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HTSeqGenie (version 4.2.0)

A NGS analysis pipeline.

Description

Libraries to perform NGS analysis.

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Version

Version

4.2.0

License

Artistic-2.0

Maintainer

Jens Reeder

Last Published

February 15th, 2017

Functions in HTSeqGenie (4.2.0)

buildShortReadReports

Build a ShortRead report

buildTallyParam

Build tally parameters

calculateCoverage

Calculate read coverage

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

Get a package file

Hashing function for vector

Package overview

initPipelineFromSaveDir

Init Pipeline environment from previous run

isAboveQualityThresh

Check for high quality reads

Merge input lanes

Merge coverage files

mergePreprocessReads

Merge after preprocessReads

mergeSummaryAlignment

Merge summary alignments

Runs the read alignment step of the pipeline

runPreprocessReads

Run the preprocesing steps of the pipeline

trimTailsByQuality

Trim off low quality tail

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

Trim/truncate a set of reads

Write Session information

Write a config file

buildGenomicFeaturesFromTxDb

Build genomic features from a TxDb object

computeBamStats

Compute record statistics from a bam file

Build a configuration file based on a list of parameters

computeCoverage

Compute the coverage vector given a bamfile

Read list of Illumina adapter seqs from package data

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

Get the list of chunk directories

buildTP53GenomeTemplate

buildTP53GenomeTemplate

getConfig.integer

Check if a config parameter is an integer

Detect reads that look like rRNA

getRandomAlignCutoff

Estimate an adapter alignment cutoff score

getTabDataFromFile

Load tabular data from the NGS pipeline result directory

Set up NGS output dir

Get traceback from tryKeepTraceback()

preprocessReads

Pipeline preprocessing

preprocessReadsChunk

Preprocess a chunk

realignIndelsGATK

Realign indels via GATK

relativeBarPlot

Make relative bar plots

Initialize the logger

listIterator.init

Create a iterator on a list

listIterator.next

Get reads from the listIterator

Log warning using the logging package

Make a directory after performing an existence check

Read and parse a configuration file

Execute function in try catch with trace function

Safely load a R data file

Show memory usage

Trim/truncate a set of reads

parse summary files from save dirs

Run the NGS analysis pipeline

Set the base directory for the chunks

Scheduled parallel processing

writeFastQFiles

Write reads to file

runPipelineConfig

Run the NGS analysis pipeline

alignReadsChunk

Genomic alignment

Align reads against genome

countGenomicFeatures

Count overlaps with genomic features

Count RNA-Seq Pipeline Genomic Features

Create a random directory with prefix in R temp dir

countGenomicFeaturesChunk

Count reads by genomic Feature

getNumberOfReadsInFASTQFile

Count reads in Fastq file

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

Detect adapter contamination

Test the presence of the parameter in the current config

makeRandomSreads

Generate a couple if random ShortReadQ, intended for testing

Read FastQ input files

Process chunk in the pipeline framework

Save an R object

TP53GenomicFeatures

Demo genomic features around the TP53 gene

statCountFeatures

Compute statistics on count features

writePreprocessAlignReport

Generate Pipeline Report

Write HTML summary

writeFeatureCountsHTML

writeFeatureCountsHTML

analyzeVariants

Calculate and process Variants

bamCountUniqueReads

Uniquely count number of reads in bam file

Check for the GATK jar file

detectAdapterContam

Detect sequencing adapter contamination

detectQualityInFASTQFile

Detect quality protocol from a FASTQ file

generateSingleGeneDERs

generateSingleGeneDERs

Hashing function for coverage

Hashing function for variants

isFirstFragment

Does a SAM flag indicate the first fragment

Log info using the logging package

Log info using the logging package

Make continuous plots of distribution function

Remove chunk directories

Compute stats on a VCF file

Reload package source code

wrap.callVariants

Variant calling

writeGenomicFeaturesReport

Generate pipeline report

writePreprocessAlignHTML

writePreprocessAlignHTML

callVariantsGATK

Variant calling via GATK

Check configuration

Filter reads by length

Filter reads by quality

FastQStreamer.release

Close the FastQStreamer

findVariantFile

Get a vcf filename given a HTSeqGenie directory

Returns memory usage in bytes

Get Read End Number

Log debug using the logging package

Load configuration file

mergeAlignReads

Merge after alignReads

Read single/paired End Bam Files

Create output directory and subdirectories for sequencing pipeline analysis outputs

setupTestFramework

setup test framework

tryKeepTraceback

Wrapper around try-catch

Update the existing config