Package: marr 1.15.0

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'))

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)

bioconductor-package

14 exports 0.71 score 57 dependencies

Last updated 2 months agofrom:50c45eb59a

Exports:Marr MarrAlpha MarrData MarrFeatures MarrFeaturesfiltered MarrFeatureVars MarrFilterData MarrPFeatures MarrPlotFeatures MarrPlotSamplepairs MarrProc MarrPSamplepairs MarrSamplepairs MarrSamplepairsfiltered

Dependencies:abind askpass Biobase BiocGenerics cli colorspace crayon curl DelayedArray dplyr fansi farver generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggplot2 glue gtable httr IRanges isoband jsonlite labeling lattice lifecycle magrittr MASS Matrix MatrixGenerics matrixStats mgcv mime munsell nlme openssl pillar pkgconfig R6 RColorBrewer Rcpp rlang S4Arrays S4Vectors scales SparseArray SummarizedExperiment sys tibble tidyselect UCSC.utils utf8 vctrs viridisLite withr XVector zlibbioc

The marr user's guide

Tusharkanti Ghosh, Max McGrath, Daisy Philtron, Katerina Kechris, Debashis Ghosh

Rendered fromMarrVignette.Rmdusingknitr::rmarkdownon Jun 30 2024.

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

Help page	Topics
S4 Class union	data.frameORSummarizedExperiment-class
Marr	Marr
the Marr class	Marr-class
Generic function that returns the Marr Alpha	MarrAlpha MarrAlpha,Marr-method
Generic function that returns the Marr Data	MarrData MarrData,Marr-method
Generic function that returns the Marr features	MarrFeatures MarrFeatures,Marr-method
Generic function that returns the Marr filtered features	MarrFeaturesfiltered MarrFeaturesfiltered,Marr-method
Generic function that returns the Marr Feature Vars	MarrFeatureVars MarrFeatureVars,Marr-method
Filter by Maximum Rank Reproducibility	MarrFilterData
Generic function that returns the Marr P Features	MarrPFeatures MarrPFeatures,Marr-method
Plot percent reproducible sample pairs per feature for pairwise replicates from 'Marr' function.	MarrPlotFeatures
Plot percent reproducible features per sample pair for pairwise replicates from 'Marr' function.	MarrPlotSamplepairs
MarrProc	MarrProc
Generic function that returns the Marr P Sample Pairs	MarrPSamplepairs MarrPSamplepairs,Marr-method
Generic function that returns the Marr sample pairs	MarrSamplepairs MarrSamplepairs,Marr-method
Generic function that returns the Marr filtered sample pairs	MarrSamplepairsfiltered MarrSamplepairsfiltered,Marr-method
Example of processed mass spectrometry dataset	msprepCOPD
S4 Class union	vectorORNull-class

Package: marr 1.15.0

marr: Maximum rank reproducibility

The marr user's guide

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