BioJuliaDoing Biology with Julia

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BioTutorials

These are still a work in progress

BioJulia Packages

TwoBit.jl Files

Read and write 2bit sequence files

Automa.jl Files

Efficient state-machine generation to quickly and correctly parse bespoke file formats

BED.jl Files

Read and write BED format files

BGZFLib.jl Files

Low-level BGZF compression library

BGZFStreams.jl Files

Read and write BGZF compressed files

BigWig.jl Files

Read and write BigWig format files

BioAlignments.jl Bioinformatics

Sequence alignment algorithms and data structures

BioGenerics.jl Other

Generic interface definitions for BioJulia packages

BioMakie.jl Bioinformatics

Visualize sequences and 3D proteins with ease

BioMarkovChains.jl Bioinformatics

Markov chain models for biological sequences

BioSequences.jl Bioinformatics

Optimized types for working with biological sequences (eg DNA, RNA, proteins)

BioServices.jl Other

Interface to biological web services and databases

BioStructures.jl Bioinformatics

Read, write, and manipulate macromolecular structures (PDB, mmCIF)

BioSymbols.jl Bioinformatics

Primitive types for nucleotides and amino acids

BufferIO.jl I/O

IO interface for buffer operations

CIGARStrings.jl Bioinformatics

Parse and manipulate CIGAR strings for sequence alignments

EcoJulia Outside Org

Ecological modeling and analysis ecosystem

FASTX.jl Files

Read and write FASTA and FASTQ files

FormatSpecimens.jl Other

Test specimens for biological file formats

GeneticVariation.jl Bioinformatics

Types and methods for working with genetic variation data

GenomicAnnotations.jl Bioinformatics

Read and write genomic annotations (GFF3, GenBank, EMBL)

GenomicFeatures.jl Bioinformatics

Genomic interval operations and data structures

GFF3.jl Files

Read and write GFF3 format files

GraphicalFragmentAssembly.jl Files

Read and write GFA format for sequence graphs

IntervalTrees.jl Other

Efficient interval tree data structures

JuliaHealth Outside Org

Health and medical informatics packages

KmerAnalysis.jl Bioinformatics

K-mer counting and analysis tools

Kmers.jl Bioinformatics

Efficient k-mer representation and operations

KWayMerges.jl Other

K-way merge algorithms for sorted iterators

MemoryViews.jl I/O

Efficient memory views for IO operations

MMTF.jl Files

Read and write MMTF macromolecular structure files

NCBIBlast.jl Bioinformatics

Interface to NCBI BLAST+ for sequence similarity searches

OpenMendel Outside Org

Statistical genetics and genomic analysis tools

PairwiseMappingFormat.jl Files

Read and write PAF alignment format

PopGen.jl Bioinformatics

Population genetics analysis and simulation

PopGenCore.jl Bioinformatics

Core types and functions for population genetics

ProteinSecondaryStructures.jl Bioinformatics

Analyze and predict protein secondary structures

ReadDatastores.jl Bioinformatics

Efficient storage and access for sequencing read data

SequenceVariation.jl Bioinformatics

Represent and manipulate sequence variations (mutations, variants)

SingleCellProjections.jl Bioinformatics

More cells? No Problem! Get UMAPs and other projections of your single cell data using the power of Sparse Matrices

SubstitutionModels.jl Bioinformatics

Nucleotide and amino acid substitution models for phylogenetics

WaveletMatrices.jl Other

Wavelet matrix data structure for fast queries

XAM.jl Files

Read and write SAM and BAM files

XAMAuxData.jl Files

Auxiliary data handling for SAM/BAM files

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BioJulia Blog

Stay up to date with the latest news, tutorials, and community updates

Julia Slack

Chat with the Julia community on Slack

Julia Discourse

Ask questions and discuss with the Julia community

Contributing to BioJulia

Learn how to contribute to BioJulia packages