HTSeqGenie: A NGS analysis pipeline.

Libraries to perform NGS analysis.

AuthorGregoire Pau, Jens Reeder
Date of publicationNone
MaintainerJens Reeder <reeder.jens@gene.com>
LicenseArtistic-2.0
Version4.4.0

View on Bioconductor

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

alignReads Man page
alignReadsChunk Man page
analyzeVariants Man page
annotateVariants Man page
bamCountUniqueReads Man page
buildConfig Man page
buildGenomicFeaturesFromTxDb Man page
buildShortReadReports Man page
buildTallyParam Man page
buildTP53FastaGenome Man page
buildTP53GenomeTemplate Man page
calculateCoverage Man page
calculateTargetLengths Man page
callVariantsGATK Man page
checkConfig Man page
checkGATKJar Man page
checkPicardJar Man page
computeBamStats Man page
computeCoverage Man page
countFeatures Man page
countGenomicFeatures Man page
countGenomicFeaturesChunk Man page
createTmpDir Man page
detectAdapterContam Man page
detectQualityInFASTQFile Man page
detectRRNA Man page
excludeVariantsByRegions Man page
FastQStreamer.getReads Man page
FastQStreamer.init Man page
FastQStreamer.release Man page
filterByLength Man page
filterQuality Man page
findVariantFile Man page
gatk Man page
generateSingleGeneDERs Man page
getAdapterSeqs Man page
getBams Man page
getChunkDirs Man page
getConfig Man page
getConfig.integer Man page
getConfig.logical Man page
getConfig.numeric Man page
getConfig.vector Man page
getEndNumber Man page
getMemoryUsage Man page
getNumberOfReadsInFASTQFile Man page
getNumericVectorDataFromFile Man page
getObjectFilename Man page
getPackageFile Man page
getRandomAlignCutoff Man page
getRRNAIds Man page
getTabDataFromFile Man page
getTraceback Man page
hashCoverage Man page
hashVariants Man page
hashVector Man page
HTSeqGenie Man page
initDirs Man page
initLog Man page
initLogger Man page
initPipelineFromConfig Man page
initPipelineFromSaveDir Man page
isAboveQualityThresh Man page
isAdapter Man page
isConfig Man page
isFirstFragment Man page
isSparse Man page
listIterator.init Man page
listIterator.next Man page
loadConfig Man page
logdebug Man page
logerror Man page
loginfo Man page
logwarn Man page
makeDir Man page
makeRandomSreads Man page
markDuplicates Man page
markDups Man page
mergeAlignReads Man page
mergeCoverage Man page
mergeLanes Man page
mergePreprocessReads Man page
mergeSummaryAlignment Man page
parseDCF Man page
parseSummaries Man page
picard Man page
plotDF Man page
preprocessReads Man page
preprocessReadsChunk Man page
processChunks Man page
readInputFiles Man page
readRNASeqEnds Man page
realignIndels Man page
realignIndelsGATK Man page
relativeBarPlot Man page
removeChunkDir Man page
resource Man page
rpkm Man page
runAlignment Man page
runPipeline Man page
runPipelineConfig Man page
runPreprocessReads Man page
safeExecute Man page
safeGetObject Man page
safeUnlink Man page
safe.yield Man page
saveWithID Man page
sclapply Man page
setChunkDir Man page
setUpDirs Man page
setupTestFramework Man page
statCountFeatures Man page
TP53GenomicFeatures Man page
traceMem Man page
trimReads Man page
trimTailsByQuality Man page
truncateReads Man page
tryKeepTraceback Man page
updateConfig Man page
vcfStat Man page
wrap.callVariants Man page
writeAudit Man page
writeConfig Man page
writeFastQFiles Man page
writeFeatureCountsHTML Man page
writeGenomicFeaturesReport Man page
writePreprocessAlignHTML Man page
writePreprocessAlignReport Man page
writeSummary Man page
writeVCF Man page

Files

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

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