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.

AuthorPaul Theodor Pyl
Date of publicationNone
MaintainerPaul Theodor Pyl <paul.theodor.pyl@gmail.com>
LicenseGPL (>= 3)
Version2.8.0

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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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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