BioJulia Packages


Software Packages developed and maintained by the BioJulia organisation.

Bio.jl

Bioinformatics and Computational Biology Infrastructure for Julia

BioFmtSpecimens

A collection of bioinformatics file format specimens to test against

IntervalTrees.jl

A data structure for efficient manipulation of sets of intervals

Automa.jl

A julia code generator for regular expressions

BufferedStreams.jl

Fast composable IO streams

BioTutorials

Tutorial Notebooks of BioJulia

Libz.jl

Fast, flexible zlib bindings.

BioSequences.jl

Biological sequences for the julia language

WaveletMatrices.jl

The Wavelet Matrix

FMIndexes.jl

FM-index for full-text search

IndexableBitVectors.jl

Fully indexable dictionaries - access/rank/select operations

BGZFStreams.jl

BGZF Stream

BioSymbols.jl

A small package introducing nucleic and amino acid primitive types

GeneticVariation.jl

Datastructures and algorithms for working with genetic variation

Dalliance.jl

Julia interface to the Dalliance genome browser

BioStructures.jl

A julia package to read, write and manipulate macromolecular structures

SubstitutionModels.jl

Biological Sequence Substitution Models for Julia

Microbiome.jl


Contributing

Documentation, guidelines, and policy on contributing to all BioJulia repositories

BioCore.jl

Core types and interfaces for BioJulia

Phylogenies.jl

The BioJulia package for working with phylogenetic trees and geneologies.

Dat.jl

Types and methods for interacting with Dat from the Julia REPL and programs.

CWL.jl

Utilities for working with the Common Workflow Language (CWL) from Julia

WAHVectors.jl

Compress bit vectors using the Word Aligned Hybrid method.

ReferenceSequences.jl

Data structure for reference sequences

NaturalSelection.jl

A package containing methods for looking at the effects of natural selection

Kmers.jl

In development: Kmer types and methods for julia

GenomicFeatures.jl

Tools for genomic features in Julia.

CountMin.jl

Count-min Sketch implementation for Julia

BioServices.jl

Julia interface to APIs for various bio-related web services

BioAlignments.jl

Sequence alignment tools

PopGen.jl

Population Genetics functions in Julia.

fogsaa

Fast Optimal Global Sequence Alignment Algorithm

FactCheck.jl

Midje-like testing for Julia

BioTools.jl

BioBridgeR.jl

Compatibility between R classes and BioJulia types for bioinformatics