Package: preprocessCore 1.75.0

Ben Bolstad

preprocessCore: A collection of pre-processing functions

A library of core preprocessing routines.

Authors:Ben Bolstad <[email protected]>

preprocessCore_1.75.0.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
preprocessCore/json (API)

# Install 'preprocessCore' in R:
install.packages('preprocessCore', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/bmbolstad/preprocesscore/issues

Uses libs:
  • openblas– Optimized BLAS

On BioConductor:preprocessCore-1.75.0(bioc 3.24)preprocessCore-1.74.0(bioc 3.23)

infrastructureopenblas

10.74 score 19 stars 216 packages 2.8k scripts 146 mentions 39 exports 0 dependencies

Last updated from:4e5bfc285f. Checks:1 ERROR, 11 WARNING, 1 OK, 1 FAIL. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksERROR217
linux-devel-arm64WARNING131
linux-devel-x86_64WARNING161
source / vignettesOK154
linux-release-arm64WARNING124
linux-release-x86_64WARNING157
macos-release-arm64WARNING84
macos-release-x86_64WARNING170
macos-oldrel-arm64WARNING134
macos-oldrel-x86_64WARNING252
windows-develWARNING146
windows-releaseWARNING126
windows-oldrelWARNING101
wasm-releaseFAIL89

Exports:colSummarizeAvgcolSummarizeAvgLogcolSummarizeBiweightcolSummarizeBiweightLogcolSummarizeLogAvgcolSummarizeLogMediancolSummarizeMediancolSummarizeMedianLogcolSummarizeMedianpolishcolSummarizeMedianpolishLogconvert.group.labelsnormalize.quantilesnormalize.quantiles.determine.targetnormalize.quantiles.in.blocksnormalize.quantiles.robustnormalize.quantiles.use.targetrcModelMedianPolishrcModelPLMrcModelPLMdrcModelPLMrrcModelPLMrcrcModelPLMrrrcModelWPLMrcModelWPLMrrcModelWPLMrcrcModelWPLMrrrma.background.correctsubColSummarizeAvgsubColSummarizeAvgLogsubColSummarizeBiweightsubColSummarizeBiweightLogsubColSummarizeLogAvgsubColSummarizeLogMediansubColSummarizeMediansubColSummarizeMedianLogsubColSummarizeMedianpolishsubColSummarizeMedianpolishLogsubrcModelMedianPolishsubrcModelPLM

Dependencies:

Readme and manuals

Help Manual

Help pageTopics
Summarize the column of matricescolSummarizeAvg colSummarizeAvgLog colSummarizeBiweight colSummarizeBiweightLog colSummarizeLogAvg colSummarizeLogMedian colSummarizeMedian colSummarizeMedianLog colSummarizeMedianpolish colSummarizeMedianpolishLog
Quantile Normalizationnormalize.quantiles
Quantile Normalization carried out separately within blocks of rowsnormalize.quantiles.in.blocks
Robust Quantile Normalizationnormalize.AffyBatch.quantiles.robust normalize.quantiles.robust
Quantile Normalization using a specified target distribution vectornormalize.quantiles.determine.target normalize.quantiles.use.target
Fit robust row-column models to a matrixrcModelPLMd
Fit robust row-column models to a matrixrcModelPLMr rcModelPLMrc rcModelPLMrr rcModelWPLMr rcModelWPLMrc rcModelWPLMrr
Fit row-column model to a matrixrcModelMedianPolish rcModelPLM rcModelWPLM
RMA Background Correctionrma.background.correct
Summarize columns when divided into groups of rowsconvert.group.labels subColSummarizeAvg subColSummarizeAvgLog subColSummarizeBiweight subColSummarizeBiweightLog subColSummarizeLogAvg subColSummarizeLogMedian subColSummarizeMedian subColSummarizeMedianLog subColSummarizeMedianpolish subColSummarizeMedianpolishLog
Fit row-column model to a matrixsubrcModelMedianPolish subrcModelPLM subrcModelWPLM