Package: OVESEG 1.29.0

Lulu Chen

OVESEG: OVESEG-test to detect tissue/cell-specific markers

An R package for multiple-group comparison to detect tissue/cell-specific marker genes among subtypes. It provides functions to compute OVESEG-test statistics, derive component weights in the mixture null distribution model and estimate p-values from weightedly aggregated permutations. Obtained posterior probabilities of component null hypotheses can also portrait all kinds of upregulation patterns among subtypes.

Authors:Lulu Chen <[email protected]>

OVESEG_1.29.0.tar.gz
OVESEG_1.29.0.zip(r-4.7)OVESEG_1.29.0.zip(r-4.6)OVESEG_1.29.0.zip(r-4.5)
OVESEG_1.29.0.tgz(r-4.6-x86_64)OVESEG_1.29.0.tgz(r-4.6-arm64)OVESEG_1.29.0.tgz(r-4.5-x86_64)OVESEG_1.29.0.tgz(r-4.5-arm64)
OVESEG_1.29.0.tar.gz(r-4.7-arm64)OVESEG_1.29.0.tar.gz(r-4.7-x86_64)OVESEG_1.29.0.tar.gz(r-4.6-arm64)OVESEG_1.29.0.tar.gz(r-4.6-x86_64)
OVESEG_1.29.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
OVESEG/json (API)

# Install 'OVESEG' in R:

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

Bug tracker:https://github.com/lululuella/oveseg/issues

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

countBT - RNAseq count data downsampled from GSE60424
RocheBT - MRNA expression data downsampled from GSE28490

On BioConductor:OVESEG-1.29.0(bioc 3.24)OVESEG-1.28.0(bioc 3.23)

software multiplecomparison cellbiology geneexpression cpp

4.30 score 2 stars 2 scripts 7 exports 30 dependencies

Last updated from:45a3e56b44. Checks:1 ERROR, 11 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	197
linux-devel-arm64	NOTE	203
linux-devel-x86_64	NOTE	218
source / vignettes	OK	575
linux-release-arm64	NOTE	237
linux-release-x86_64	NOTE	248
macos-release-arm64	NOTE	162
macos-release-x86_64	NOTE	255
macos-oldrel-arm64	NOTE	106
macos-oldrel-x86_64	NOTE	355
windows-devel	NOTE	153
windows-release	NOTE	147
windows-oldrel	NOTE	146
wasm-release	OK	173

Exports:nullDistri OVESEGtest OVESEGtstat OVEtstatPermTopM patternDistri postProbNull pvalueWeightedEst

Dependencies:abind BH Biobase BiocGenerics BiocParallel codetools cpp11 DelayedArray fdrtool formatR futile.logger futile.options generics GenomicRanges IRanges lambda.r lattice limma Matrix MatrixGenerics matrixStats Rcpp S4Arrays S4Vectors Seqinfo snow SparseArray statmod SummarizedExperiment XVector

OVESEG User Manual

Rendered fromOVESEG.Rmdusingknitr::rmarkdown

Last update: 2019-01-14
Started: 2019-01-13

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
OVESEG: A package for marker gene test.	OVESEG-package OVESEG
RNAseq count data downsampled from GSE60424	countBT
Probability of one group being upregulated under null	nullDistri
OVESEG-test	OVESEGtest
OVESEG-test statistics	OVESEGtstat
OVESEG-test statistics after permuting top M groups	OVEtstatPermTopM
Probabilities of all upregulation patterns	patternDistri
Posterior probabilities of each component null hypothesis	postProbNull
p-value by weighted permutation scheme	pvalueWeightedEst
mRNA expression data downsampled from GSE28490 (Roche)	RocheBT