Modify a set of reference sequences using a set of variants
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Documentation for package ‘transmogR’ version 1.4.0
Help Pages
| cleanVariants | Check provided variants for compatibility |
| cleanVariants-method | Check provided variants for compatibility |
| cleanVariants-methods | Check provided variants for compatibility |
| digestSalmon | Parse the output from salmon |
| genomogrify | Mogrify a genome using a set of variants |
| genomogrify-method | Mogrify a genome using a set of variants |
| genomogrify-methods | Mogrify a genome using a set of variants |
| indelcator | Substitute InDels into one or more sequences |
| indelcator-method | Substitute InDels into one or more sequences |
| overlapsByVar | Count overlaps by variant type |
| overlapsByVar-method | Count overlaps by variant type |
| overlapsByVar-methods | Count overlaps by variant type |
| owl | OverWrite Letters in an XStringSet |
| owl-method | OverWrite Letters in an XStringSet |
| parY | Get the PAR-Y Regions From a Seqinfo Object |
| parY-method | Get the PAR-Y Regions From a Seqinfo Object |
| parY-methods | Get the PAR-Y Regions From a Seqinfo Object |
| shiftByVar | Calculate new exon co-ordinates |
| sjFromExons | Obtain Splice-Junctions from Exons and Transcripts |
| transmogrify | Mogrify a transcriptome using a set of variants |
| transmogrify-method | Mogrify a transcriptome using a set of variants |
| transmogrify-methods | Mogrify a transcriptome using a set of variants |
| upsetVarByCol | Show Variants by Impacted Columns |
| varTags | Create a set of tags indicating overlap status with variants |
| varTypes | Identify SNVs, Insertions and Deletions |