ArrayExpressHTS: ArrayExpress High Throughput Sequencing Processing Pipeline
Version 1.26.0

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

AuthorAngela Goncalves, Andrew Tikhonov
Bioconductor views RNASeq Sequencing
Date of publicationNone
MaintainerAngela Goncalves <filimon@ebi.ac.uk>, Andrew Tikhonov <andrew@ebi.ac.uk>
LicenseArtistic License 2.0
Version1.26.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("ArrayExpressHTS")

Popular 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
See all...

All man pages Function index File listing

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

Functions

ASCIIconvert Source code
ArrayExpressHTS Man page Source code
ArrayExpressHTSFastQ Man page Source code
addOptions Source code Source code
addPackageVariables Source code Source code
addPathToPATH Source code
align Source code
align_bowtie Source code
align_bwa Source code
align_tophat Source code
annot_to_iranges Source code
appendStatusText Source code
assignOneProject Source code
assignPipelineOptions Source code Source code
assignProjects Source code
assignStopOnWarnings Source code
assignSubmID Source code
attachExperimentData Source code
bamParam Source code
bam_to_list Source code
bam_to_occurrencetab Source code
bamlist_to_alignedread Source code
calculate_dustyScore Source code
call_count Source code
call_cufflinks Source code
call_estimator Source code
call_mmseq Source code
call_none Source code
call_normalisator Source code
call_samtools Source code
call_tmm Source code
checkAndDefineBasePath Source code Source code
checkAndDefineReferencePath Source code Source code
checkAndDefineToolOptions Source code Source code
checkOneTool Source code Source code
checkProjectErrors Source code
checkReference Source code
checkToolExists Source code Source code
checkURLAvailable Source code
checkURLResourcesAvailable Source code
check_indexes Source code
cleanupAfterExecution Source code
cleanupCluster Source code
compareProjects Source code
count_polyL Source code
count_reads_per_feature Source code
createAEprojects Source code
createDefaultProject Source code
createDirAndBackup Source code
createFastQProjects Source code
createOptions Source code Source code
createServerLog Source code
create_feature_data Source code
cufflinks_to_countmatrix Source code
cufflinks_to_dataframe Source code
cufflinks_to_granges Source code
cufflinks_to_iranges Source code
downloadENADataFile Source code
download_annotation Source code
exprs_table_to_dataframe Source code
fasta_to_list Source code
fastq_to_dataframe Source code
fastq_to_shortreadq Source code
fastqquality_to_integer Source code
filterENAData Source code
filter_chr Source code
filter_shortread_by_sequence Source code
filterbam Source code
finalCountdown Source code
findUsefulRange Source code
fixReference Source code
fixReferenceDoubleY Source code
fixedOptions Source code
flagToBitStr Source code
flag_is_firstmate Source code
flag_is_mapped Source code
flag_is_mapped_and_proper Source code
flag_is_secondmate Source code
flag_meaning Source code
flagint_to_bit Source code
getAEExpDescription Source code
getAEExpType Source code
getAEExperimentPathBase Source code
getAEIDFFilename Source code
getAEIDFURL Source code
getAERawDataFilenames Source code
getAESDRFFilename Source code
getAESDRFURL Source code
getAlignerDefaultOptions Source code
getAllHTSAccessionsFromAE Source code
getAssayNameFromSDRF Source code
getCluster Source code
getCurrentRefVersion Source code
getDataFromSDRF Source code
getDefaultFilteringOptions Man page Source code
getDefaultProcessingOptions Man page Source code
getDefaultRCloudOptions Man page Source code
getDefaultReferenceDir Source code
getENAAccessionPrefixes Source code
getENAAccessionRecord Source code
getENAExpIDForAEAcc Source code
getENAExpIDFromSDRF Source code
getENAFastqPathBase Source code
getENAFastqURLBase Source code
getENARunIDForExpID Source code
getEnsemblAnnotation Source code
getEnsemblReference Source code
getExpStatus Source code
getExperimentDescriptors Source code
getFactorValueFromSDRF Source code
getFirstAvailableLayout Source code
getHTSAccessionsFromAE Source code
getHTSRNASeqAccessionsFromAE Source code
getLibrarySelectionFromSDRF Source code
getLibraryStrategyFromSDRF Source code
getMark Source code
getMatchedText Source code
getOptionPathComponent Source code
getOrganismFromSDRF Source code
getPackageVariable Source code Source code
getPipelineOption Man page Source code Source code
getPipelineOptions Man page Source code Source code
getReadLength0 Source code
getRunIDFromSDRF Source code
getRunStatus Source code
getSAMLineInfo Source code
getSDRFforAccession Source code
getSubmID Source code
getSupportedOrganisms Source code
getSupportedSelectionRowIndexes Source code
getSupportedStrategyRowIndexes Source code
getToolName Source code Source code
getToolOptionNames Source code Source code
getTraceMark Source code Source code
get_DE Source code
get_annotation Source code
get_annotation_RData_name Source code
get_chr_representation Source code
get_fastq_quality0 Source code
get_fastq_quality_scale Source code
grepAllENAAccessions Source code
grepSDRFForENAAccessions Source code
gtf_to_dataframe Source code
indexReference Source code
initDefaultProject Source code
initEnvironmentVariables Source code
initPackageVariables Source code Source code
initPipelineOptions Source code Source code
isOrganismSupported Source code
isPackageVariableDefined Source code Source code
isRCloud Man page Source code
is_polyX Source code
length_raw_reads Source code
loadENAData Source code
locateInSystem Source code Source code
locateInToolBase Source code Source code
log.error Source code
log.info Source code
log.warning Source code
makeAEFilesURL Source code
makeAEIDFURL Source code
makeAESDRFFilenames Source code
makeAESDRFURLs Source code
makeClusterLogFolder Source code
makeENAExpURL Source code
makeENAFastqFileName Source code
makeENAFastqURL Source code
make_filt_indexes Source code
make_indexes_old Source code
mapAEtoENAviaENADataFile Source code
mapAEtoENAviaHTTP Source code
map_quality_scale0 Source code
mergeOptions Source code
mmseq_to_dataframe Source code
move_files Source code
myHTMLplot Source code
number_aligned_reads Source code
number_raw_reads Source code
obtainENAFastQDataFiles Source code
onLoad Source code
onUnload Source code
parseFlag Source code
peekPSRExpId Source code
peekPSRFolder Source code
peekPSRRunId Source code
phred_to_average_qual Source code
phred_to_avgqual Source code
pileup_to_dataframe Source code
plot_DE_length Source code
plot_DE_report Source code
plot_N_distrib Source code
plot_aligned_report Source code
plot_avgbasequal_boxplots Source code
plot_avgbasequal_distrib Source code
plot_bars_totalunique Source code
plot_basecall_per_cycle Source code
plot_basecall_per_cycle_log Source code
plot_chromosome_distrib Source code
plot_compared_hits Source code
plot_compared_raw_report Source code
plot_dustyScore_distrib Source code
plot_dustyScore_distribs Source code
plot_hits Source code
plot_insertsize Source code
plot_insize_boxplot Source code
plot_mapq Source code
plot_mapq_distribution Source code
plot_multiplealigns_hist Source code
plot_multiplealigns_vs_complexity Source code
plot_polyX Source code
plot_quality_per_cycle Source code
plot_ranges Source code
plot_raw_report Source code
plot_readoccurence_cdf Source code
plot_repeatedreads_vs_complexity Source code
plot_scatter_samples Source code
plot_strand_distrib Source code
plot_transcript_distrib Source code
pokePSRExpId Source code
pokePSRFolder Source code
pokePSRRunId Source code
polyX_size Source code
prepareAnnotation Man page Source code
prepareCluster Source code
prepareReference Man page Source code
print.memory.usage Source code
printFlag Source code
processOneProject Source code
processOneProjectAlignment Source code
processOneProjectAlnReport Source code
processOneProjectEstimation Source code
processOneProjectRawReport Source code
projectSummary Source code
readData Source code
readENADataForExpID Source code
readENADataForRunID Source code
readIDF Source code
readSDRF Source code
read_gtf Source code
recordAlignedProperties Source code
reflen_to_dataframe Source code
reftype_to_filename Source code
registerExpStepCompleted Source code
registerExpStepFailure Source code
registerExpStepStarted Source code
registerExpStepStatusText Source code
registerExpStepWarning Source code
registerRunStepCompleted Source code
registerRunStepFailure Source code
registerRunStepStarted Source code
registerRunStepStatusText Source code
registerRunStepWarning Source code
removePathFromPATH Source code
replacePathInPATH Source code
resetProjectErrors Source code
runProjects Source code
run_cmds Source code
sam_addXS Source code
scanAllENAData Source code
scanSupportedOrganisms Source code
searchBiomart Source code
sendReminder Source code
setCluster Source code
setExpStatus Source code
setPackageVariable Source code Source code
setPipelineOption Source code Source code
setPipelineOptions Man page Source code Source code
setProjectData Source code
setRunStatus Source code
setUserOptions Source code
setupBaseFolder Source code
setupDataFolder Source code
setupPSRFolder Source code
setupPSRLogging Source code
setupSUBM_ID Source code
shortread_to_dataframe Source code
shortread_to_tab Source code
shortread_to_unique Source code
standardise Source code
std Source code
stringids_to_dataframe Source code
stringset_to_dustyscore Source code
stripOffQuotas Source code
table_pileup_summary Source code
table_transcript_overlap Source code
table_transcriptome_vs_genome Source code
to_dataframe Source code
to_expressionset Source code
toolFolderName Source code Source code
trace.enter Source code Source code
trace.exit Source code Source code
transcriptome_to_dataframe Source code
un_std Source code
updateExpStatusOnExit Source code
updateRunStatusOnExit Source code
verify_fqfiles Source code
writePropertyFile Source code
xstringset_to_hitcount Source code

Files

DESCRIPTION
NAMESPACE
R
R/ae2enamap.R
R/cluster.R
R/comparedAnalysis.R
R/comparedPlots.R
R/defaults.R
R/functions.R
R/logutil.R
R/memutil.R
R/onload.R
R/options.R
R/optutil.R
R/package.R
R/pipeline.R
R/project_options.R
R/proputil.R
R/psrutil.R
R/reference.R
R/singlePlots.R
R/trace.R
R/traceutil.R
R/tweaked.R
R/utils.R
R/vars.R
R/varutil.R
build
build/vignette.rds
inst
inst/NEWS
inst/doc
inst/doc/ArrayExpressHTS.R
inst/doc/ArrayExpressHTS.Rnw
inst/doc/ArrayExpressHTS.pdf
inst/expdata
inst/expdata/testExperiment
inst/expdata/testExperiment/data
inst/expdata/testExperiment/data/SRR017233.fastq
inst/expdata/testExperiment/data/SRR017234.fastq
inst/expdata/testExperiment/data/SRR017235.fastq
inst/expdata/testExperiment/data/SRR017236.fastq
inst/expdata/testExperiment/data/SRR017237.fastq
inst/expdata/testExperiment/data/SRR017238.fastq
inst/expdata/testExperiment/data/SRR017239.fastq
inst/expdata/testExperiment/data/SRR017240.fastq
inst/expdata/testExperiment/data/SRR017241.fastq
inst/expdata/testExperiment/data/SRR017242.fastq
inst/expdata/testExperiment/data/SRR017243.fastq
inst/expdata/testExperiment/data/SRR017244.fastq
inst/expdata/testExperiment/data/SRR017245.fastq
inst/expdata/testExperiment/data/SRR017246.fastq
inst/expdata/testExperiment/data/SRR017247.fastq
inst/expdata/testExperiment/data/SRR017248.fastq
inst/expdata/testExperiment/data/testExperiment.idf.txt
inst/expdata/testExperiment/data/testExperiment.sdrf.txt
inst/script
inst/script/gtf2txt.pl
man
man/ArrayExpressHTS.Rd
man/ArrayExpressHTSFastQ.Rd
man/isRCloud.Rd
man/package-options.Rd
man/prepareAnnotation.Rd
man/prepareReference.Rd
man/processing-options.Rd
src
src/Makevars
src/addXS.c
src/fltbam.c
src/functions.c
src/hashtable.c
src/hashtable.h
src/hashtable_itr.c
src/hashtable_itr.h
src/hashtable_private.h
src/hashtable_utility.c
src/hashtable_utility.h
vignettes
vignettes/ArrayExpressHTS.Rnw
ArrayExpressHTS documentation built on May 20, 2017, 9:49 p.m.

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