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:Karolis Uziela and Antti Honkela

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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

2.30 score 1 scripts 273 downloads 1 mentions 1 exports 117 dependencies

Last updated 5 months agofrom:711f89508c. Checks:2 ERROR, 6 WARNING. Indexed: yes.

TargetResultLatest binary
Doc / VignettesFAILMar 01 2025
R-4.5-winWARNINGMar 01 2025
R-4.5-macWARNINGMar 01 2025
R-4.5-linuxERRORMar 01 2025
R-4.4-winWARNINGMar 01 2025
R-4.4-macWARNINGMar 01 2025
R-4.3-winWARNINGMar 01 2025
R-4.3-macWARNINGMar 01 2025

Exports:calc_prebs

Dependencies:abindade4affyaffyioapeaskpassbase64encBHBiobaseBiocGenericsBiocManagerBiocParallelBiocStylebiomformatBiostringsbitopsbookdownbslibcachemcliclustercodetoolscolorspacecpp11crayoncurldata.tableDelayedArraydigestevaluatefansifarverfastmapfontawesomeforeachformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesggplot2gluegtablehighrhtmltoolshttrigraphIRangesisobanditeratorsjquerylibjsonliteknitrlabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemulttestmunsellnlmeopensslpermutephyloseqpillarpixmappkgconfigplyrpreprocessCoreR6rappdirsRColorBrewerRcppRcppArmadilloreshape2rhdf5rhdf5filtersRhdf5libRhtslibrlangrmarkdownRPARsamtoolsS4ArraysS4VectorssassscalessnowspSparseArraystringistringrSummarizedExperimentsurvivalsystibbletinytexUCSC.utilsutf8vctrsveganviridisLitewithrxfunXVectoryaml

Readme and manuals

Help Manual

Help pageTopics
Calculate PREBS valuescalc_prebs
PREBS packageprebs-package prebs