Package: DoubleExpSeq 1.1

DoubleExpSeq: Differential Exon Usage Test for RNA-Seq Data via Empirical Bayes Shrinkage of the Dispersion Parameter

Differential exon usage test for RNA-Seq data via an empirical Bayes shrinkage method for the dispersion parameter the utilizes inclusion-exclusion data to analyze the propensity to skip an exon across groups. The input data consists of two matrices where each row represents an exon and the columns represent the biological samples. The first matrix is the count of the number of reads expressing the exon for each sample. The second matrix is the count of the number of reads that either express the exon or explicitly skip the exon across the samples, a.k.a. the total count matrix. Dividing the two matrices yields proportions representing the propensity to express the exon versus skipping the exon for each sample.

Authors:Sean Ruddy

DoubleExpSeq_1.1.tar.gz
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DoubleExpSeq.pdf |DoubleExpSeq.html
DoubleExpSeq/json (API)

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

Peer review:

Datasets:
  • counts - Exon Inclusion Counts
  • groups - Group Structure of the Toy Data Set
  • offsets - Exon Total Counts

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

1.20 score 16 scripts 203 downloads 5 exports 1 dependencies

Last updated 9 years agofrom:ecb9a92130. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 11 2024
R-4.5-winOKOct 11 2024
R-4.5-linuxOKOct 11 2024
R-4.4-winOKOct 11 2024
R-4.4-macOKOct 11 2024
R-4.3-winOKOct 11 2024
R-4.3-macOKOct 11 2024

Exports:DB.MAPlotDBGLM1EstimateDEBDispEstimateWEBDispoptimPlot

Dependencies:numDeriv