addSeq | Add sequence column to GRanges object |
checkFormat | Check format of TE annotation file |
chunk | Chunk vector |
chunkFiles | Split files into equally sized chunks |
curateGenes | Curation of gene intervals |
curateTEs | Curation of TE intervals |
deduplicateBAM | Deduplicates SAM/BAM files using umi-tools |
downsamp | Downsamples data in long data.frame format |
getTSS | Extract TSS coordinates from Gencode |
grapes-fin-grapes | Fast matching |
importBAM | Parallel import of BAM files |
importDFAM | Import TE intervals in DFAM format |
importRMSK | Import TE intervals in Repeatmasker format |
importTEs | Import TE intervals in common file formats |
importUCSC | Import TE intervals in UCSC table browser format |
longToSparse | Transforms long data.frame into sparse matrix |
mafft | Compute multiple sequence alignment |
msaToLong | Transforms multiple sequence alignment into long data.frame |
mutateReads | Randomly mutate read sequences |
mutateSeqs | Randomly mutate DNA sequences |
Reputils | Reputils |
splitBAM | Splits BAM file per chromosome |
varmean | Computes variance over mean |
writeMM2 | Export (sparse) matrix in matrix market format Much faster... |
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