s312569

clj-biosequence

A Clojure library designed to make the manipulation of biological sequence data easier.

bioreader

clj-fasta

Parser for fasta formatted sequences.

clj-gff3

A gff3 parsing library for Clojure.

clj-uniprot

Parser for uniprot sequences in XML format.

clj-blast

Parser for BLAST results.

clj-genbank

A Clojure interface to GenBank

clj-tandem

Parser for X! Tandem XML formatted result files.

clj-translate

DNA and RNA translation library.

run-tandem

vmaths

Some common maths functions for vectors.

biodb

Some utilities for storing biological sequences in SQL databases.

biomarket

clj-interproscan

A Clojure library for running Interproscan and parsing the results.

clj-mzml

A Clojure library for parsing mzML files.

clj-pepxml

A Clojure library for parsing pepxml files.

clj-protease

Some simple utilities for analysing protease cleavage of protein sequences.

clj-reciprocal-blast

Clojure library for running reciprocal blast.

clj-signalp

A Clojure library for running signalP and parsing the results.

clj-text

Wraps Stanford CoreNLP

clj-tmhmm

A Clojure library for running TMHMM and parsing the results

clojure-opennlp

Natural Language Processing in Clojure (opennlp)

core

Clojure wrapper for the Stanford CoreNLP Java library

hierarchical-cluster

jellydb

A website and backend for annotating and displaying integrated transcriptomics and proteomics data.

msproteomicstools

Some hopefully useful tools for mass spectrometry applied to proteomics

protein-report

Protein and peptide reports in csv format from X! Tandem xml result files.

qhshiny

reverse-database

Creates a reversed database for MS/MS searches

uniprot2fasta

Converts a UniProt XML formatted file into a FASTA file.