Package: HTSeqGenie 4.37.0

Jens Reeder

HTSeqGenie: A NGS analysis pipeline.

Libraries to perform NGS analysis.

Authors:Gregoire Pau, Jens Reeder

HTSeqGenie_4.37.0.tar.gz

HTSeqGenie_4.37.0.tgz(r-4.4-any)HTSeqGenie_4.35.0.tgz(r-4.3-any)
HTSeqGenie_4.37.0.tar.gz(r-4.5-noble)HTSeqGenie_4.37.0.tar.gz(r-4.4-noble)
HTSeqGenie_4.37.0.tgz(r-4.4-emscripten)HTSeqGenie_4.37.0.tgz(r-4.3-emscripten)
HTSeqGenie.pdf |HTSeqGenie.html✨
HTSeqGenie/json (API)
NEWS

# Install 'HTSeqGenie' in R:

install.packages('HTSeqGenie', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

On BioConductor:HTSeqGenie-4.37.0(bioc 3.21)HTSeqGenie-4.36.0(bioc 3.20)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

3.48 score 4 scripts 176 downloads 12 mentions 110 exports 86 dependencies

Last updated 20 days agofrom:721d51cdcf. Checks:ERROR: 4. Indexed: yes.

Target	Result	Date
Doc / Vignettes	FAIL	Nov 03 2024
R-4.5-linux	ERROR	Nov 03 2024
R-4.4-mac	ERROR	Nov 03 2024
R-4.3-mac	ERROR	Oct 17 2024

Exports:alignReads analyzeVariants annotateVariants bamCountUniqueReads buildConfig buildGenomicFeaturesFromTxDb buildTP53FastaGenome calculateCoverage calculateTargetLengths checkConfig checkGATKJar checkPicardJar computeBamStats computeCoverage countGenomicFeatures countGenomicFeaturesChunk detectAdapterContam detectQualityInFASTQFile detectRRNA FastQStreamer.getReads FastQStreamer.init FastQStreamer.release filterByLength filterQuality findVariantFile gatk getBams getChunkDirs getConfig getConfig.integer getConfig.logical getConfig.numeric getConfig.vector getEndNumber getMemoryUsage getNumberOfReadsInFASTQFile getNumericVectorDataFromFile getObjectFilename getPackageFile getRRNAIds getTabDataFromFile getTraceback hashCoverage hashVariants hashVector initDirs initLog initLogger initPipelineFromConfig initPipelineFromSaveDir isAboveQualityThresh isAdapter isConfig listIterator.init listIterator.next loadConfig logdebug logerror loginfo logwarn makeDir markDuplicates markDups mergeAlignReads mergeCoverage mergeLanes mergePreprocessReads mergeSummaryAlignment parseDCF parseSummaries plotDF preprocessReads processChunks readInputFiles readRNASeqEnds realignIndels relativeBarPlot removeChunkDir resource rpkm runAlignment runPipeline runPipelineConfig runPreprocessReads safe.yield safeExecute safeGetObject safeUnlink saveWithID sclapply setUpDirs setupTestFramework statCountFeatures TP53GenomicFeatures traceMem trimReads trimTailsByQuality truncateReads tryKeepTraceback updateConfig vcfStat wrap.callVariants writeAudit writeConfig writeFastQFiles writeFeatureCountsHTML writeGenomicFeaturesReport writePreprocessAlignReport writeSummary writeVCF

Dependencies:abind AnnotationDbi askpass BH Biobase BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob BSgenome cachem Cairo chipseq cli codetools cpp11 crayon curl DBI DelayedArray deldir fastmap formatR futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges glue gmapR httr hwriter interp IRanges jpeg jsonlite KEGGREST lambda.r lattice latticeExtra lifecycle MASS Matrix MatrixGenerics matrixStats memoise mime openssl pkgconfig plogr png pwalign R6 RColorBrewer Rcpp RcppEigen RCurl restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors ShortRead snow SparseArray SummarizedExperiment sys UCSC.utils VariantAnnotation VariantTools vctrs XML XVector yaml zlibbioc

Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.

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Readme and manuals

Help Manual

Help page	Topics
Calculate and process Variants	analyzeVariants
Annotate variants via vep	annotateVariants
Build genomic features from a TxDb object	buildGenomicFeaturesFromTxDb
Variant calling via GATK	callVariantsGATK
Check for the GATK jar file	checkGATKJar
Detect rRNA Contamination in Reads	detectRRNA
Filter variants by regions	excludeVariantsByRegions
gatk	gatk
generateSingleGeneDERs	generateSingleGeneDERs
Detect reads that look like rRNA	getRRNAIds
Load tabular data from the NGS pipeline result directory	getTabDataFromFile
Hashing function for coverage	hashCoverage
Hashing function for variants	hashVariants
Hashing function for vector	hashVector
Package overview	HTSeqGenie
isSparse	isSparse
markDuplicates	markDuplicates
markDups	markDups
realignIndels	realignIndels
Realign indels via GATK	realignIndelsGATK
Run the NGS analysis pipeline	runPipeline
Run the NGS analysis pipeline	runPipelineConfig
setup test framework	setupTestFramework
Demo genomic features around the TP53 gene	TP53GenomicFeatures
Compute stats on a VCF file	vcfStat
Variant calling	wrap.callVariants
writeVCF	writeVCF