Package: prebs 1.47.0
Karolis Uziela
prebs: Probe region expression estimation for RNA-seq data for improved microarray comparability
The prebs package aims at making RNA-sequencing (RNA-seq) data more comparable to microarray data. The comparability is achieved by summarizing sequencing-based expressions of probe regions using a modified version of RMA algorithm. The pipeline takes mapped reads in BAM format as an input and produces either gene expressions or original microarray probe set expressions as an output.
Authors:
prebs_1.47.0.tar.gz
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prebs.pdf |prebs.html✨
prebs/json (API)
NEWS
| # Install 'prebs' in R: |
| install.packages('prebs', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:prebs-1.47.0(bioc 3.21)prebs-1.46.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
immunooncologymicroarrayrnaseqsequencinggeneexpressionpreprocessing
Last updated 4 months agofrom:711f89508c. Checks:2 ERROR, 6 WARNING. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | FAIL | Jan 30 2025 |
| R-4.5-win | WARNING | Jan 30 2025 |
| R-4.5-mac | WARNING | Jan 30 2025 |
| R-4.5-linux | ERROR | Jan 30 2025 |
| R-4.4-win | WARNING | Jan 30 2025 |
| R-4.4-mac | WARNING | Jan 30 2025 |
| R-4.3-win | WARNING | Jan 30 2025 |
| R-4.3-mac | WARNING | Jan 30 2025 |
Exports:calc_prebs
Dependencies:abindade4affyaffyioapeaskpassbase64encBHBiobaseBiocGenericsBiocManagerBiocParallelBiocStylebiomformatBiostringsbitopsbookdownbslibcachemcliclustercodetoolscolorspacecpp11crayoncurldata.tableDelayedArraydigestevaluatefansifarverfastmapfontawesomeforeachformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesggplot2gluegtablehighrhtmltoolshttrigraphIRangesisobanditeratorsjquerylibjsonliteknitrlabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemulttestmunsellnlmeopensslpermutephyloseqpillarpixmappkgconfigplyrpreprocessCoreR6rappdirsRColorBrewerRcppRcppArmadilloreshape2rhdf5rhdf5filtersRhdf5libRhtslibrlangrmarkdownRPARsamtoolsS4ArraysS4VectorssassscalessnowspSparseArraystringistringrSummarizedExperimentsurvivalsystibbletinytexUCSC.utilsutf8vctrsveganviridisLitewithrxfunXVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Calculate PREBS values | calc_prebs |
| PREBS package | prebs-package prebs |
