Package: OVESEG 1.23.0

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_1.23.0.tar.gz
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OVESEG.pdf |OVESEG.html✨
OVESEG/json (API)
NEWS

# 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:

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

On BioConductor:OVESEG-1.23.0(bioc 3.21)OVESEG-1.22.0(bioc 3.20)

software multiplecomparison cellbiology geneexpression cpp

4.00 score 1 stars 2 scripts 206 downloads 7 exports 42 dependencies

Last updated 2 months agofrom:ec068d0283. Checks:OK: 1 NOTE: 8. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Dec 18 2024
R-4.5-win-x86_64	NOTE	Dec 18 2024
R-4.5-linux-x86_64	NOTE	Dec 18 2024
R-4.4-win-x86_64	NOTE	Dec 18 2024
R-4.4-mac-x86_64	NOTE	Dec 18 2024
R-4.4-mac-aarch64	NOTE	Dec 18 2024
R-4.3-win-x86_64	NOTE	Dec 18 2024
R-4.3-mac-x86_64	NOTE	Dec 18 2024
R-4.3-mac-aarch64	NOTE	Dec 18 2024

Exports:nullDistri OVESEGtest OVESEGtstat OVEtstatPermTopM patternDistri postProbNull pvalueWeightedEst

Dependencies:abind askpass BH Biobase BiocGenerics BiocParallel codetools cpp11 crayon curl DelayedArray fdrtool formatR futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicRanges httr IRanges jsonlite lambda.r lattice limma Matrix MatrixGenerics matrixStats mime openssl R6 Rcpp S4Arrays S4Vectors snow SparseArray statmod SummarizedExperiment sys UCSC.utils XVector zlibbioc

OVESEG User Manual

Lulu Chen

Rendered fromOVESEG.Rmdusingknitr::rmarkdownon Dec 18 2024.

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