ArrayExpressHTS: ArrayExpress High Throughput Sequencing Processing Pipeline

RNA-Seq processing pipeline for public ArrayExpress experiments or local datasets

Author
Angela Goncalves, Andrew Tikhonov
Date of publication
None
Maintainer
Angela Goncalves <filimon@ebi.ac.uk>, Andrew Tikhonov <andrew@ebi.ac.uk>
License
Artistic License 2.0
Version
1.24.0

View on Bioconductor

Man pages

ArrayExpressHTS
ExpressionSet for RNA-Seq experiment submitted in...
ArrayExpressHTSFastQ
ExpressionSet for RNA-Seq raw data files
isRCloud
Check the code is running on R-Cloud
package-options
Functions to work with package level options
prepareAnnotation
Prepare annotation data for the RNA-Seq Pipeline
prepareReference
Prepare reference data for the RNA-Seq Pipeline
processing-options
Functions to work with ArrayExpressHTS processing options

Files in this package

ArrayExpressHTS/DESCRIPTION
ArrayExpressHTS/NAMESPACE
ArrayExpressHTS/R
ArrayExpressHTS/R/ae2enamap.R
ArrayExpressHTS/R/cluster.R
ArrayExpressHTS/R/comparedAnalysis.R
ArrayExpressHTS/R/comparedPlots.R
ArrayExpressHTS/R/defaults.R
ArrayExpressHTS/R/functions.R
ArrayExpressHTS/R/logutil.R
ArrayExpressHTS/R/memutil.R
ArrayExpressHTS/R/onload.R
ArrayExpressHTS/R/options.R
ArrayExpressHTS/R/optutil.R
ArrayExpressHTS/R/package.R
ArrayExpressHTS/R/pipeline.R
ArrayExpressHTS/R/project_options.R
ArrayExpressHTS/R/proputil.R
ArrayExpressHTS/R/psrutil.R
ArrayExpressHTS/R/reference.R
ArrayExpressHTS/R/singlePlots.R
ArrayExpressHTS/R/trace.R
ArrayExpressHTS/R/traceutil.R
ArrayExpressHTS/R/tweaked.R
ArrayExpressHTS/R/utils.R
ArrayExpressHTS/R/vars.R
ArrayExpressHTS/R/varutil.R
ArrayExpressHTS/build
ArrayExpressHTS/build/vignette.rds
ArrayExpressHTS/inst
ArrayExpressHTS/inst/NEWS
ArrayExpressHTS/inst/doc
ArrayExpressHTS/inst/doc/ArrayExpressHTS.R
ArrayExpressHTS/inst/doc/ArrayExpressHTS.Rnw
ArrayExpressHTS/inst/doc/ArrayExpressHTS.pdf
ArrayExpressHTS/inst/expdata
ArrayExpressHTS/inst/expdata/testExperiment
ArrayExpressHTS/inst/expdata/testExperiment/data
ArrayExpressHTS/inst/expdata/testExperiment/data/SRR017233.fastq
ArrayExpressHTS/inst/expdata/testExperiment/data/SRR017234.fastq
ArrayExpressHTS/inst/expdata/testExperiment/data/SRR017235.fastq
ArrayExpressHTS/inst/expdata/testExperiment/data/SRR017236.fastq
ArrayExpressHTS/inst/expdata/testExperiment/data/SRR017237.fastq
ArrayExpressHTS/inst/expdata/testExperiment/data/SRR017238.fastq
ArrayExpressHTS/inst/expdata/testExperiment/data/SRR017239.fastq
ArrayExpressHTS/inst/expdata/testExperiment/data/SRR017240.fastq
ArrayExpressHTS/inst/expdata/testExperiment/data/SRR017241.fastq
ArrayExpressHTS/inst/expdata/testExperiment/data/SRR017242.fastq
ArrayExpressHTS/inst/expdata/testExperiment/data/SRR017243.fastq
ArrayExpressHTS/inst/expdata/testExperiment/data/SRR017244.fastq
ArrayExpressHTS/inst/expdata/testExperiment/data/SRR017245.fastq
ArrayExpressHTS/inst/expdata/testExperiment/data/SRR017246.fastq
ArrayExpressHTS/inst/expdata/testExperiment/data/SRR017247.fastq
ArrayExpressHTS/inst/expdata/testExperiment/data/SRR017248.fastq
ArrayExpressHTS/inst/expdata/testExperiment/data/testExperiment.idf.txt
ArrayExpressHTS/inst/expdata/testExperiment/data/testExperiment.sdrf.txt
ArrayExpressHTS/inst/script
ArrayExpressHTS/inst/script/gtf2txt.pl
ArrayExpressHTS/man
ArrayExpressHTS/man/ArrayExpressHTS.Rd
ArrayExpressHTS/man/ArrayExpressHTSFastQ.Rd
ArrayExpressHTS/man/isRCloud.Rd
ArrayExpressHTS/man/package-options.Rd
ArrayExpressHTS/man/prepareAnnotation.Rd
ArrayExpressHTS/man/prepareReference.Rd
ArrayExpressHTS/man/processing-options.Rd
ArrayExpressHTS/src
ArrayExpressHTS/src/Makevars
ArrayExpressHTS/src/addXS.c
ArrayExpressHTS/src/fltbam.c
ArrayExpressHTS/src/functions.c
ArrayExpressHTS/src/hashtable.c
ArrayExpressHTS/src/hashtable.h
ArrayExpressHTS/src/hashtable_itr.c
ArrayExpressHTS/src/hashtable_itr.h
ArrayExpressHTS/src/hashtable_private.h
ArrayExpressHTS/src/hashtable_utility.c
ArrayExpressHTS/src/hashtable_utility.h
ArrayExpressHTS/vignettes
ArrayExpressHTS/vignettes/ArrayExpressHTS.Rnw