Package: fastLiquidAssociation 1.49.0

Tina Gunderson

fastLiquidAssociation: functions for genome-wide application of Liquid Association

This package extends the function of the LiquidAssociation package for genome-wide application. It integrates a screening method into the LA analysis to reduce the number of triplets to be examined for a high LA value and provides code for use in subsequent significance analyses.

Authors:Tina Gunderson

fastLiquidAssociation_1.49.0.tar.gz
fastLiquidAssociation_1.49.0.zip(r-4.7)fastLiquidAssociation_1.49.0.zip(r-4.6)fastLiquidAssociation_1.49.0.zip(r-4.5)
fastLiquidAssociation_1.49.0.tgz(r-4.6-any)fastLiquidAssociation_1.49.0.tgz(r-4.5-any)
fastLiquidAssociation_1.49.0.tar.gz(r-4.7-any)fastLiquidAssociation_1.49.0.tar.gz(r-4.6-any)
fastLiquidAssociation_1.49.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
fastLiquidAssociation/json (API)

# Install 'fastLiquidAssociation' in R:

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

Datasets:

testmat - Example results from fastMLA requiring all significance methods

On BioConductor:fastLiquidAssociation-1.49.0(bioc 3.24)fastLiquidAssociation-1.48.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

software geneexpression genetics pathways cellbiology

3.30 score 3 scripts 1 mentions 3 exports 105 dependencies

Last updated from:a5e403d15e. Checks:1 ERROR, 7 WARNING, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	226
linux-devel-x86_64	WARNING	322
source / vignettes	OK	366
linux-release-x86_64	WARNING	361
macos-release-arm64	WARNING	201
macos-oldrel-arm64	WARNING	172
windows-devel	WARNING	243
windows-release	WARNING	254
windows-oldrel	WARNING	235
wasm-release	OK	227

Exports:fastboots.GLA fastMLA mass.CNM

Dependencies:AnnotationDbi askpass backports base64enc Biobase BiocGenerics Biostrings bit bit64 blob broom bslib cachem checkmate cli cluster codetools colorspace cpp11 crayon curl data.table DBI digest doParallel dplyr dynamicTreeCut evaluate farver fastcluster fastmap fontawesome foreach foreign Formula fs geepack generics ggplot2 glue gridExtra gtable highr Hmisc htmlTable htmltools htmlwidgets httr impute IRanges isoband iterators jquerylib jsonlite KEGGREST knitr labeling lattice lifecycle LiquidAssociation magrittr MASS Matrix matrixStats memoise mime nnet openssl org.Sc.sgd.db pillar pkgconfig png preprocessCore purrr R6 rappdirs RColorBrewer Rcpp rlang rmarkdown rpart RSQLite rstudioapi S4Vectors S7 sass scales Seqinfo stringi stringr survival sys tibble tidyr tidyselect tinytex utf8 vctrs viridisLite WGCNA withr xfun XVector yaml yeastCC

fastLiquidAssociation Vignette

Rendered fromfastLiquidAssociation.Rnwusingutils::Sweave

Last update: 2017-10-23
Started: 2014-04-11

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Functions to extend liquid association (LA) analysis for genome-wide use	fastLiquidAssociation-package fastLiquidAssociation
Function to parallelize bootstrapping for MLA robust estimates.	fastboots.GLA fastboots.GLA,ANY,matrix-method fastboots.GLA-class fastboots.GLA-methods
Function to more efficiently screen for gene triplets for those with a high liquid association value.	fastMLA fastMLA,matrix-method fastMLA-class fastMLA-methods
Function to obtain CNM significance estimates from an object result of fastMLA.	mass.CNM mass.CNM,matrix,data.frame-method mass.CNM-class mass.CNM-methods
Example results from fastMLA requiring all significance methods	testmat