varity 0.11.0
Released under the Apache License, Version 2.0
Variant translation library for Clojure.
Installation
To install, add the following dependency to your project or build file:
[varity "0.11.0"]
Namespaces
varity.chain
Functions to read, index, and search the chain format. See https://genome.ucsc.edu/goldenPath/help/chain.html for the detail chain format specifications.
Public variables and functions:
varity.fusion
NOTE: This algorithm was initially developed at Cancer Precision Medicine Center, Japanese Foundation for Cancer Research and Xcoo re-implemented it with Clojure.
Public variables and functions:
varity.lift
Functions to convert a genome coordinate between assemblies.
Public variables and functions:
varity.ref-gene
Handles refGene.txt(.gz) and ncbiRefSeq.txt(.gz) content.
Public variables and functions:
- cds->genomic-pos
- cds-coord
- cds-coord->genomic-pos
- cds-pos
- cds-region
- cds-seq
- exon-ranges->intron-ranges
- exon-seq
- find-ens-g-id
- find-ens-t-id
- in-any-exon?
- in-cds?
- in-exon?
- index
- load-gencode
- load-gff3
- load-gtf
- load-ref-genes
- load-ref-seqs
- max-tx-margin
- read-coding-sequence
- read-exon-sequence
- read-transcript-sequence
- ref-genes
- rna-accession?
- seek-gene-region
- tx-region
varity.vcf-to-hgvs
Functions to convert a VCF-style variant into HGVS.
Public variables and functions: