Package: h5vc 2.41.0

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

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h5vc.pdf |h5vc.html✨
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-2.41.0(bioc 3.21)h5vc-2.40.0(bioc 3.20)

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

curl bzip2 xz-utils zlib cpp

3.00 score 2 scripts 36 exports 86 dependencies

Last updated 3 months agofrom:2b58d0934f. Checks:4 ERROR, 5 WARNING. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	FAIL	Jan 16 2025
R-4.5-win-x86_64	WARNING	Jan 16 2025
R-4.5-linux-x86_64	WARNING	Jan 16 2025
R-4.4-win-x86_64	WARNING	Jan 16 2025
R-4.4-mac-x86_64	WARNING	Jan 16 2025
R-4.4-mac-aarch64	WARNING	Jan 16 2025
R-4.3-win-x86_64	ERROR	Jan 16 2025
R-4.3-mac-x86_64	ERROR	Jan 16 2025
R-4.3-mac-aarch64	ERROR	Jan 16 2025

Exports:applyTallies bases batchTallies batchTallyParam binGenome binnedAFs binnedCoverage callVariantsPaired callVariantsPairedFisher callVariantsSingle collectTallies defineBlocks encodeDNAString formatGenomicPosition geom_h5vc getChromSize getSampleData h5dapply h5readBlock mergeTallies mergeTallyFiles mismatchPlot mutationSpectrum plotMutationSpectrum prepareForHDF5 prepareTallyFile rerunBatchTallies resizeCohort setSampleData tallyBAM tallyRanges tallyRangesBatch tallyRangesToFile vcConfParams writeReference writeToTallyFile

Dependencies:abind askpass backports base64enc BatchJobs BBmisc BH BiocGenerics BiocParallel Biostrings bit bit64 bitops blob brew cachem checkmate cli codetools colorspace cpp11 crayon curl data.table DBI digest fansi farver fastmap formatR futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggplot2 glue gridExtra gtable h5vcData httr IRanges isoband jsonlite labeling lambda.r lattice lifecycle magrittr MASS Matrix memoise mgcv mime munsell nlme openssl pillar pkgconfig plogr plyr R6 RColorBrewer Rcpp reshape rhdf5 rhdf5filters Rhdf5lib Rhtslib rlang Rsamtools RSQLite S4Vectors scales sendmailR snow stringi sys tibble UCSC.utils utf8 vctrs viridisLite withr XVector

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Managing alignment tallies using a hdf5 backend	h5vc-package h5vc
Preparing the results of tallyBAM for writing to an HDF5 tally file	applyTallies
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 genome	binnedAFs
Variant calling	callDeletionsPaired callVariantsPaired vcConfParams
Paired variant calling using fisher tests	callVariantsPairedFisher
Single sample variant calling	callVariantsSingle
Coverage analysis	binnedCoverage
geom_h5vc	geom_h5vc
Reading and writing sample data from / to a tally file	getSampleData setSampleData
h5dapply	h5dapply h5dapply,GRanges-method h5dapply,IRanges-method h5dapply,numeric-method
h5readBlock	h5readBlock
helper functions	defineBlocks encodeDNAString formatGenomicPosition getChromSize
Merging the prepared results from multiple bam file tallies into one block that can be written to the HDF5 tally file	mergeTallies
Merging multiple tally files into one	mergeTallyFiles
mismatchPlot	mismatchPlot
Mutation spectrum analyses	bases mutationSpectrum variantCalls
Plotting a mutation spectrum	plotMutationSpectrum
Preparing the results of tallyBAM for writing to an HDF5 tally file	prepareForHDF5
prepareTallyFile	prepareTallyFile resizeCohort
tallyBAM	tallyBAM
Tallying function with a 'GRanges' interface.	tallyRanges tallyRangesBatch tallyRangesToFile
Filling the Reference dataset in a tally file from a DNAString	writeReference
Writing data to an HDF5 tally file	writeToTallyFile