Package: fluentGenomics 1.25.0

Stuart Lee

fluentGenomics: A plyranges and tximeta workflow

An extended workflow using the plyranges and tximeta packages for fluent genomic data analysis. Use tximeta to correctly import RNA-seq transcript quantifications and summarize them to gene counts for downstream analysis. Use plyranges for clearly expressing operations over genomic coordinates and to combine results from differential expression and differential accessibility analyses.

Authors:Stuart Lee [aut, cre], Michael Love [aut, ctb]

fluentGenomics_1.25.0.tar.gz
fluentGenomics_1.25.0.zip(r-4.7-any)fluentGenomics_1.25.0.zip(r-4.6-any)fluentGenomics_1.25.0.zip(r-4.5-any)
fluentGenomics_1.25.0.tgz(r-4.6-any)fluentGenomics_1.25.0.tgz(r-4.5-any)
fluentGenomics_1.25.0.tar.gz(r-4.7-any)fluentGenomics_1.25.0.tar.gz(r-4.6-any)
fluentGenomics_1.25.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
fluentGenomics/json (API)

# Install 'fluentGenomics' in R:

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

Bug tracker:https://github.com/sa-lee/fluentgenomics/issues

Datasets:

peaks - Summarised ATAC-seq peaks as a GRanges object

On BioConductor:fluentGenomics-1.25.0(workflows 3.24)fluentGenomics-1.24.0(workflows 3.23)

workflow basicworkflow geneexpressionworkflow atac-seq bioconductor genomics rna-seq

4.80 score 7 stars 9 scripts 1 exports 72 dependencies

Last updated from:fc9849dc92. Checks:2 ERROR, 7 WARNING, 1 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	198
linux-devel	WARNING	393
source / vignettes	ERROR	300
linux-release	WARNING	382
macos-release	WARNING	211
macos-oldrel	WARNING	204
windows-devel	WARNING	261
windows-release	WARNING	265
windows-oldrel	WARNING	261
wasm-release	OK	157