rnaseqcomp: Benchmarks for RNA-seq Quantification Pipelines

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.

Author
Mingxiang Teng and Rafael A. Irizarry
Date of publication
None
Maintainer
Mingxiang Teng <tengmx@gmail.com>
License
GPL-3
Version
1.4.0
URLs

View on Bioconductor

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

Files in this package

rnaseqcomp/DESCRIPTION
rnaseqcomp/NAMESPACE
rnaseqcomp/R
rnaseqcomp/R/AllClasses.R
rnaseqcomp/R/plot2TX.R
rnaseqcomp/R/plotFC.R
rnaseqcomp/R/plotNE.R
rnaseqcomp/R/plotROC.R
rnaseqcomp/R/plotSD.R
rnaseqcomp/R/signalCalibrate.R
rnaseqcomp/R/simdata.R
rnaseqcomp/build
rnaseqcomp/build/vignette.rds
rnaseqcomp/data
rnaseqcomp/data/datalist
rnaseqcomp/data/simdata.RData
rnaseqcomp/inst
rnaseqcomp/inst/CITATION
rnaseqcomp/inst/NEWS
rnaseqcomp/inst/doc
rnaseqcomp/inst/doc/rnaseqcomp.R
rnaseqcomp/inst/doc/rnaseqcomp.Rmd
rnaseqcomp/inst/doc/rnaseqcomp.pdf
rnaseqcomp/man
rnaseqcomp/man/check_rnaseqcomp.Rd
rnaseqcomp/man/plot2TX.Rd
rnaseqcomp/man/plotFC.Rd
rnaseqcomp/man/plotNE.Rd
rnaseqcomp/man/plotROC.Rd
rnaseqcomp/man/plotSD.Rd
rnaseqcomp/man/rnaseqcomp-class.Rd
rnaseqcomp/man/signalCalibrate.Rd
rnaseqcomp/man/simdata.Rd
rnaseqcomp/vignettes
rnaseqcomp/vignettes/rnaseqcomp.Rmd
rnaseqcomp/vignettes/rnaseqcomp.bib