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HTSeqGenie (version 3.20.0)

A NGS analysis pipeline.

Description

Libraries to perform NGS analysis.

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Version

Version

3.20.0

License

Artistic-2.0

Maintainer

Jens Reeder

Last Published

February 15th, 2017

Functions in HTSeqGenie (3.20.0)

buildTP53FastaGenome

buildTP53FastaGenome

Align reads against genome

consolidateByRead

Consolidate Paired-End Alignments by Read Names

alignReadsChunk

Genomic alignment

excludeVariantsByRegions

Filter variants by regions

Count RNA-Seq Pipeline Genomic Features

FastQStreamer.getReads

Get FastQ reads from the FastQ streamer

Read list of Illumina adapter seqs from package data

Get bam files of a pipeline run

computeBamStats

Compute record statistics from a bam file

computeCoverage

Compute the coverage vector given a bamfile

findVariantFile

Get a vcf filename given a HTSeqGenie directory

getNumberOfReadsInFASTQFile

Count reads in Fastq file

getNumericVectorDataFromFile

Load data as numerical values

initPipelineFromConfig

Init pipeline environment

buildTP53GenomeTemplate

buildTP53GenomeTemplate

listIterator.init

Create a iterator on a list

countGenomicFeatures

Count overlaps with genomic features

countGenomicFeaturesChunk

Count reads by genomic Feature

Get the list of chunk directories

Log warning using the logging package

getConfig.integer

Check if a config parameter is an integer

listIterator.next

Get reads from the listIterator

Make a directory after performing an existence check

Make continuous plots of distribution function

preprocessReads

Pipeline preprocessing

Runs the read alignment step of the pipeline

Run the NGS analysis pipeline

Create output directory and subdirectories for sequencing pipeline analysis outputs

Set the base directory for the chunks

writeGenomicFeaturesReport

Generate pipeline report

writeFeatureCountsHTML

writeFeatureCountsHTML

trimTailsByQuality

Trim off low quality tail

Trim/truncate a set of reads

getObjectFilename

Get a filename given a directory and the object name

Initialize the logger

Set up NGS output dir

Get a package file

isAboveQualityThresh

Check for high quality reads

initPipelineFromSaveDir

Init Pipeline environment from previous run

getTabDataFromFile

Load tabular data from the NGS pipeline result directory

Get traceback from tryKeepTraceback()

isFirstFragment

Does a SAM flag indicate the first fragment

Merge coverage files

Merge input lanes

Reload package source code

Safely load a R data file

Trim/truncate a set of reads

tryKeepTraceback

Wrapper around try-catch

Write HTML summary

makeRandomSreads

Generate a couple if random ShortReadQ, intended for testing

parse summary files from save dirs

Read and parse a configuration file

Read FastQ input files

wrap.callVariants

Variant calling

Write Session information

Read Paired End Bam Files

buildShortReadReports

Build a ShortRead report

buildTallyParam

Build tally parameters

calculateCoverage

Calculate read coverage

calculateTargetLengths

Plot target length for paired end

FastQStreamer.init

Open a streaming connection to a FastQ file

FastQStreamer.release

Close the FastQStreamer

Get Read End Number

Returns memory usage in bytes

Package overview

Hashing function for vector

Log debug using the logging package

mergeAlignReads

Merge after alignReads

Load configuration file

preprocessReadsChunk

Preprocess a chunk

Process chunk in the pipeline framework

realignIndelsGATK

Realign indels via GATK

runPipelineConfig

Run the NGS analysis pipeline

runPreprocessReads

Run the preprocesing steps of the pipeline

Update the existing config

Compute stats on a VCF file

writePreprocessAlignHTML

writePreprocessAlignHTML

writePreprocessAlignReport

Generate Pipeline Report

analyzeVariants

Calculate and process Variants

Check for the GATK jar file

bamCountUniqueReads

Uniquely count number of reads in bam file

Create a random directory with prefix in R temp dir

Filter reads by length

detectAdapterContam

Detect sequencing adapter contamination

Filter reads by quality

getRandomAlignCutoff

Estimate an adapter alignment cutoff score

Detect reads that look like rRNA

Hashing function for coverage

Hashing function for variants

Detect adapter contamination

Test the presence of the parameter in the current config

Log info using the logging package

Log info using the logging package

relativeBarPlot

Make relative bar plots

plotDepthByStrand

Plot Read Depth of Variants by Strand

Remove chunk directories

Save an R object

Scheduled parallel processing

setupTestFramework

setup test framework

statCountFeatures

Compute statistics on count features

Write a config file

writeFastQFiles

Write reads to file

Build a configuration file based on a list of parameters

buildGenomicFeaturesFromTxDb

Build genomic features from a TxDb object

callVariantsGATK

Variant calling via GATK

Check configuration

getConfig.logical

Check if a config parameter has a logical value

Get a configuration parameter

Detect rRNA Contamination in Reads

detectQualityInFASTQFile

Detect quality protocol from a FASTQ file

getConfig.numeric

Check if a config parameter is a numeric

getConfig.vector

Return values of a config variable as vector

mergePreprocessReads

Merge after preprocessReads

mergeSummaryAlignment

Merge summary alignments

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

Execute function in try catch with trace function

TP53GenomicFeatures

Demo genomic features around the TP53 gene

Show memory usage