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'))

Peer review:

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 250 downloads 1 mentions 1 exports 117 dependencies

Last updated 23 days agofrom:711f89508c. Checks:ERROR: 2 WARNING: 5. Indexed: yes.

TargetResultDate
Doc / VignettesFAILOct 31 2024
R-4.5-winWARNINGOct 31 2024
R-4.5-linuxERROROct 31 2024
R-4.4-winWARNINGOct 31 2024
R-4.4-macWARNINGOct 31 2024
R-4.3-winWARNINGOct 31 2024
R-4.3-macWARNINGOct 31 2024

Exports:calc_prebs

Dependencies:abindade4affyaffyioapeaskpassbase64encBHBiobaseBiocGenericsBiocManagerBiocParallelBiocStylebiomformatBiostringsbitopsbookdownbslibcachemcliclustercodetoolscolorspacecpp11crayoncurldata.tableDelayedArraydigestevaluatefansifarverfastmapfontawesomeforeachformatRfsfutile.loggerfutile.optionsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesggplot2gluegtablehighrhtmltoolshttrigraphIRangesisobanditeratorsjquerylibjsonliteknitrlabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemulttestmunsellnlmeopensslpermutephyloseqpillarpixmappkgconfigplyrpreprocessCoreR6rappdirsRColorBrewerRcppRcppArmadilloreshape2rhdf5rhdf5filtersRhdf5libRhtslibrlangrmarkdownRPARsamtoolsS4ArraysS4VectorssassscalessnowspSparseArraystringistringrSummarizedExperimentsurvivalsystibbletinytexUCSC.utilsutf8vctrsveganviridisLitewithrxfunXVectoryamlzlibbioc

Readme and manuals

Help Manual

Help pageTopics
Calculate PREBS valuescalc_prebs
PREBS packageprebs-package prebs