Introduction | Quick Start Guide | Plotting | Writing Your Own Analysis Method | Reproducing or Adding to a Previous Run | Note on Subsampling
Package: subSeq 1.43.0
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_1.43.0.tar.gz
subSeq_1.43.0.zip(r-4.7)subSeq_1.43.0.zip(r-4.6)subSeq_1.43.0.zip(r-4.5)
subSeq_1.43.0.tgz(r-4.6-any)subSeq_1.43.0.tgz(r-4.5-any)
subSeq_1.43.0.tar.gz(r-4.7-any)subSeq_1.43.0.tar.gz(r-4.6-any)
subSeq_1.43.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
subSeq/json (API)
| # 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
Datasets:
On BioConductor:subSeq-1.43.0(bioc 3.24)subSeq-1.42.0(bioc 3.23)
immunooncologysequencingtranscriptionrnaseqgeneexpressiondifferentialexpression
Last updated from:44f42964ed. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 167 | ||
| linux-devel-x86_64 | NOTE | 319 | ||
| source / vignettes | OK | 244 | ||
| linux-release-x86_64 | NOTE | 342 | ||
| macos-release-arm64 | NOTE | 319 | ||
| macos-oldrel-arm64 | NOTE | 125 | ||
| windows-devel | NOTE | 222 | ||
| windows-release | NOTE | 209 | ||
| windows-oldrel | NOTE | 209 | ||
| wasm-release | OK | 178 |
Exports:combineSubsamplesgenerateSubsampledMatrixgetSeedsubsample
Dependencies:BiobaseBiocGenericsclicpp11data.tabledigestdplyrfarvergenericsggplot2gluegtableisobandlabelinglifecyclemagrittrpillarpkgconfigplyrpurrrqvalueR6RColorBrewerRcppreshape2rlangS7scalesstringistringrtibbletidyrtidyselectutf8vctrsviridisLitewithr
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 |
