Introduction | Installation | Loading precomputed RNA-seq counts | Inferring sample groups | Working with GCT files | Session info
Package: phantasusLite 1.11.4
Alexey Sergushichev
phantasusLite: Loading and annotation RNA-seq counts matrices
PhantasusLite – a lightweight package with helper functions of general interest extracted from phantasus package. In parituclar it simplifies working with public RNA-seq datasets from GEO by providing access to the remote HSDS repository with the precomputed gene counts from ARCHS4 and DEE2 projects.
Authors:
phantasusLite_1.11.4.tar.gz
phantasusLite_1.11.4.zip(r-4.7-any)phantasusLite_1.11.4.zip(r-4.6-any)phantasusLite_1.11.4.zip(r-4.5-any)
phantasusLite_1.11.4.tgz(r-4.6-any)phantasusLite_1.11.4.tgz(r-4.5-any)
phantasusLite_1.11.4.tar.gz(r-4.7-any)phantasusLite_1.11.4.tar.gz(r-4.6-any)
phantasusLite_1.11.4.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
phantasusLite/json (API)
| # Install 'phantasusLite' in R: |
| install.packages('phantasusLite', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/alserglab/phantasuslite/issues
On BioConductor:phantasusLite-1.11.4(bioc 3.24)phantasusLite-1.10.0(bioc 3.23)
geneexpressiontranscriptomicsrnaseq
Last updated from:6c4a67c9b2. Checks:1 WARNING, 5 NOTE, 2 OK, 2 ERROR. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 204 | ||
| linux-devel-x86_64 | NOTE | 354 | ||
| source / vignettes | OK | 254 | ||
| linux-release-x86_64 | NOTE | 311 | ||
| macos-release-arm64 | NOTE | 220 | ||
| macos-oldrel-arm64 | ERROR | 224 | ||
| windows-devel-x86_64 | NOTE | 210 | ||
| windows-release-x86_64 | ERROR | 179 | ||
| windows-oldrel-x86_64 | NOTE | 207 | ||
| wasm-release | OK | 131 |
Exports:getHSDSFileListinferConditionloadCountsFromH5FileHSDSloadCountsFromHSDSreadGctwriteGct
Dependencies:abindaskpassBiobaseBiocGenericsclicurldata.tableDelayedArraygenericsgluehttrIRangesjsonlitelatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmimeopensslR6rhdf5clientrjsonrlangS4ArraysS4VectorsSparseArraystringistringrsysvctrsXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Returns list of all HDF5-files on HSDS-server | getHSDSFileList |
| Adds condition to the annotation. | inferCondition |
| Load count matrix from remote HDF5-file | loadCountsFromH5FileHSDS |
| Load count matrix from HDF5-files. | loadCountsFromHSDS |
| Reads ExpressionSet from a GCT file. | readGct |
| Saves ExpressionSet to a GCT file (version 1.3). | writeGct |
