Package: marr 1.17.0

Tusharkanti Ghosh

marr: Maximum rank reproducibility

marr (Maximum Rank Reproducibility) is a nonparametric approach that detects reproducible signals using a maximal rank statistic for high-dimensional biological data. In this R package, we implement functions that measures the reproducibility of features per sample pair and sample pairs per feature in high-dimensional biological replicate experiments. The user-friendly plot functions in this package also plot histograms of the reproducibility of features per sample pair and sample pairs per feature. Furthermore, our approach also allows the users to select optimal filtering threshold values for the identification of reproducible features and sample pairs based on output visualization checks (histograms). This package also provides the subset of data filtered by reproducible features and/or sample pairs.

Authors:Tusharkanti Ghosh [aut, cre], Max McGrath [aut], Daisy Philtron [aut], Katerina Kechris [aut], Debashis Ghosh [aut, cph]

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NEWS

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

Peer review:

Bug tracker:https://github.com/ghoshlab/marr/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • msprepCOPD - Example of processed mass spectrometry dataset

On BioConductor:marr-1.15.0(bioc 3.20)marr-1.14.0(bioc 3.19)

qualitycontrolmetabolomicsmassspectrometryrnaseqchipseq

4.60 score 2 stars 4 scripts 166 downloads 14 exports 57 dependencies

Last updated 23 days agofrom:88e44eebc6. Checks:OK: 9. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 30 2024
R-4.5-win-x86_64OKOct 31 2024
R-4.5-linux-x86_64OKOct 30 2024
R-4.4-win-x86_64OKOct 31 2024
R-4.4-mac-x86_64OKOct 31 2024
R-4.4-mac-aarch64OKOct 31 2024
R-4.3-win-x86_64OKOct 31 2024
R-4.3-mac-x86_64OKOct 31 2024
R-4.3-mac-aarch64OKOct 31 2024

Exports:MarrMarrAlphaMarrDataMarrFeaturesMarrFeaturesfilteredMarrFeatureVarsMarrFilterDataMarrPFeaturesMarrPlotFeaturesMarrPlotSamplepairsMarrProcMarrPSamplepairsMarrSamplepairsMarrSamplepairsfiltered

Dependencies:abindaskpassBiobaseBiocGenericsclicolorspacecrayoncurlDelayedArraydplyrfansifarvergenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegtablehttrIRangesisobandjsonlitelabelinglatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemunsellnlmeopensslpillarpkgconfigR6RColorBrewerRcpprlangS4ArraysS4VectorsscalesSparseArraySummarizedExperimentsystibbletidyselectUCSC.utilsutf8vctrsviridisLitewithrXVectorzlibbioc

The marr user's guide

Rendered fromMarrVignette.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2021-04-28
Started: 2020-10-23