Package: phantasusLite 1.5.0
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_1.5.0.tar.gz
phantasusLite_1.5.0.zip(r-4.5)phantasusLite_1.5.0.zip(r-4.4)phantasusLite_1.5.0.zip(r-4.3)
phantasusLite_1.5.0.tgz(r-4.4-any)phantasusLite_1.5.0.tgz(r-4.3-any)
phantasusLite_1.5.0.tar.gz(r-4.5-noble)phantasusLite_1.5.0.tar.gz(r-4.4-noble)
phantasusLite_1.5.0.tgz(r-4.4-emscripten)phantasusLite_1.5.0.tgz(r-4.3-emscripten)
phantasusLite.pdf |phantasusLite.html✨
phantasusLite/json (API)
NEWS
| # Install 'phantasusLite' in R: |
| install.packages('phantasusLite', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/ctlab/phantasuslite/issues
On BioConductor:phantasusLite-1.5.0(bioc 3.21)phantasusLite-1.4.0(bioc 3.20)
geneexpressiontranscriptomicsrnaseq
Last updated 2 months agofrom:13aa8ea999. Checks:OK: 1 NOTE: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 18 2024 |
| R-4.5-win | NOTE | Dec 18 2024 |
| R-4.5-linux | NOTE | Dec 18 2024 |
| R-4.4-win | NOTE | Dec 18 2024 |
| R-4.4-mac | NOTE | Dec 18 2024 |
| R-4.3-win | NOTE | Dec 18 2024 |
| R-4.3-mac | NOTE | Dec 18 2024 |
Exports:getHSDSFileListinferConditionloadCountsFromH5FileHSDSloadCountsFromHSDSreadGctwriteGct
Dependencies:abindaskpassBiobaseBiocGenericsclicrayoncurldata.tableDelayedArraygenericsgluehttrIRangesjsonlitelatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmimeopensslR6rhdf5clientrjsonrlangS4ArraysS4VectorsSparseArraystringistringrsysvctrsXVectorzlibbioc
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 |
