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HTSeqGenie (version 3.18.0)

A NGS analysis pipeline.

Description

Libraries to perform NGS analysis.

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Version

Version

3.18.0

License

Artistic-2.0

Maintainer

Jens Reeder

Last Published

February 15th, 2017

Functions in HTSeqGenie (3.18.0)

buildShortReadReports

Build a ShortRead report

buildTallyParam

Build tally parameters

consolidateByRead

Consolidate Paired-End Alignments by Read Names

Count RNA-Seq Pipeline Genomic Features

excludeVariantsByRegions

Filter variants by regions

FastQStreamer.getReads

Get FastQ reads from the FastQ streamer

Filter reads by length

Filter reads by quality

getConfig.numeric

Check if a config parameter is a numeric

getConfig.vector

Return values of a config variable as vector

Hashing function for vector

Package overview

isFirstFragment

Does a SAM flag indicate the first fragment

makeRandomSreads

Generate a couple if random ShortReadQ, intended for testing

mergeSummaryAlignment

Merge summary alignments

mergePreprocessReads

Merge after preprocessReads

Read Paired End Bam Files

Read FastQ input files

Create output directory and subdirectories for sequencing pipeline analysis outputs

Set the base directory for the chunks

Trim/truncate a set of reads

trimTailsByQuality

Trim off low quality tail

analyzeVariants

Calculate and process Variants

bamCountUniqueReads

Uniquely count number of reads in bam file

calculateCoverage

Calculate read coverage

calculateTargetLengths

Plot target length for paired end

detectQualityInFASTQFile

Detect quality protocol from a FASTQ file

Detect rRNA Contamination in Reads

Get bam files of a pipeline run

Hashing function for variants

Hashing function for coverage

Read list of Illumina adapter seqs from package data

initPipelineFromSaveDir

Init Pipeline environment from previous run

Log info using the logging package

isAboveQualityThresh

Check for high quality reads

Read and parse a configuration file

Log info using the logging package

parse summary files from save dirs

getNumberOfReadsInFASTQFile

Count reads in Fastq file

computeBamStats

Compute record statistics from a bam file

computeCoverage

Compute the coverage vector given a bamfile

Set up NGS output dir

getNumericVectorDataFromFile

Load data as numerical values

Initialize the logger

Detect adapter contamination

Test the presence of the parameter in the current config

Merge coverage files

Merge input lanes

Make continuous plots of distribution function

Run the NGS analysis pipeline

preprocessReads

Pipeline preprocessing

Runs the read alignment step of the pipeline

Write a config file

writeFastQFiles

Write reads to file

Reload package source code

Execute function in try catch with trace function

Overloaded yield(...) method catching truncated exceptions for FastqStreamer

Update the existing config

Compute stats on a VCF file

writeFeatureCountsHTML

writeFeatureCountsHTML

writeGenomicFeaturesReport

Generate pipeline report

Align reads against genome

alignReadsChunk

Genomic alignment

countGenomicFeaturesChunk

Count reads by genomic Feature

countGenomicFeatures

Count overlaps with genomic features

getObjectFilename

Get a filename given a directory and the object name

findVariantFile

Get a vcf filename given a HTSeqGenie directory

Get a package file

getTabDataFromFile

Load tabular data from the NGS pipeline result directory

Get traceback from tryKeepTraceback()

listIterator.init

Create a iterator on a list

listIterator.next

Get reads from the listIterator

mergeAlignReads

Merge after alignReads

realignIndelsGATK

Realign indels via GATK

Save an R object

Scheduled parallel processing

setupTestFramework

setup test framework

statCountFeatures

Compute statistics on count features

writePreprocessAlignHTML

writePreprocessAlignHTML

writePreprocessAlignReport

Generate Pipeline Report

buildTP53FastaGenome

buildTP53FastaGenome

Check for the GATK jar file

buildTP53GenomeTemplate

buildTP53GenomeTemplate

Create a random directory with prefix in R temp dir

detectAdapterContam

Detect sequencing adapter contamination

Get a configuration parameter

getConfig.logical

Check if a config parameter has a logical value

Get Read End Number

initPipelineFromConfig

Init pipeline environment

Returns memory usage in bytes

buildGenomicFeaturesFromTxDb

Build genomic features from a TxDb object

callVariantsGATK

Variant calling via GATK

Build a configuration file based on a list of parameters

Check configuration

Load configuration file

Log debug using the logging package

Make a directory after performing an existence check

Log warning using the logging package

Process chunk in the pipeline framework

preprocessReadsChunk

Preprocess a chunk

FastQStreamer.init

Open a streaming connection to a FastQ file

Get the list of chunk directories

getConfig.integer

Check if a config parameter is an integer

getRandomAlignCutoff

Estimate an adapter alignment cutoff score

FastQStreamer.release

Close the FastQStreamer

Detect reads that look like rRNA

plotDepthByStrand

Plot Read Depth of Variants by Strand

runPipelineConfig

Run the NGS analysis pipeline

runPreprocessReads

Run the preprocesing steps of the pipeline

Trim/truncate a set of reads

tryKeepTraceback

Wrapper around try-catch

relativeBarPlot

Make relative bar plots

Remove chunk directories

Safely load a R data file

Show memory usage

TP53GenomicFeatures

Demo genomic features around the TP53 gene

Write HTML summary

wrap.callVariants

Variant calling

Write Session information