Explore @BioJulia Open Source projects

BioJulia

Stars
1,410
Global Org. Rank 12,167 (Top 4 %)
Registered almost 11 years ago
Most used languages

Julia
88.5 %

Jupyter Notebook
4.9 %

C++
1.6 %

HTML
1.6 %

JavaScript
1.6 %

Roff 1.6 %

Bio.jl

[DEPRECATED] Bioinformatics and Computational Biology Infrastructure for Julia

Julia

257

Automa.jl

A julia code generator for regular expressions

Julia

187

BioSequences.jl

Biological sequences for the julia language

Julia

136

BioStructures.jl

A Julia package to read, write and manipulate macromolecular structures

Julia

GenomeGraphs.jl

A modern genomics framework for julia

Julia

BioAlignments.jl

Sequence alignment tools

Julia

BioMakie.jl

Plotting and interface tools for biology.

Julia

FASTX.jl

Parse and process FASTA and FASTQ formatted files of biological sequences.

Julia

PopGen.jl

Population Genetics in Julia

Julia

IntervalTrees.jl

A data structure for efficient manipulation of sets of intervals

Julia

BioFmtSpecimens

A collection of bioinformatics file format specimens to test against

Roff

GeneticVariation.jl

Datastructures and algorithms for working with genetic variation

Julia

BioTutorials

Tutorial Notebooks of BioJulia

Jupyter Notebook

GenomicFeatures.jl

Tools for genomic features in Julia.

Julia

BioCore.jl

Core types and interfaces for BioJulia packages

Julia

BioSymbols.jl

Nucleic and amino acid primitive types

Julia

Libz.jl

Fast, flexible zlib bindings.

Julia

XAM.jl

Parse and process SAM and BAM formatted files

Julia

FMIndexes.jl

FM-index for full-text search

Julia

BioServices.jl

Julia interface to APIs for various bio-related web services

Julia

MemoryViews.jl

Simple, low-level views into memory in Julia

Julia

SingleCellProjections.jl

Analysis of Single Cell Expression data in Julia

Julia

Kmers.jl

In development: Kmer types and methods for julia

Julia

SubstitutionModels.jl

Biological Sequence Substitution Models for Julia

Julia

GenomicAnnotations.jl

Julia

Contributing

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

BGZFStreams.jl

BGZF Stream

Julia

IndexableBitVectors.jl

Fully indexable dictionaries - access/rank/select operations

Jupyter Notebook

ProteinSecondaryStructures.jl

Wrapper to protein secondary structure calculation packages

Julia

Codecs.jl

Common data encoding algorithms

Julia

ReadDatastores.jl

Datastores for reads, not your papa's FASTQ files.

Julia

KmerAnalysis.jl

K-mer counting algorithms and count-data utilities for the BioJulia framework

Julia

WaveletMatrices.jl

The Wavelet Matrix

Julia

BioGenerics.jl

Generic methods, types and modules for the BioJulia ecosystem.

Julia

GenomeBrowsers.jl

Julia

FormatSpecimens.jl

Biological file format specimens for testing packages, and functions to assist in testing.

Julia

BioJuliaRegistry

The BioJulia package registry

BioFetch.jl

Easily fetch biological sequences from online sources

Julia

SequenceVariation.jl

Biological sequence variation

Julia

TwoBit.jl

Support for working with 2Bit formatted sequence data files

Julia

Phylogenies.jl

The BioJulia package for working with phylogenetic trees and geneologies.

Julia

PopGen.jl_archive

Population Genetics functions in Julia.

Julia

GFF3.jl

Julia

MMTF.jl

A julia package to parse and write MMTF file

Julia

biojulia.github.io

BioJulia's Website

HTML

PopGenCore.jl

Core utilities for PopGen.jl, including the PopData type and file IO

Julia

BED.jl

Julia

NaturalSelection.jl

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

Julia

CWL.jl

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

talks

Slides and materials for talks about BioJulia

Jupyter Notebook

Dat.jl

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

BigWig.jl

Julia

biojulia_handbook

MicrobiomePlots.jl

BBI.jl

BigBed.jl

BioJuliaDocs

BioBridgeR.jl

Compatibility between R classes and BioJulia types for bioinformatics

Julia

ragel7

Ragel 7 fork with a few Julia fixes

C++

ReferenceSequences.jl

Data structure for reference sequences

Julia

WAHVectors.jl

Compress bit vectors using the Word Aligned Hybrid method.

Julia

KmerAnalysisMakie.jl

Makie recpies for visualising KmerAnalysis types and results.

Julia

assets

Logos and other assets

JavaScript

Indexes.jl

Julia

NCBIBlast.jl

Thin wrapper around NCBI's BLAST+ CLI https://www.ncbi.nlm.nih.gov/books/NBK569856/

Julia

abstracts

Abstracts for conference talks, posters, and papers

BSG.jl

A wrapper for the BSG library and suite of tools

juju

A version manager for Julia

BioJulia-stickers

Stickers and logos for BioJulia packages

GraphicalFragmentAssembly.jl

Parser for the GFA format

Julia

Community-Issues

Repo to track BioJulia organisation level issues.

BioJulia

Top repositories