Package: fluentGenomics 1.24.0
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:
fluentGenomics_1.24.0.tar.gz
fluentGenomics_1.24.0.zip(r-4.7-any)fluentGenomics_1.24.0.zip(r-4.6-any)fluentGenomics_1.24.0.zip(r-4.5-any)
fluentGenomics_1.24.0.tgz(r-4.6-any)fluentGenomics_1.24.0.tgz(r-4.5-any)
fluentGenomics_1.24.0.tar.gz(r-4.7-any)fluentGenomics_1.24.0.tar.gz(r-4.6-any)
fluentGenomics_1.24.0.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-release.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/sa-lee/fluentgenomics/issues
- peaks - Summarised ATAC-seq peaks as a GRanges object
workflowbasicworkflowgeneexpressionworkflowatac-seqbioconductorgenomicsrna-seq
Last updated from:ab4340df7c (on RELEASE_3_23). Checks:1 ERROR, 9 OK. Indexed: no.
A new build is currently in progress.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 198 | ||
| linux-devel | OK | 380 | ||
| source / vignettes | OK | 418 | ||
| linux-release | OK | 386 | ||
| macos-release | OK | 301 | ||
| macos-oldrel | OK | 228 | ||
| windows-devel | OK | 314 | ||
| windows-release | OK | 282 | ||
| windows-oldrel | OK | 265 | ||
| wasm-release | OK | 162 |
Exports:cache_atac_se
Dependencies:abindaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopscigarilloclicliprcodetoolscpp11crayoncurlDelayedArraydplyrformatRfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicRangesgluehmshttrIRangesjsonlitelambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmimeopensslpillarpkgconfigplyrangesprettyunitsprogressR6RCurlreadrrestfulrRhtslibrjsonrlangRsamtoolsrtracklayerS4ArraysS4VectorsSeqinfosnowSparseArraySummarizedExperimentsystibbletidyselecttzdbutf8vctrsvroomwithrXMLXVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Download, retrieve and cache macrophage ATAC seq results | cache_atac_se |
| Summarised ATAC-seq peaks as a GRanges object | peaks |
