BioJulia/biojulia_handbook BioJulia/biojulia_handbook

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BioJulia/biojulia_handbook
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BioJulia

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Repository Details

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1

Bio.jl

[DEPRECATED] Bioinformatics and Computational Biology Infrastructure for Julia
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BioSequences.jl

Biological sequences for the julia language
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A Julia package to read, write and manipulate macromolecular structures
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5

GenomeGraphs.jl

A modern genomics framework for julia
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BioAlignments.jl

Sequence alignment tools
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7

BioMakie.jl

Plotting and interface tools for biology.
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FASTX.jl

Parse and process FASTA and FASTQ formatted files of biological sequences.
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9

PopGen.jl

Population Genetics in Julia
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IntervalTrees.jl

A data structure for efficient manipulation of sets of intervals
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BioFmtSpecimens

A collection of bioinformatics file format specimens to test against
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12

GeneticVariation.jl

Datastructures and algorithms for working with genetic variation
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BioTutorials

Tutorial Notebooks of BioJulia
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14

GenomicFeatures.jl

Tools for genomic features in Julia.
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BioCore.jl

Core types and interfaces for BioJulia packages
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16

BioSymbols.jl

Nucleic and amino acid primitive types
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17

Libz.jl

Fast, flexible zlib bindings.
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18

XAM.jl

Parse and process SAM and BAM formatted files
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19

FMIndexes.jl

FM-index for full-text search
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20

BioServices.jl

Julia interface to APIs for various bio-related web services
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21

MemoryViews.jl

Simple, low-level views into memory in Julia
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22

SingleCellProjections.jl

Analysis of Single Cell Expression data in Julia
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23

Kmers.jl

In development: Kmer types and methods for julia
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24

SubstitutionModels.jl

Biological Sequence Substitution Models for Julia
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25

GenomicAnnotations.jl

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26

Contributing

Documentation, guidelines, and policy on contributing to all BioJulia repositories
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BGZFStreams.jl

BGZF Stream
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28

IndexableBitVectors.jl

Fully indexable dictionaries - access/rank/select operations
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29

ProteinSecondaryStructures.jl

Wrapper to protein secondary structure calculation packages
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30

Codecs.jl

Common data encoding algorithms
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31

ReadDatastores.jl

Datastores for reads, not your papa's FASTQ files.
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32

KmerAnalysis.jl

K-mer counting algorithms and count-data utilities for the BioJulia framework
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33

WaveletMatrices.jl

The Wavelet Matrix
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34

BioGenerics.jl

Generic methods, types and modules for the BioJulia ecosystem.
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35

GenomeBrowsers.jl

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36

FormatSpecimens.jl

Biological file format specimens for testing packages, and functions to assist in testing.
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37

BioJuliaRegistry

The BioJulia package registry
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38

BioFetch.jl

Easily fetch biological sequences from online sources
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39

SequenceVariation.jl

Biological sequence variation
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40

TwoBit.jl

Support for working with 2Bit formatted sequence data files
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41

Phylogenies.jl

The BioJulia package for working with phylogenetic trees and geneologies.
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42

PopGen.jl_archive

Population Genetics functions in Julia.
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43

GFF3.jl

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44

MMTF.jl

A julia package to parse and write MMTF file
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45

biojulia.github.io

BioJulia's Website
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46

PopGenCore.jl

Core utilities for PopGen.jl, including the PopData type and file IO
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47

BED.jl

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48

NaturalSelection.jl

A package containing methods for looking at the effects of natural selection
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49

CWL.jl

Utilities for working with the Common Workflow Language (CWL) from Julia
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50

talks

Slides and materials for talks about BioJulia
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51

Dat.jl

Types and methods for interacting with Dat from the Julia REPL and programs.
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52

BigWig.jl

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53

MicrobiomePlots.jl

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54

BBI.jl

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55

BigBed.jl

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56

BioJuliaDocs

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57

BioBridgeR.jl

Compatibility between R classes and BioJulia types for bioinformatics
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58

ragel7

Ragel 7 fork with a few Julia fixes
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59

ReferenceSequences.jl

Data structure for reference sequences
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60

WAHVectors.jl

Compress bit vectors using the Word Aligned Hybrid method.
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61

KmerAnalysisMakie.jl

Makie recpies for visualising KmerAnalysis types and results.
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62

assets

Logos and other assets
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63

Indexes.jl

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64

NCBIBlast.jl

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

Abstracts for conference talks, posters, and papers
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66

BSG.jl

A wrapper for the BSG library and suite of tools
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67

juju

A version manager for Julia
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68

BioJulia-stickers

Stickers and logos for BioJulia packages
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69

GraphicalFragmentAssembly.jl

Parser for the GFA format
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70

Community-Issues

Repo to track BioJulia organisation level issues.
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