SIEVEseq: Unified Differential Expression, Variability and Skewness Analysis for RNA-Seq Data

Package: SIEVEseq 0.0.0

Hongxiang Li

SIEVEseq: Unified Differential Expression, Variability and Skewness Analysis for RNA-Seq Data

Provides a unified framework for the simultaneous testing of differential expression, variability, and skewness of genes using RNA-Seq data. The framework adopts a compositional data analysis approach for modelling RNA-Seq count data, applies the centered log-ratio transformation to obtain continuous variables, and uses the skew-normal distribution for statistical inference. Methods are described in Li and Khang (bioRxiv preprint, 2024, version 3) <doi:10.1101/2024.04.09.588804>.

Authors:Hongxiang Li [aut, cre], Tsung Fei Khang [aut]

SIEVEseq_0.0.0.tar.gz
SIEVEseq_0.0.0.tar.gz(r-4.7-any)SIEVEseq_0.0.0.tar.gz(r-4.6-any)
SIEVEseq_0.0.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
SIEVEseq/json (API)

# Install 'SIEVEseq' in R:

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

Bug tracker:https://github.com/divo-lee/sieveseq/issues

Datasets:

clrCounts1 - Simulated CLR-transformed count table
clrCounts2 - Simulated DV genes CLR-transformed count table
clrCounts3 - Simulated DE genes CLR-transformed count table

On CRAN:

2.00 score 7 exports 27 dependencies

Last updated from:c610429b45. Checks:2 WARNING, 2 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	WARNING	153
source / vignettes	OK	235
linux-release-x86_64	WARNING	141
wasm-release	OK	116

Exports:clr.SN.fit clrDE clrDV clrSeq clrSIEVE SN.plot violin.plot.SIEVE

Dependencies:cli cpp11 farver ggplot2 glue gtable isoband labeling lattice lifecycle MASS Matrix MatrixModels mnormt numDeriv quantreg R6 RColorBrewer rlang S7 scales sn SparseM survival vctrs viridisLite withr

SIEVEseq Introduction

Rendered fromSIEVEseq_Introduction.Rmdusingknitr::rmarkdown

Help page	Topics
Fit the skew-normal distribution to CLR-transformed RNA-Seq data	clr.SN.fit
Simulated CLR-transformed count table	clrCounts1
Simulated DV genes CLR-transformed count table	clrCounts2
Simulated DE genes CLR-transformed count table	clrCounts3
Differential Expression (DE) Test of CLR-transformed RNA-Seq Data	clrDE
Differential variability (DV) test of CLR-transformed RNA-Seq data	clrDV
Fit the skew-normal model to CLR-transformed RNA-Seq data for 2 groups	clrSeq
Simultaneous Differential Expression, Variability and Skewness Analysis Using RNA-Seq Data	clrSIEVE
Distribution of CLR-transformed counts	SN.plot
Violin plots	violin.plot.SIEVE

Help page

Topics

Fit the skew-normal distribution to CLR-transformed RNA-Seq data

clr.SN.fit

Simulated CLR-transformed count table

clrCounts1

Simulated DV genes CLR-transformed count table

clrCounts2

Simulated DE genes CLR-transformed count table

clrCounts3

Differential Expression (DE) Test of CLR-transformed RNA-Seq Data

clrDE