HTSeqGenie: A NGS analysis pipeline.

Libraries to perform NGS analysis.

Author
Gregoire Pau, Jens Reeder
Date of publication
None
Maintainer
Jens Reeder <reeder.jens@gene.com>
License
Artistic-2.0
Version
4.4.0

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