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

Files in this package

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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