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HTSeqGenie (version 4.2.0)
A NGS analysis pipeline.
Description
Libraries to perform NGS analysis.
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Version
4.2.0
3.20.0
3.18.0
3.16.1
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Version
4.2.0
License
Artistic-2.0
Maintainer
Jens Reeder
Last Published
January 1st, 1970
Functions in HTSeqGenie (4.2.0)
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buildShortReadReports
Build a ShortRead report
buildTallyParam
Build tally parameters
calculateCoverage
Calculate read coverage
detectRRNA
Detect rRNA Contamination in Reads
excludeVariantsByRegions
Filter variants by regions
getObjectFilename
Get a filename given a directory and the object name
calculateTargetLengths
Plot target length for paired end
getPackageFile
Get a package file
hashVector
Hashing function for vector
HTSeqGenie
Package overview
initPipelineFromSaveDir
Init Pipeline environment from previous run
isAboveQualityThresh
Check for high quality reads
mergeLanes
Merge input lanes
mergeCoverage
Merge coverage files
mergePreprocessReads
Merge after preprocessReads
mergeSummaryAlignment
Merge summary alignments
runAlignment
Runs the read alignment step of the pipeline
rpkm
Calculate RPKM
runPreprocessReads
Run the preprocesing steps of the pipeline
trimTailsByQuality
Trim off low quality tail
safe.yield
Overloaded yield(...) method catching truncated exceptions for FastqStreamer
truncateReads
Trim/truncate a set of reads
writeAudit
Write Session information
writeConfig
Write a config file
buildGenomicFeaturesFromTxDb
Build genomic features from a TxDb object
computeBamStats
Compute record statistics from a bam file
buildConfig
Build a configuration file based on a list of parameters
computeCoverage
Compute the coverage vector given a bamfile
getAdapterSeqs
Read list of Illumina adapter seqs from package data
getBams
Get bam files of a pipeline run
FastQStreamer.getReads
Get FastQ reads from the FastQ streamer
FastQStreamer.init
Open a streaming connection to a FastQ file
getConfig.numeric
Check if a config parameter is a numeric
getConfig.vector
Return values of a config variable as vector
buildTP53FastaGenome
buildTP53FastaGenome
getChunkDirs
Get the list of chunk directories
buildTP53GenomeTemplate
buildTP53GenomeTemplate
getConfig.integer
Check if a config parameter is an integer
getRRNAIds
Detect reads that look like rRNA
getRandomAlignCutoff
Estimate an adapter alignment cutoff score
getTabDataFromFile
Load tabular data from the NGS pipeline result directory
initDirs
Set up NGS output dir
getTraceback
Get traceback from tryKeepTraceback()
preprocessReads
Pipeline preprocessing
preprocessReadsChunk
Preprocess a chunk
realignIndelsGATK
Realign indels via GATK
relativeBarPlot
Make relative bar plots
initLog
Initialize the logger
listIterator.init
Create a iterator on a list
listIterator.next
Get reads from the listIterator
logwarn
Log warning using the logging package
makeDir
Make a directory after performing an existence check
parseDCF
Read and parse a configuration file
safeExecute
Execute function in try catch with trace function
safeGetObject
Safely load a R data file
traceMem
Show memory usage
trimReads
Trim/truncate a set of reads
writeVCF
writeVCF
parseSummaries
parse summary files from save dirs
runPipeline
Run the NGS analysis pipeline
setChunkDir
Set the base directory for the chunks
sclapply
Scheduled parallel processing
writeFastQFiles
Write reads to file
runPipelineConfig
Run the NGS analysis pipeline
alignReadsChunk
Genomic alignment
alignReads
Align reads against genome
countGenomicFeatures
Count overlaps with genomic features
countFeatures
Count RNA-Seq Pipeline Genomic Features
createTmpDir
Create a random directory with prefix in R temp dir
countGenomicFeaturesChunk
Count reads by genomic Feature
getNumberOfReadsInFASTQFile
Count reads in Fastq file
getConfig
Get a configuration parameter
getNumericVectorDataFromFile
Load data as numerical values
getConfig.logical
Check if a config parameter has a logical value
initPipelineFromConfig
Init pipeline environment
initLogger
Init loggers
isAdapter
Detect adapter contamination
isConfig
Test the presence of the parameter in the current config
makeRandomSreads
Generate a couple if random ShortReadQ, intended for testing
markDuplicates
markDuplicates
readInputFiles
Read FastQ input files
processChunks
Process chunk in the pipeline framework
safeUnlink
safeUnlink
saveWithID
Save an R object
TP53GenomicFeatures
Demo genomic features around the TP53 gene
statCountFeatures
Compute statistics on count features
writePreprocessAlignReport
Generate Pipeline Report
writeSummary
Write HTML summary
writeFeatureCountsHTML
writeFeatureCountsHTML
analyzeVariants
Calculate and process Variants
bamCountUniqueReads
Uniquely count number of reads in bam file
checkGATKJar
Check for the GATK jar file
detectAdapterContam
Detect sequencing adapter contamination
detectQualityInFASTQFile
Detect quality protocol from a FASTQ file
checkPicardJar
checkPicardJar
gatk
gatk
generateSingleGeneDERs
generateSingleGeneDERs
hashCoverage
Hashing function for coverage
hashVariants
Hashing function for variants
isFirstFragment
Does a SAM flag indicate the first fragment
isSparse
isSparse
logerror
Log info using the logging package
loginfo
Log info using the logging package
picard
picard
plotDF
Make continuous plots of distribution function
removeChunkDir
Remove chunk directories
vcfStat
Compute stats on a VCF file
resource
Reload package source code
wrap.callVariants
Variant calling
writeGenomicFeaturesReport
Generate pipeline report
writePreprocessAlignHTML
writePreprocessAlignHTML
callVariantsGATK
Variant calling via GATK
checkConfig
Check configuration
filterByLength
Filter reads by length
filterQuality
Filter reads by quality
FastQStreamer.release
Close the FastQStreamer
findVariantFile
Get a vcf filename given a HTSeqGenie directory
getMemoryUsage
Returns memory usage in bytes
getEndNumber
Get Read End Number
logdebug
Log debug using the logging package
loadConfig
Load configuration file
markDups
markDups
mergeAlignReads
Merge after alignReads
readRNASeqEnds
Read single/paired End Bam Files
realignIndels
realignIndels
setUpDirs
Create output directory and subdirectories for sequencing pipeline analysis outputs
setupTestFramework
setup test framework
tryKeepTraceback
Wrapper around try-catch
updateConfig
Update the existing config