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)
Version2.8.1

View on Bioconductor

Functions

applyTallies Man page
bases Man page
batchTallies Man page
batchTallyParam Man page
binGenome Man page
binnedAFs Man page
binnedCoverage Man page
callDeletionsPaired Man page
callVariantsPaired Man page
callVariantsPairedFisher Man page
callVariantsSingle Man page
collectTallies Man page
defineBlocks Man page
encodeDNAString Man page
formatGenomicPosition Man page
geom_h5vc Man page
getChromSize Man page
getSampleData Man page
h5dapply Man page
h5dapply,GRanges-method Man page
h5dapply,IRanges-method Man page
h5dapply,numeric-method Man page
h5readBlock Man page
h5vc Man page
h5vc-package Man page
mergeTallies Man page
mergeTallyFiles Man page
mismatchPlot Man page
mutationSpectrum Man page
plotMutationSpectrum Man page
prepareForHDF5 Man page
prepareTallyFile Man page
rerunBatchTallies Man page
resizeCohort Man page
setSampleData Man page
tallyBAM Man page
tallyRanges Man page
tallyRangesBatch Man page
tallyRangesToFile Man page
variantCalls Man page
vcConfParams Man page
writeReference Man page
writeToTallyFile Man page

Files

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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All documentation is copyright its authors; we didn't write any of that.