Package: ABSSeq 1.67.0

Wentao Yang

ABSSeq: ABSSeq: a new RNA-Seq analysis method based on modelling absolute expression differences

Inferring differential expression genes by absolute counts difference between two groups, utilizing Negative binomial distribution and moderating fold-change according to heterogeneity of dispersion across expression level.

Authors:Wentao Yang

ABSSeq_1.67.0.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ABSSeq/json (API)

# Install 'ABSSeq' in R:

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

Datasets:

simuN5 - Simulated study with random outliers

On BioConductor:ABSSeq-1.67.0(bioc 3.24)ABSSeq-1.66.0(bioc 3.23)

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

differentialexpression

4.62 score 1 packages 2 scripts 7 mentions 34 exports 4 dependencies

Last updated from:a18cc3f69e. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	143
linux-devel-x86_64	NOTE	217
source / vignettes	OK	420
linux-release-x86_64	NOTE	215
macos-release-arm64	NOTE	183
macos-oldrel-arm64	NOTE	163
windows-devel	NOTE	132
windows-release	NOTE	127
windows-oldrel	NOTE	143
wasm-release	OK	96

Exports:ABSDataSet ABSSeq ABSSeqlm aFoldcomplexDesign callDEs callParameter callParameterwithoutReplicates counts counts<-estimateSizeFactorsForMatrix excounts excounts<-genAFold groups groups<-LevelstoNormFC LevelstoNormFC<-maxRates maxRates<-minimalDispersion minimalDispersion<-minRates minRates<-normalFactors normMethod normMethod<-paired paired<-plotDifftoBase qtotalNormalized ReplaceOutliersByMAD results sFactors sFactors<-

Dependencies:lattice limma locfit statmod

ABSSeq

Rendered fromABSSeq.Rnwusingutils::Sweave

Last update: 2017-08-30
Started: 2014-03-27

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
ABSDataSet object and constructors	ABSDataSet ABSDataSet-class SumInfo-class [[<-,SumInfo,character,missing-method
Differential expression analysis based on the total counts difference.	ABSSeq
Differential expression analysis for complex desgin.	ABSSeqlm
Calculate parameters for differential expression test base on absolute counts differences	aFoldcomplexDesign
Testing the differential expression by counts difference	callDEs
Calculate parameters for differential expression test base on absolute counts differences	callParameter
Calculate parameters for differential expression test base on absolute counts differences without replicates	callParameterwithoutReplicates
Accessors for the 'counts' slot of a ABSDataSet object.	counts counts,ABSDataSet-method counts<- counts<-,ABSDataSet,matrix-method
Low-level function to estimate size factors with robust regression.	estimateSizeFactorsForMatrix
Accessors for the 'excounts' slot of a ABSDataSet object.	excounts excounts,ABSDataSet-method excounts<- excounts<-,ABSDataSet,matrix-method
Calculate parameters for differential expression test base on absolute counts differences	genAFold
Accessors for the 'groups' slot of a ABSDataSet object.	groups groups,ABSDataSet-method groups<- groups<-,ABSDataSet,factor-method
Accessors for the 'LevelstoNormFC' slot of a ABSDataSet object.	LevelstoNormFC LevelstoNormFC,ABSDataSet-method LevelstoNormFC<- LevelstoNormFC<-,ABSDataSet,numeric-method
Accessors for the 'maxRates' slot of a ABSDataSet object.	maxRates maxRates,ABSDataSet-method maxRates<- maxRates<-,ABSDataSet,numeric-method
Accessors for the 'minDispersion' slot of a ABSDataSet object.	minimalDispersion minimalDispersion,ABSDataSet-method minimalDispersion<- minimalDispersion<-,ABSDataSet,numeric-method
Accessors for the 'minRates' slot of a ABSDataSet object.	minRates minRates,ABSDataSet-method minRates<- minRates<-,ABSDataSet,numeric-method
Estimating size factors from the reads count table	normalFactors
Accessors for the 'normMethod' slot of a ABSDataSet object.	normMethod normMethod,ABSDataSet-method normMethod<- normMethod<-,ABSDataSet,character-method
Accessors for the 'paired' slot of a ABSDataSet object.	paired paired,ABSDataSet-method paired<- paired<-,ABSDataSet,logical-method
Plot absolute log2 fold-change against base mean of expression	plotDifftoBase
Estimating size factors from the reads count table via ranking	qtotalNormalized
Replacing outliers by moderated MAD	ReplaceOutliersByMAD
Accessor functions for the result from a ABSDataSet	results results,ABSDataSet-method
Accessors for the 'sizeFactor' slot of a ABSDataSet object.	sFactors sFactors,ABSDataSet-method sFactors<- sFactors<-,ABSDataSet,numeric-method
Simulated study with random outliers	simuN5