Package: subSeq 1.37.0
Andrew J. Bass
subSeq: Subsampling of high-throughput sequencing count data
Subsampling of high throughput sequencing count data for use in experiment design and analysis.
Authors:
subSeq_1.37.0.tar.gz
subSeq_1.37.0.zip(r-4.5)subSeq_1.37.0.zip(r-4.4)subSeq_1.37.0.zip(r-4.3)
subSeq_1.37.0.tgz(r-4.4-any)subSeq_1.37.0.tgz(r-4.3-any)
subSeq_1.37.0.tar.gz(r-4.5-noble)subSeq_1.37.0.tar.gz(r-4.4-noble)
subSeq_1.37.0.tgz(r-4.4-emscripten)subSeq_1.37.0.tgz(r-4.3-emscripten)
subSeq.pdf |subSeq.html✨
subSeq/json (API)
NEWS
| # Install 'subSeq' in R: |
| install.packages('subSeq', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/storeylab/subseq/issues
On BioConductor:subSeq-1.37.0(bioc 3.21)subSeq-1.36.0(bioc 3.20)
immunooncologysequencingtranscriptionrnaseqgeneexpressiondifferentialexpression
Last updated 3 months agofrom:694bd4dcb5. Checks:1 OK, 3 NOTE, 3 ERROR. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Dec 30 2024 |
| R-4.5-win | ERROR | Dec 30 2024 |
| R-4.5-linux | NOTE | Dec 30 2024 |
| R-4.4-win | ERROR | Dec 30 2024 |
| R-4.4-mac | NOTE | Dec 30 2024 |
| R-4.3-win | ERROR | Dec 30 2024 |
| R-4.3-mac | NOTE | Dec 30 2024 |
Exports:combineSubsamplesgenerateSubsampledMatrixgetSeedsubsample
Dependencies:BiobaseBiocGenericsclicolorspacecpp11data.tabledigestdplyrfansifarvergenericsggplot2gluegtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigplyrpurrrqvalueR6RColorBrewerRcppreshape2rlangscalesstringistringrtibbletidyrtidyselectutf8vctrsviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| combine multiple subsamples objects | combineSubsamples |
| Generate the read matrix corresponding to a particular level | generateSubsampledMatrix |
| Extract the global random seed from a subsamples object | getSeed |
| ExpressionSet results from Hammer et al 2010 | hammer |
| plot metrics as a function of subsampled read depth | plot.subsamples |
| plot metrics as a function of subsampled read depth | plot.summary.subsamples |
| Subsampling results using the hammer dataset | ss |
| Subsample reads and perform statistical testing on each sample | subsample |
| calculate summary statistics for each subsampled depth in a subsamples object | summary.subsamples |
