Man pages for tanaylab/reputils
Utility functions for working with transposable elements

addSeqAdd sequence column to GRanges object
checkFormatCheck format of TE annotation file
chunkChunk vector
chunkFilesSplit files into equally sized chunks
curateGenesCuration of gene intervals
curateTEsCuration of TE intervals
deduplicateBAMDeduplicates SAM/BAM files using umi-tools
downsampDownsamples data in long data.frame format
getTSSExtract TSS coordinates from Gencode
grapes-fin-grapesFast matching
importBAMParallel import of BAM files
importDFAMImport TE intervals in DFAM format
importRMSKImport TE intervals in Repeatmasker format
importTEsImport TE intervals in common file formats
importUCSCImport TE intervals in UCSC table browser format
longToSparseTransforms long data.frame into sparse matrix
mafftCompute multiple sequence alignment
msaToLongTransforms multiple sequence alignment into long data.frame
mutateReadsRandomly mutate read sequences
mutateSeqsRandomly mutate DNA sequences
ReputilsReputils
splitBAMSplits BAM file per chromosome
varmeanComputes variance over mean
writeMM2Export (sparse) matrix in matrix market format Much faster...
tanaylab/reputils documentation built on Nov. 5, 2019, 9:58 a.m.