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 <firstname.lastname@example.org>|
|License||GPL (>= 3)|
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
getSampleData: Reading and writing sample data from / to a tally file
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
mutationSpectrum: Mutation spectrum analyses
plotMutationSpectrum: Plotting a mutation spectrum
prepareForHDF5: Preparing the results of tallyBAM for writing to an HDF5...
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