h5vc: Managing alignment tallies using a hdf5 backend

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

Author
Paul Theodor Pyl
Date of publication
None
Maintainer
Paul Theodor Pyl <paul.theodor.pyl@gmail.com>
License
GPL (>= 3)
Version
2.8.0

View on Bioconductor

Man pages

applyTallies
Preparing the results of tallyBAM for writing to an HDF5...
batchTallies
Tallying bam files in parallel using 'BatchJobs' on high...
binGenome
Function for binning a genome.
binnedAFs
Estimate allelic frequency distributions in bins along the...
callVariants
Variant calling
callVariantsFisher
Paired variant calling using fisher tests
callVariantsSingle
Single sample variant calling
coverage
Coverage analysis
geom_h5vc
geom_h5vc
getSampleData
Reading and writing sample data from / to a tally file
h5dapply
h5dapply
h5readBlock
h5readBlock
h5vc-package
Managing alignment tallies using a hdf5 backend
helpers
helper functions
mergeTallies
Merging the prepared results from multiple bam file tallies...
mergeTallyFiles
Merging multiple tally files into one
mismatchPlot
mismatchPlot
mutationSpectrum
Mutation spectrum analyses
plotMutationSpectrum
Plotting a mutation spectrum
prepareForHDF5
Preparing the results of tallyBAM for writing to an HDF5...
prepareTallyFile
prepareTallyFile
tallyBAM
tallyBAM
tallyRanges
Tallying function with a 'GRanges' interface.
writeReference
Filling the Reference dataset in a tally file from a...
writeToTallyFile
Writing data to an HDF5 tally file

Files in this package

h5vc/DESCRIPTION
h5vc/NAMESPACE
h5vc/R
h5vc/R/applyTallies.R
h5vc/R/call.variants.R
h5vc/R/call.variants.fisher.R
h5vc/R/call.variants.single.R
h5vc/R/coverage.R
h5vc/R/get.sample.metadata.R
h5vc/R/getChromSize.R
h5vc/R/h5apply.R
h5vc/R/h5readBlock.R
h5vc/R/helpers.R
h5vc/R/mergeTallyFiles.r
h5vc/R/mutation.spectrum.R
h5vc/R/plotting.R
h5vc/R/prepareForHDF5.R
h5vc/R/prepareTallyFile.R
h5vc/R/set.sample.metadata.R
h5vc/R/tally.in.ranges.r
h5vc/R/tallyBAM.R
h5vc/R/write.reference.R
h5vc/build
h5vc/build/vignette.rds
h5vc/data
h5vc/data/bases.rda
h5vc/inst
h5vc/inst/CITATION
h5vc/inst/doc
h5vc/inst/doc/bioc_adapted.css
h5vc/inst/doc/h5vc.simple.genome.browser.R
h5vc/inst/doc/h5vc.simple.genome.browser.Rmd
h5vc/inst/doc/h5vc.simple.genome.browser.html
h5vc/inst/doc/h5vc.tour.R
h5vc/inst/doc/h5vc.tour.Rmd
h5vc/inst/doc/h5vc.tour.html
h5vc/inst/extdata
h5vc/inst/unitTests
h5vc/inst/unitTests/expected.counts.txt
h5vc/inst/unitTests/insert.bam
h5vc/inst/unitTests/insert.bam.bai
h5vc/inst/unitTests/test_tallyBAM.R
h5vc/man
h5vc/man/applyTallies.Rd
h5vc/man/batchTallies.Rd
h5vc/man/binGenome.Rd
h5vc/man/binnedAFs.Rd
h5vc/man/callVariants.Rd
h5vc/man/callVariantsFisher.Rd
h5vc/man/callVariantsSingle.Rd
h5vc/man/coverage.Rd
h5vc/man/geom_h5vc.Rd
h5vc/man/getSampleData.Rd
h5vc/man/h5dapply.Rd
h5vc/man/h5readBlock.Rd
h5vc/man/h5vc-package.Rd
h5vc/man/helpers.Rd
h5vc/man/mergeTallies.Rd
h5vc/man/mergeTallyFiles.Rd
h5vc/man/mismatchPlot.Rd
h5vc/man/mutationSpectrum.Rd
h5vc/man/plotMutationSpectrum.Rd
h5vc/man/prepareForHDF5.Rd
h5vc/man/prepareTallyFile.Rd
h5vc/man/tallyBAM.Rd
h5vc/man/tallyRanges.Rd
h5vc/man/writeReference.Rd
h5vc/man/writeToTallyFile.Rd
h5vc/src
h5vc/src/Makevars
h5vc/src/Makevars.common
h5vc/src/Makevars.win
h5vc/src/tallyBAM.cpp
h5vc/tests
h5vc/tests/runTests.R
h5vc/vignettes
h5vc/vignettes/bioc_adapted.css
h5vc/vignettes/example.plot.1.png
h5vc/vignettes/example.plot.2.png
h5vc/vignettes/example.plot.3.png
h5vc/vignettes/example.plot.4.png
h5vc/vignettes/example.plot.5.png
h5vc/vignettes/h5vc.simple.genome.browser.Rmd
h5vc/vignettes/h5vc.tour.Rmd
h5vc/vignettes/mutation.spectrum.example.png
h5vc/vignettes/tally.file.layout.png