rnaseqcomp: Benchmarks for RNA-seq Quantification Pipelines
Version 1.6.0

Several quantitative and visualized benchmarks for RNA-seq quantification pipelines. Two-condition quantifications for genes, transcripts, junctions or exons by each pipeline with necessary meta information should be organized into numeric matrices in order to proceed the evaluation.

AuthorMingxiang Teng and Rafael A. Irizarry
Bioconductor views QualityControl RNASeq Visualization
Date of publicationNone
MaintainerMingxiang Teng <tengmx@gmail.com>
LicenseGPL-3
Version1.6.0
URL https://github.com/tengmx/rnaseqcomp
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("rnaseqcomp")

Getting started

README.md
The rnaseqcomp user's guide

Popular man pages

plotFC: Estimate And Plot Fold Change Accuracy
plotNE: Estimate And Plot Express And Non-express Features
plotROC: Estimate And Plot Differential Expression
plotSD: Estimate And Plot Median Standard Deviation
rnaseqcomp-class: rnaseqcomp
signalCalibrate: Quantification Filtering And Calibration
simdata: Example of Quantifications on Simulation Data
See all...

All man pages Function index File listing

Man pages

check_rnaseqcomp: Sanity Check of S4 rnaseqcomp Class
plot2TX: Estimate And Plot Transcript Proportion Difference
plotFC: Estimate And Plot Fold Change Accuracy
plotNE: Estimate And Plot Express And Non-express Features
plotROC: Estimate And Plot Differential Expression
plotSD: Estimate And Plot Median Standard Deviation
rnaseqcomp-class: rnaseqcomp
signalCalibrate: Quantification Filtering And Calibration
simdata: Example of Quantifications on Simulation Data

Functions

check_rnaseqcomp Man page Source code
plot2TX Man page Source code
plotFC Man page Source code
plotNE Man page Source code
plotROC Man page Source code
plotSD Man page Source code
rnaseqcomp-class Man page
signalCalibrate Man page Source code
simdata Man page

Files

DESCRIPTION
NAMESPACE
R
R/AllClasses.R
R/plot2TX.R
R/plotFC.R
R/plotNE.R
R/plotROC.R
R/plotSD.R
R/signalCalibrate.R
R/simdata.R
README.md
build
build/vignette.rds
data
data/datalist
data/simdata.RData
inst
inst/CITATION
inst/NEWS
inst/doc
inst/doc/rnaseqcomp.R
inst/doc/rnaseqcomp.Rmd
inst/doc/rnaseqcomp.pdf
man
man/check_rnaseqcomp.Rd
man/plot2TX.Rd
man/plotFC.Rd
man/plotNE.Rd
man/plotROC.Rd
man/plotSD.Rd
man/rnaseqcomp-class.Rd
man/signalCalibrate.Rd
man/simdata.Rd
vignettes
vignettes/rnaseqcomp.Rmd
vignettes/rnaseqcomp.bib
rnaseqcomp documentation built on May 20, 2017, 11:03 p.m.

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