC	plotICVarianceExplained
Samples of gene expression	samples_data
Save PDF report with analysis of each independent component	saveReport
Set orientation for independent components	setOrientation
Sort dataframe	sortDataFrame
Survival analysis based on significant IC	survivalAnalysis