Package: discordant 1.29.0

McGrath Max

discordant: The Discordant Method: A Novel Approach for Differential Correlation

Discordant is an R package that identifies pairs of features that correlate differently between phenotypic groups, with application to -omics data sets. Discordant uses a mixture model that “bins” molecular feature pairs based on their type of coexpression or coabbundance. Algorithm is explained further in "Differential Correlation for Sequencing Data"" (Siska et al. 2016).

Authors:Charlotte Siska [aut], McGrath Max [aut, cre], Katerina Kechris [aut, cph, ths]

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NEWS

# Install 'discordant' in R:

install.packages('discordant', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/siskac/discordant/issues

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

TCGA_Breast_RNASeq - TCGA Breast Cancer RNASeq Sample Dataset
TCGA_Breast_RNASeq_voom - TCGA Breast Cancer RNASeq Sample Dataset
TCGA_Breast_miRNASeq - Example breast miRNA-Seq count dataset.
TCGA_Breast_miRNASeq_voom - Example breast miRNA-Seq voom-transformed count dataset.
TCGA_GBM_miRNA_microarray - TCGA Glioblastoma Multiforme miRNA Sample Dataset
TCGA_GBM_transcript_microarray - TCGA Glioblastoma Multiforme Transcript Sample Dataset

On BioConductor:discordant-1.29.0(bioc 3.20)discordant-1.28.0(bioc 3.19)

bioconductor-package

4 exports 1.16 score 24 dependencies

Last updated 2 months agofrom:866e1fffc4

Exports:createVectors discordantRun fishersTrans splitMADOutlier

Dependencies:Biobase BiocGenerics biwt cli DEoptimR dplyr fansi generics glue gtools lifecycle magrittr MASS pillar pkgconfig R6 Rcpp rlang robustbase tibble tidyselect utf8 vctrs withr

The discordant R Package: A Novel Approach to Differential Correlation

Charlotte Siska, Max McGrath, Katerina Kechris

Rendered fromUsing_discordant.Rmdusingknitr::rmarkdownon Jun 19 2024.

Last update: 2021-10-15
Started: 2021-08-04

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Create correlation coefficient vectors based on bivariate data	createVectors
discordant: A Novel Approach for Differential Correlation	discordant
Run Discordant Algorithm	discordantRun
Fisher Transformation of Pearson Correlation Coefficients to Z Scores	fishersTrans
Outliers using left and right MAD	splitMADOutlier
Example breast miRNA-Seq count dataset.	TCGA_Breast_miRNASeq
Example breast miRNA-Seq voom-transformed count dataset.	TCGA_Breast_miRNASeq_voom
TCGA Breast Cancer RNASeq Sample Dataset	TCGA_Breast_RNASeq
TCGA Breast Cancer RNASeq Sample Dataset	TCGA_Breast_RNASeq_voom
TCGA Glioblastoma Multiforme miRNA Sample Dataset	TCGA_GBM_miRNA_microarray
TCGA Glioblastoma Multiforme Transcript Sample Dataset	TCGA_GBM_transcript_microarray