HTSeqGenie: A NGS analysis pipeline.
Version 4.6.0

Libraries to perform NGS analysis.

AuthorGregoire Pau, Jens Reeder
Date of publicationNone
MaintainerJens Reeder <reeder.jens@gene.com>
LicenseArtistic-2.0
Version4.6.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("HTSeqGenie")

Popular man pages

bamCountUniqueReads: Uniquely count number of reads in bam file
buildTP53GenomeTemplate: buildTP53GenomeTemplate
computeBamStats: Compute record statistics from a bam file
preprocessReads: Pipeline preprocessing
realignIndelsGATK: Realign indels via GATK
rpkm: Calculate RPKM
trimTailsByQuality: Trim off low quality tail
See all...

All man pages Function index File listing

Man pages

alignReads: Align reads against genome
alignReadsChunk: Genomic alignment
analyzeVariants: Calculate and process Variants
annotateVariants: Annotate variants via vep
bamCountUniqueReads: Uniquely count number of reads in bam file
buildConfig: Build a configuration file based on a list of parameters
buildGenomicFeaturesFromTxDb: Build genomic features from a TxDb object
buildShortReadReports: Build a ShortRead report
buildTallyParam: Build tally parameters
buildTP53FastaGenome: buildTP53FastaGenome
buildTP53GenomeTemplate: buildTP53GenomeTemplate
calculateCoverage: Calculate read coverage
calculateTargetLengths: Plot target length for paired end
callVariantsGATK: Variant calling via GATK
checkConfig: Check configuration
checkGATKJar: Check for the GATK jar file
checkPicardJar: checkPicardJar
computeBamStats: Compute record statistics from a bam file
computeCoverage: Compute the coverage vector given a bamfile
countFeatures: Count RNA-Seq Pipeline Genomic Features
countGenomicFeatures: Count overlaps with genomic features
countGenomicFeaturesChunk: Count reads by genomic Feature
createTmpDir: Create a random directory with prefix in R temp dir
detectAdapterContam: Detect sequencing adapter contamination
detectQualityInFASTQFile: Detect quality protocol from a FASTQ file
detectRRNA: Detect rRNA Contamination in Reads
excludeVariantsByRegions: Filter variants by regions
FastQStreamer.getReads: Get FastQ reads from the FastQ streamer
FastQStreamer.init: Open a streaming connection to a FastQ file
FastQStreamer.release: Close the FastQStreamer
filterByLength: Filter reads by length
filterQuality: Filter reads by quality
findVariantFile: Get a vcf filename given a HTSeqGenie directory
gatk: gatk
generateSingleGeneDERs: generateSingleGeneDERs
getAdapterSeqs: Read list of Illumina adapter seqs from package data
getBams: Get bam files of a pipeline run
getChunkDirs: Get the list of chunk directories
getConfig: Get a configuration parameter
getConfig.integer: Check if a config parameter is an integer
getConfig.logical: Check if a config parameter has a logical value
getConfig.numeric: Check if a config parameter is a numeric
getConfig.vector: Return values of a config variable as vector
getEndNumber: Get Read End Number
getMemoryUsage: Returns memory usage in bytes
getNumberOfReadsInFASTQFile: Count reads in Fastq file
getNumericVectorDataFromFile: Load data as numerical values
getObjectFilename: Get a filename given a directory and the object name
getPackageFile: Get a package file
getRandomAlignCutoff: Estimate an adapter alignment cutoff score
getRRNAIds: Detect reads that look like rRNA
getTabDataFromFile: Load tabular data from the NGS pipeline result directory
getTraceback: Get traceback from tryKeepTraceback()
hashCoverage: Hashing function for coverage
hashVariants: Hashing function for variants
hashVector: Hashing function for vector
HTSeqGenie: Package overview
initDirs: Set up NGS output dir
initLog: Initialize the logger
initLogger: Init loggers
initPipelineFromConfig: Init pipeline environment
initPipelineFromSaveDir: Init Pipeline environment from previous run
isAboveQualityThresh: Check for high quality reads
isAdapter: Detect adapter contamination
isConfig: Test the presence of the parameter in the current config
isFirstFragment: Does a SAM flag indicate the first fragment
isSparse: isSparse
listIterator.init: Create a iterator on a list
listIterator.next: Get reads from the listIterator
loadConfig: Load configuration file
logdebug: Log debug using the logging package
logerror: Log info using the logging package
loginfo: Log info using the logging package
logwarn: Log warning using the logging package
makeDir: Make a directory after performing an existence check
makeRandomSreads: Generate a couple if random ShortReadQ, intended for testing
markDuplicates: markDuplicates
markDups: markDups
mergeAlignReads: Merge after alignReads
mergeCoverage: Merge coverage files
mergeLanes: Merge input lanes
mergePreprocessReads: Merge after preprocessReads
mergeSummaryAlignment: Merge summary alignments
parseDCF: Read and parse a configuration file
parseSummaries: parse summary files from save dirs
picard: picard
plotDF: Make continuous plots of distribution function
preprocessReads: Pipeline preprocessing
preprocessReadsChunk: Preprocess a chunk
processChunks: Process chunk in the pipeline framework
readInputFiles: Read FastQ input files
readRNASeqEnds: Read single/paired End Bam Files
realignIndels: realignIndels
realignIndelsGATK: Realign indels via GATK
relativeBarPlot: Make relative bar plots
removeChunkDir: Remove chunk directories
resource: Reload package source code
rpkm: Calculate RPKM
runAlignment: Runs the read alignment step of the pipeline
runPipeline: Run the NGS analysis pipeline
runPipelineConfig: Run the NGS analysis pipeline
runPreprocessReads: Run the preprocesing steps of the pipeline
safeExecute: Execute function in try catch with trace function
safeGetObject: Safely load a R data file
safeUnlink: safeUnlink
safe.yield: Overloaded yield(...) method catching truncated exceptions...
saveWithID: Save an R object
sclapply: Scheduled parallel processing
setChunkDir: Set the base directory for the chunks
setUpDirs: Create output directory and subdirectories for sequencing...
setupTestFramework: setup test framework
statCountFeatures: Compute statistics on count features
TP53GenomicFeatures: Demo genomic features around the TP53 gene
traceMem: Show memory usage
trimReads: Trim/truncate a set of reads
trimTailsByQuality: Trim off low quality tail
truncateReads: Trim/truncate a set of reads
tryKeepTraceback: Wrapper around try-catch
updateConfig: Update the existing config
vcfStat: Compute stats on a VCF file
wrap.callVariants: Variant calling
writeAudit: Write Session information
writeConfig: Write a config file
writeFastQFiles: Write reads to file
writeFeatureCountsHTML: writeFeatureCountsHTML
writeGenomicFeaturesReport: Generate pipeline report
writePreprocessAlignHTML: writePreprocessAlignHTML
writePreprocessAlignReport: Generate Pipeline Report
writeSummary: Write HTML summary
writeVCF: writeVCF

Functions

FastQStreamer.getReads Man page Source code
FastQStreamer.init Man page Source code
FastQStreamer.release Man page Source code
HTSeqGenie Man page
IDverify Source code
TP53GenomicFeatures Man page Source code
addHandler Source code
alignReads Man page Source code
alignReadsChunk Man page Source code
analyzeVariants Man page Source code
annotateVariants Man page Source code
bamCountUniqueReads Man page Source code
buildAnalyzedBam Source code
buildAnyFastaGenome Source code
buildCallingFilters Source code
buildConfig Man page Source code
buildGenomicFeaturesFromTxDb Man page Source code
buildGsnapArgs Source code
buildGsnapParams Source code
buildShortReadReports Man page Source code
buildTP53FastaGenome Man page Source code
buildTP53GenomeTemplate Man page Source code
buildTallyParam Man page Source code
calcExonsCovered Source code
calcGenomicFeaturesDetected Source code
calcHitsByGenomicFeature Source code
calculateCoverage Man page Source code
calculateTargetLengths Man page Source code
callGenotypes Source code
callVariantsGATK Man page Source code
callVariantsVariantTools Source code
catBams Source code
checkConfig Man page Source code
checkConfig.GATK Source code
checkConfig.alignReads Source code
checkConfig.analyzeVariants Source code
checkConfig.analyzeVariants.VT Source code
checkConfig.countGenomicFeatures Source code
checkConfig.coverage Source code
checkConfig.debug Source code
checkConfig.detectAdapterContam Source code
checkConfig.detectRRNA Source code
checkConfig.filterQuality Source code
checkConfig.input Source code
checkConfig.markDuplicates Source code
checkConfig.noextraparameters Source code
checkConfig.output Source code
checkConfig.realignIndels Source code
checkConfig.shortReadReport Source code
checkConfig.system Source code
checkConfig.template Source code
checkConfig.trimReads Source code
checkGATKJar Man page Source code
checkInputConfigs Source code
checkPicardJar Man page Source code
checkVEP Source code
computeBamStats Man page Source code
computeCoverage Man page Source code
computeCoverageStats Source code
computeWidth Source code
countFeatures Man page Source code
countGenomicFeatures Man page Source code
countGenomicFeaturesChunk Man page Source code
create.result.link.table Source code
createQAReport Source code
createSummaryAlignment Source code
createSummaryCounts Source code
createTmpDir Man page Source code
detectAdapterContam Man page Source code
detectQualityInFASTQFile Man page Source code
detectRRNA Man page Source code
doMergeLanes Source code
dotboxplot Source code
estimateCutoffs Source code
estimateFragmentLength Source code
excludeVariantsByRegions Man page Source code
filterByLength Man page Source code
filterGATKVars Source code
filterQuality Man page Source code
finalCallFromIndividualQACalls Source code
findTemplate Source code
findVariantFile Man page Source code
gatk Man page Source code
generateCountFeaturesPlots Source code
generateSingleGeneDERs Man page Source code
get.random.chunk.dir.name Source code
getAdapterSeqs Man page Source code
getAllSummaries Source code
getAnalyzedBamFile Source code
getBamType Source code
getBams Man page Source code
getChunkDirs Man page Source code
getConfig Man page Source code
getConfig.integer Man page Source code
getConfig.logical Man page Source code
getConfig.numeric Man page Source code
getConfig.vector Man page Source code
getEffectiveReadLengths Source code
getEndNumber Man page Source code
getGenomeSegments Source code
getGmapGenome Source code
getMemoryUsage Man page Source code
getNumberOfReadsInFASTQFile Man page Source code
getNumericVectorDataFromFile Man page Source code
getObjectFilename Man page Source code
getPackageFile Man page Source code
getRRNAIds Man page Source code
getRandomAlignCutoff Man page Source code
getTabDataFromFile Man page Source code
getTraceback Man page Source code
hashCoverage Man page Source code
hashVariants Man page Source code
hashVector Man page Source code
heatmap Source code
how_many Source code
initDirs Man page Source code
initLog Man page Source code
initLogger Man page Source code
initPipelineFromConfig Man page Source code
initPipelineFromSaveDir Man page Source code
isAboveQualityThresh Man page Source code
isAdapter Man page Source code
isConfig Man page Source code
isFirstFragment Man page Source code
isSparse Man page Source code
listIterator.init Man page Source code
listIterator.next Man page Source code
loadConfig Man page Source code
logReset Source code
logdebug Man page Source code
logerror Man page Source code
loginfo Man page Source code
loglevel Source code
logwarn Man page Source code
makeDir Man page Source code
makePreprocessAlignPlots Source code
makeRandomSreads Man page Source code
makeReadFiltering Source code
markDuplicates Man page Source code
markDups Man page Source code
mergeAlignReads Man page Source code
mergeBAMsAcrossDirs Source code
mergeBams Source code
mergeCountGenomicFeatures Source code
mergeCounts Source code
mergeCoverage Man page Source code
mergeDetectAdapterContam Source code
mergeLanes Man page Source code
mergePreprocessReads Man page Source code
mergePreprocessedFastQ Source code
mergeSummaryAlignment Man page Source code
mergeSummaryCounts Source code
mergeSummaryPreprocess Source code
onLoad Source code
parseDCF Man page Source code
parseSummaries Man page Source code
picard Man page Source code
plot.in.out.min.max.readlength Source code
plot.perc.reads.bad Source code
plot.perc.reads.good Source code
plot.quartile.target.length Source code
plot.reads.bad Source code
plot.reads.good Source code
plotAlignmentSummary Source code
plotBamStatsSummary Source code
plotCountGFSummary Source code
plotCountGFbyFeatureSummary Source code
plotDF Man page Source code
plotGenesDetected Source code
plotJunctionReads Source code
plotPreprocessSummary Source code
plotReadMappingsPerChr Source code
plotVariantsSummary Source code
plot_hist Source code
postFilterVariants Source code
postMergeChecks Source code
preMergeChecks Source code
preprocessReads Man page Source code
preprocessReadsChunk Man page Source code
processChunks Man page Source code
readInputFiles Man page Source code
readRNASeqEnds Man page Source code
realignIndels Man page Source code
realignIndelsGATK Man page Source code
realignOne Source code
relativeBarPlot Man page Source code
removeChunkDir Man page Source code
reportFailedRuns Source code
resource Man page Source code
rpkm Man page Source code
runAlignment Man page Source code
runPipeline Man page Source code
runPipelineConfig Man page Source code
runPreprocessReads Man page Source code
safe.file.rename Source code
safe.yield Man page Source code
safeExecute Man page Source code
safeGetObject Man page Source code
safeUnlink Man page Source code
sanityCheck Source code
saveCoverage Source code
saveVTvars Source code
saveWithID Man page Source code
sclapply Man page Source code
setChunkDir Man page Source code
setLevel Source code
setUpDirs Man page Source code
setupTestFramework Man page Source code
statCountFeatures Man page Source code
traceMem Man page Source code
trimReads Man page Source code
trimTailsByQuality Man page Source code
truncateReads Man page Source code
tryKeepTraceback Man page Source code
updateConfig Man page Source code
vcfStat Man page Source code
wrap.callVariants Man page Source code
wrapGsnap Source code
writeAudit Man page Source code
writeConfig Man page Source code
writeFastQFiles Man page Source code
writeFeatureCountsHTML Man page Source code
writeGenomicFeaturesReport Man page Source code
writePreprocessAlignHTML Man page Source code
writePreprocessAlignReport Man page Source code
writeSummary Man page Source code
writeToConsole Source code
writeToFile Source code
writeVCF Man page Source code
zipUp Source code

Files

.BBSoptions
DESCRIPTION
NAMESPACE
NEWS
R
R/TP53GenomicFeatures.R
R/alignReads.R
R/analyzeVariants.R
R/bamUtils.R
R/buildGenomicFeaturesFromTxDb.R
R/checkConfig.R
R/config.R
R/countGenomicFeatures.R
R/coverage.R
R/createSummaryCounts.R
R/detectAdapterContam.R
R/detectRRNA.R
R/filterQuality.R
R/gatk.R
R/initPipeline.R
R/io.R
R/logging.R
R/mergeLanes.R
R/picard.R
R/preprocessReads.R
R/reportPipelineQA.R
R/runPipeline.R
R/summaries.R
R/targetLengths.R
R/testHelpers.R
R/tools.R
R/trimReads.R
R/wrapGsnap.R
R/zzz.R
build
build/vignette.rds
inst
inst/config
inst/config/default-config.txt
inst/doc
inst/doc/HTSeqGenie.R
inst/doc/HTSeqGenie.Rnw
inst/doc/HTSeqGenie.pdf
inst/extdata
inst/extdata/H1993_TP53_subset2500_1.fastq.gz
inst/extdata/H1993_TP53_subset2500_2.fastq.gz
inst/extdata/adapter_data
inst/extdata/adapter_data/Illumina_adapters.curated.paired_end_1.fasta
inst/extdata/adapter_data/Illumina_adapters.curated.paired_end_2.fasta
inst/extdata/adapter_data/Illumina_adapters.curated.single_end.fasta
inst/extdata/adapter_data/Illumina_adapters.paired_end.fasta
inst/test-data
inst/test-data/Realigner
inst/test-data/Realigner/KRAS_TP53_demo.dict
inst/test-data/Realigner/jiggling_indels.bam
inst/test-data/Realigner/jiggling_indels.bam.bai
inst/test-data/Realigner/jiggling_indels_tp53_kras.bam
inst/test-data/Realigner/jiggling_indels_tp53_kras.bam.bai
inst/test-data/SAM634406-subsample-config.txt
inst/test-data/SAM634406-subsample_R1.gz
inst/test-data/SAM634406-subsample_R2.gz
inst/test-data/bam_files_unit_test_PE
inst/test-data/bam_files_unit_test_PE/processed.aligner_input_1.fastq
inst/test-data/bam_files_unit_test_PE/processed.aligner_input_2.fastq
inst/test-data/bam_files_unit_test_PE/test_pe.gsnap.merged.concordant_mult.bam
inst/test-data/bam_files_unit_test_PE/test_pe.gsnap.merged.concordant_mult.bam.bai
inst/test-data/bam_files_unit_test_PE/test_pe.gsnap.merged.concordant_transloc.bam
inst/test-data/bam_files_unit_test_PE/test_pe.gsnap.merged.concordant_transloc.bam.bai
inst/test-data/bam_files_unit_test_PE/test_pe.gsnap.merged.concordant_uniq.bam
inst/test-data/bam_files_unit_test_PE/test_pe.gsnap.merged.concordant_uniq.bam.bai
inst/test-data/bam_files_unit_test_PE/test_pe.gsnap.merged.halfmapping_mult.bam
inst/test-data/bam_files_unit_test_PE/test_pe.gsnap.merged.halfmapping_mult.bam.bai
inst/test-data/bam_files_unit_test_PE/test_pe.gsnap.merged.halfmapping_transloc.bam
inst/test-data/bam_files_unit_test_PE/test_pe.gsnap.merged.halfmapping_transloc.bam.bai
inst/test-data/bam_files_unit_test_PE/test_pe.gsnap.merged.halfmapping_uniq.bam
inst/test-data/bam_files_unit_test_PE/test_pe.gsnap.merged.halfmapping_uniq.bam.bai
inst/test-data/bam_files_unit_test_PE/test_pe.gsnap.merged.nomapping.bam
inst/test-data/bam_files_unit_test_PE/test_pe.gsnap.merged.nomapping.bam.bai
inst/test-data/bam_files_unit_test_PE/test_pe.gsnap.merged.paired_mult.bam
inst/test-data/bam_files_unit_test_PE/test_pe.gsnap.merged.paired_mult.bam.bai
inst/test-data/bam_files_unit_test_PE/test_pe.gsnap.merged.paired_uniq_inv.bam
inst/test-data/bam_files_unit_test_PE/test_pe.gsnap.merged.paired_uniq_inv.bam.bai
inst/test-data/bam_files_unit_test_PE/test_pe.gsnap.merged.paired_uniq_long.bam
inst/test-data/bam_files_unit_test_PE/test_pe.gsnap.merged.paired_uniq_long.bam.bai
inst/test-data/bam_files_unit_test_PE/test_pe.gsnap.merged.paired_uniq_scr.bam
inst/test-data/bam_files_unit_test_PE/test_pe.gsnap.merged.paired_uniq_scr.bam.bai
inst/test-data/bam_files_unit_test_PE/test_pe.gsnap.merged.unpaired_mult.bam
inst/test-data/bam_files_unit_test_PE/test_pe.gsnap.merged.unpaired_mult.bam.bai
inst/test-data/bam_files_unit_test_PE/test_pe.gsnap.merged.unpaired_transloc.bam
inst/test-data/bam_files_unit_test_PE/test_pe.gsnap.merged.unpaired_transloc.bam.bai
inst/test-data/bam_files_unit_test_PE/test_pe.gsnap.merged.unpaired_uniq.bam
inst/test-data/bam_files_unit_test_PE/test_pe.gsnap.merged.unpaired_uniq.bam.bai
inst/test-data/braf_v600.vcf
inst/test-data/empty.bam
inst/test-data/ndup-marked.bam
inst/test-data/ndup-unmarked.bam
inst/test-data/reads.fastq.gz
inst/test-data/test_config.txt
inst/test-data/test_config_single_end.txt
inst/test-data/test_highqualSpliceInPE2SharedExonWithPE1.bam
inst/test-data/test_picard_dups.bam
inst/test-data/tp53_dbsnp.Rdata
inst/test-data/tp53_rmsk.bed
inst/test-data/truncated.fastq.gz
inst/test-data/unit_tests_1.fastq
inst/test-data/unit_tests_2.fastq
inst/test-data/variant_calling
inst/test-data/variant_calling/one_variant_no_filtered.bam
inst/test-data/variant_calling/one_variant_no_filtered.bam.bai
inst/test-data/variant_calling/test_set.merged.uniques.bam
inst/test-data/variant_calling/test_set.merged.uniques.bam.bai
inst/test-data/variant_calling/test_set.pair1.fastq
inst/test-data/variant_calling/test_set.pair2.fastq
inst/test-data/variant_calling/tp53_test.bam
inst/test-data/variant_calling/tp53_test.bam.bai
inst/unitTests
inst/unitTests/runTests.R
inst/unitTests/runit.alignReads.R
inst/unitTests/runit.analyzeVariants.R
inst/unitTests/runit.bamUtils.R
inst/unitTests/runit.buildGenomicFeatures.R
inst/unitTests/runit.calculateCoverage.R
inst/unitTests/runit.checkConfig.R
inst/unitTests/runit.config.R
inst/unitTests/runit.detectAdapterContam.R
inst/unitTests/runit.detectRRNA.R
inst/unitTests/runit.filterQuality.R
inst/unitTests/runit.gatk.R
inst/unitTests/runit.io.R
inst/unitTests/runit.mergeLanes.R
inst/unitTests/runit.picard.R
inst/unitTests/runit.preprocessReads.R
inst/unitTests/runit.readRNASeqEnds.R
inst/unitTests/runit.reportPipelineQA.R
inst/unitTests/runit.runPipeline.R
inst/unitTests/runit.targetLengths.R
inst/unitTests/runit.tools.R
inst/unitTests/runit.trimReads.R
man
man/FastQStreamer.getReads.Rd
man/FastQStreamer.init.Rd
man/FastQStreamer.release.Rd
man/HTSeqGenie.Rd
man/TP53GenomicFeatures.Rd
man/alignReads.Rd
man/alignReadsChunk.Rd
man/analyzeVariants.Rd
man/annotateVariants.Rd
man/bamCountUniqueReads.Rd
man/buildConfig.Rd
man/buildGenomicFeaturesFromTxDb.Rd
man/buildShortReadReports.Rd
man/buildTP53FastaGenome.Rd
man/buildTP53GenomeTemplate.Rd
man/buildTallyParam.Rd
man/calculateCoverage.Rd
man/calculateTargetLengths.Rd
man/callVariantsGATK.Rd
man/checkConfig.Rd
man/checkGATKJar.Rd
man/checkPicardJar.Rd
man/computeBamStats.Rd
man/computeCoverage.Rd
man/countFeatures.Rd
man/countGenomicFeatures.Rd
man/countGenomicFeaturesChunk.Rd
man/createTmpDir.Rd
man/detectAdapterContam.Rd
man/detectQualityInFASTQFile.Rd
man/detectRRNA.Rd
man/excludeVariantsByRegions.Rd
man/filterByLength.Rd
man/filterQuality.Rd
man/findVariantFile.Rd
man/gatk.Rd
man/generateSingleGeneDERs.Rd
man/getAdapterSeqs.Rd
man/getBams.Rd
man/getChunkDirs.Rd
man/getConfig.Rd
man/getConfig.integer.Rd
man/getConfig.logical.Rd
man/getConfig.numeric.Rd
man/getConfig.vector.Rd
man/getEndNumber.Rd
man/getMemoryUsage.Rd
man/getNumberOfReadsInFASTQFile.Rd
man/getNumericVectorDataFromFile.Rd
man/getObjectFilename.Rd
man/getPackageFile.Rd
man/getRRNAIds.Rd
man/getRandomAlignCutoff.Rd
man/getTabDataFromFile.Rd
man/getTraceback.Rd
man/hashCoverage.Rd
man/hashVariants.Rd
man/hashVector.Rd
man/initDirs.Rd
man/initLog.Rd
man/initLogger.Rd
man/initPipelineFromConfig.Rd
man/initPipelineFromSaveDir.Rd
man/isAboveQualityThresh.Rd
man/isAdapter.Rd
man/isConfig.Rd
man/isFirstFragment.Rd
man/isSparse.Rd
man/listIterator.init.Rd
man/listIterator.next.Rd
man/loadConfig.Rd
man/logdebug.Rd
man/logerror.Rd
man/loginfo.Rd
man/logwarn.Rd
man/makeDir.Rd
man/makeRandomSreads.Rd
man/markDuplicates.Rd
man/markDups.Rd
man/mergeAlignReads.Rd
man/mergeCoverage.Rd
man/mergeLanes.Rd
man/mergePreprocessReads.Rd
man/mergeSummaryAlignment.Rd
man/parseDCF.Rd
man/parseSummaries.Rd
man/picard.Rd
man/plotDF.Rd
man/preprocessReads.Rd
man/preprocessReadsChunk.Rd
man/processChunks.Rd
man/readInputFiles.Rd
man/readRNASeqEnds.Rd
man/realignIndels.Rd
man/realignIndelsGATK.Rd
man/relativeBarPlot.Rd
man/removeChunkDir.Rd
man/resource.Rd
man/rpkm.Rd
man/runAlignment.Rd
man/runPipeline.Rd
man/runPipelineConfig.Rd
man/runPreprocessReads.Rd
man/safe.yield.Rd
man/safeExecute.Rd
man/safeGetObject.Rd
man/safeUnlink.Rd
man/saveWithID.Rd
man/sclapply.Rd
man/setChunkDir.Rd
man/setUpDirs.Rd
man/setupTestFramework.Rd
man/statCountFeatures.Rd
man/traceMem.Rd
man/trimReads.Rd
man/trimTailsByQuality.Rd
man/truncateReads.Rd
man/tryKeepTraceback.Rd
man/updateConfig.Rd
man/vcfStat.Rd
man/wrap.callVariants.Rd
man/writeAudit.Rd
man/writeConfig.Rd
man/writeFastQFiles.Rd
man/writeFeatureCountsHTML.Rd
man/writeGenomicFeaturesReport.Rd
man/writePreprocessAlignHTML.Rd
man/writePreprocessAlignReport.Rd
man/writeSummary.Rd
man/writeVCF.Rd
tests
tests/doRUnit.R
vignettes
vignettes/HTSeqGenie.Rnw
vignettes/RNASeq-pipeline-3.pdf
vignettes/gene_models.jpeg
HTSeqGenie documentation built on May 20, 2017, 9:17 p.m.

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