Package: h5vc 2.47.0

Paul Theodor Pyl

h5vc: Managing alignment tallies using a hdf5 backend

This package contains functions to interact with tally data from NGS experiments that is stored in HDF5 files.

Authors:Paul Theodor Pyl

h5vc_2.47.0.tar.gz
h5vc_2.47.0.zip(r-4.7)h5vc_2.47.0.zip(r-4.6)h5vc_2.47.0.zip(r-4.5)
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manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
h5vc/json (API)

# Install 'h5vc' in R:
install.packages('h5vc', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))
Uses libs:
  • curl– Easy-to-use client-side URL transfer library
  • bzip2– High-quality block-sorting file compressor library
  • xz-utils– XZ-format compression library
  • zlib– Compression library
  • c++– GNU Standard C++ Library v3
Datasets:
  • bases - Mutation spectrum analyses

On BioConductor:h5vc-2.47.0(bioc 3.24)h5vc-2.46.0(bioc 3.23)

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

curlbzip2xz-utilszlibcpp

3.60 score 6 scripts 869 downloads 1 mentions 36 exports 77 dependencies

Last updated from:1dd9f53d27. Checks:1 ERROR, 11 NOTE, 1 OK, 1 FAIL. Indexed: yes.

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Exports:applyTalliesbasesbatchTalliesbatchTallyParambinGenomebinnedAFsbinnedCoveragecallVariantsPairedcallVariantsPairedFishercallVariantsSinglecollectTalliesdefineBlocksencodeDNAStringformatGenomicPositiongeom_h5vcgetChromSizegetSampleDatah5dapplyh5readBlockmergeTalliesmergeTallyFilesmismatchPlotmutationSpectrumplotMutationSpectrumprepareForHDF5prepareTallyFilererunBatchTalliesresizeCohortsetSampleDatatallyBAMtallyRangestallyRangesBatchtallyRangesToFilevcConfParamswriteReferencewriteToTallyFile

Dependencies:abindaskpassbackportsbase64encBatchJobsBBmiscBHBiocGenericsbiocmakeBiocParallelBiostringsbitbit64bitopsblobbrewcachemcheckmateclicodetoolscpp11crayoncurldata.tableDBIdigestdir.expiryfarverfastmapfilelockformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicRangesggplot2gluegridExtragtableh5vcDatahttrIRangesisobandjsonlitelabelinglambda.rlifecyclememoisemimeopensslpkgconfigplyrR6RColorBrewerRcppreshaperhdf5rhdf5filtersRhdf5libRhtslibrlangRsamtoolsRSQLiteS4VectorsS7scalessendmailRSeqinfosnowstringisysUCSC.utilsvctrsviridisLitewithrXVector

h5vc -- Tour
h5vc -- Scalabale nucleotide tallies using HDF5 | Motivation | Nucleotide Tally Definition | A practical example | Ranges interface | Creating tally files | Extracting tallies from the bam files | Checking if everything worked | Mutation Spectrum Analysis | Parallelisation | Using Clusters
Rendered fromh5vc.tour.Rmdusingknitr::rmarkdown

Last update: 2025-01-22
Started: 2014-01-28

Building a minimal genome browser with h5vc and shiny
Prerequisites | The Data | The Shiny App | ui.R | server.R | Including Variant Calls | Calling the variants | Extending the functionality of the genome browser | Changes to the interface | Changes to the server-side computations | Conclusions
Rendered fromh5vc.simple.genome.browser.Rmdusingknitr::rmarkdown

Last update: 2019-02-12
Started: 2013-09-24

Readme and manuals

Help Manual

Help pageTopics
Managing alignment tallies using a hdf5 backendh5vc-package h5vc
Preparing the results of tallyBAM for writing to an HDF5 tally fileapplyTallies
Tallying bam files in parallel using 'BatchJobs' on high performance compute clusters (HPC)batchTallies batchTallyParam collectTallies rerunBatchTallies
Function for binning a genome.binGenome
Estimate allelic frequency distributions in bins along the genomebinnedAFs
Variant callingcallDeletionsPaired callVariantsPaired vcConfParams
Paired variant calling using fisher testscallVariantsPairedFisher
Single sample variant callingcallVariantsSingle
Coverage analysisbinnedCoverage
geom_h5vcgeom_h5vc
Reading and writing sample data from / to a tally filegetSampleData setSampleData
h5dapplyh5dapply h5dapply,GRanges-method h5dapply,IRanges-method h5dapply,numeric-method
h5readBlockh5readBlock
helper functionsdefineBlocks encodeDNAString formatGenomicPosition getChromSize
Merging the prepared results from multiple bam file tallies into one block that can be written to the HDF5 tally filemergeTallies
Merging multiple tally files into onemergeTallyFiles
mismatchPlotmismatchPlot
Mutation spectrum analysesbases mutationSpectrum variantCalls
Plotting a mutation spectrumplotMutationSpectrum
Preparing the results of tallyBAM for writing to an HDF5 tally fileprepareForHDF5
prepareTallyFileprepareTallyFile resizeCohort
tallyBAMtallyBAM
Tallying function with a 'GRanges' interface.tallyRanges tallyRangesBatch tallyRangesToFile
Filling the Reference dataset in a tally file from a DNAStringwriteReference
Writing data to an HDF5 tally filewriteToTallyFile