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