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BioJulia

Bioinformatics and Computational Biology in Julia
Collective - Host: opensource - https://opencollective.com/biojulia - Website: https://biojulia.net - Code: https://github.com/BioJulia

[WIP] Add genetic distance calculations under different substitution models

github.com/BioJulia/SubstitutionModels.jl - jangevaare opened this pull request over 7 years ago
Drop Julia 0.5

github.com/BioJulia/GenomicFeatures.jl - bicycle1885 opened this pull request over 7 years ago
Drop Julia 0.5 support

github.com/BioJulia/GenomicFeatures.jl - bicycle1885 opened this issue over 7 years ago
Fix most of 0.7 depwarns

github.com/BioJulia/Libz.jl - yuyichao opened this pull request over 7 years ago
Minor optimization of loop unrolling

github.com/BioJulia/Automa.jl - bicycle1885 opened this pull request over 7 years ago
[WIP] Decompose Bio.Align and Bio.Intervals

github.com/BioJulia/Bio.jl - SabrinaJaye opened this pull request over 7 years ago
get_bio_fmt_specimens() has started failing

github.com/BioJulia/GeneticVariation.jl - tkelman opened this issue over 7 years ago
Just a heads up...

github.com/BioJulia/Bio.jl - sbromberger opened this issue over 7 years ago
Julia v0.6 install error, feasible version for package BioSequences.

github.com/BioJulia/GenomicFeatures.jl - CorySimon opened this issue over 7 years ago
Julia v0.6 compatability

github.com/BioJulia/Bio.jl - CorySimon opened this issue over 7 years ago
[RTR]: Update get_fmt_specimens method

github.com/BioJulia/BioCore.jl - SabrinaJaye opened this pull request over 7 years ago
Update xor syntax to 0.6

github.com/BioJulia/GeneticVariation.jl - SabrinaJaye opened this pull request over 7 years ago
Drop julia 0.5 support

github.com/BioJulia/BioSymbols.jl - SabrinaJaye opened this issue over 7 years ago
Drop julia 0.5 support

github.com/BioJulia/GeneticVariation.jl - SabrinaJaye opened this issue over 7 years ago
make index types immutable

github.com/BioJulia/GenomicFeatures.jl - bicycle1885 opened this pull request over 7 years ago
Drop support of Julia 0.5

github.com/BioJulia/BioAlignments.jl - bicycle1885 opened this pull request over 7 years ago
add block compressed BED and GFF3 files

github.com/BioJulia/BioFmtSpecimens - bicycle1885 opened this pull request over 7 years ago
Release metadata

github.com/BioJulia/BioCore.jl - SabrinaJaye opened this issue over 7 years ago
Support tabix

github.com/BioJulia/GenomicFeatures.jl - bicycle1885 opened this pull request over 7 years ago
generate amino acid parser with Automa.jl

github.com/BioJulia/BioSymbols.jl - bicycle1885 opened this pull request over 7 years ago
Update .travis.yml for Julia 0.6

github.com/BioJulia/Libz.jl - femtotrader opened this pull request over 7 years ago
Installing BioJulia using Docker

github.com/BioJulia/Bio.jl - bicycle1885 opened this issue over 7 years ago
update code generator functions for Automa 0.3

github.com/BioJulia/BioCore.jl - bicycle1885 opened this pull request over 7 years ago
Installation of Bio.jl master branch; HttpParser fails

github.com/BioJulia/Bio.jl - weinstockj opened this issue over 7 years ago
Restructure docs

github.com/BioJulia/BioSymbols.jl - bicycle1885 opened this pull request over 7 years ago
Simplified methods

github.com/BioJulia/BioBridgeR.jl - SabrinaJaye opened this pull request over 7 years ago
Fix potential protect-unprotect stack imbalance

github.com/BioJulia/BioBridgeR.jl - SabrinaJaye opened this pull request over 7 years ago
Setup appveyor

github.com/BioJulia/BioBridgeR.jl - SabrinaJaye opened this pull request over 7 years ago
Setup Travis

github.com/BioJulia/BioBridgeR.jl - SabrinaJaye opened this pull request over 7 years ago
fix docstrings

github.com/BioJulia/BioSymbols.jl - bicycle1885 opened this pull request over 7 years ago
Method generalisations

github.com/BioJulia/BioSymbols.jl - SabrinaJaye opened this pull request over 7 years ago
fix appveyor.yml

github.com/BioJulia/BioAlignments.jl - bicycle1885 opened this pull request over 7 years ago
Pass the CI

github.com/BioJulia/Bio.jl - SabrinaJaye opened this pull request over 7 years ago
add read and write methods for Strand

github.com/BioJulia/GenomicFeatures.jl - bicycle1885 opened this pull request over 7 years ago
add read and write methods for VirtualOffset

github.com/BioJulia/BGZFStreams.jl - bicycle1885 opened this pull request over 7 years ago
CI failure

github.com/BioJulia/Bio.jl - bicycle1885 opened this issue over 7 years ago
NG86 methods

github.com/BioJulia/GeneticVariation.jl - SabrinaJaye opened this pull request over 7 years ago
New data structure for biomolecular structures

github.com/BioJulia/Bio.jl - bicycle1885 opened this issue over 7 years ago
Fix a couple bugs in findfirst.

github.com/BioJulia/IntervalTrees.jl - dcjones opened this pull request over 7 years ago
Remove Iterators.jl dependency (not used)

github.com/BioJulia/Bio.jl - iamed2 opened this pull request over 7 years ago
Recursive finite state machines?

github.com/BioJulia/Automa.jl - richardreeve opened this issue over 7 years ago
Decompose Var

github.com/BioJulia/Bio.jl - SabrinaJaye opened this pull request over 7 years ago
Add the proportion distance

github.com/BioJulia/GeneticVariation.jl - SabrinaJaye opened this pull request over 7 years ago
Add optional filter functions to eachoverlap, and a findfirst function.

github.com/BioJulia/GenomicFeatures.jl - dcjones opened this pull request over 7 years ago
Add optional filter predicates to intersect, and a findfirst function

github.com/BioJulia/IntervalTrees.jl - dcjones opened this pull request over 7 years ago
MASH Distances

github.com/BioJulia/GeneticVariation.jl - SabrinaJaye opened this pull request over 7 years ago
findfirst and haskey for IntervalCollection

github.com/BioJulia/Bio.jl - dcjones opened this pull request over 7 years ago
Redirecting index.html

github.com/BioJulia/GenomicFeatures.jl - SabrinaJaye opened this pull request over 7 years ago
Discriminate between exact Interval matches and overlaps

github.com/BioJulia/Bio.jl - phaverty opened this issue over 7 years ago
alternate name for `intersect` method?

github.com/BioJulia/Bio.jl - phaverty opened this issue over 7 years ago
StringField broken on Julia 0.6

github.com/BioJulia/Bio.jl - phaverty opened this issue over 7 years ago
Site counting

github.com/BioJulia/GeneticVariation.jl - SabrinaJaye opened this pull request over 7 years ago
First site draft

github.com/BioJulia/biojulia.github.io - SabrinaJaye opened this pull request over 7 years ago
support Julia v0.6

github.com/BioJulia/BioAlignments.jl - bicycle1885 opened this pull request over 7 years ago
BCF IO

github.com/BioJulia/GeneticVariation.jl - SabrinaJaye opened this pull request over 7 years ago
BioCore.Testing module

github.com/BioJulia/BioCore.jl - SabrinaJaye opened this pull request over 7 years ago
Complete Bio.Seq decomposition

github.com/BioJulia/Bio.jl - SabrinaJaye opened this pull request over 7 years ago
Define an abstract type for phylogenies and genealogies.

github.com/BioJulia/Phylogenies.jl - SabrinaJaye opened this issue over 7 years ago
Julia v0.6

github.com/BioJulia/GenomicFeatures.jl - bicycle1885 opened this pull request over 7 years ago
Test on Bio.Var

github.com/BioJulia/Bio.jl - bicycle1885 opened this issue over 7 years ago
Release 0.2.1

github.com/BioJulia/IntervalTrees.jl - bicycle1885 opened this pull request over 7 years ago
remove unused exported names

github.com/BioJulia/Bio.jl - bicycle1885 opened this pull request over 7 years ago
fix importing in Bio.Var

github.com/BioJulia/Bio.jl - bicycle1885 opened this pull request over 7 years ago
fix some syntax for Julia 0.6

github.com/BioJulia/IndexableBitVectors.jl - bicycle1885 opened this pull request over 7 years ago
Fix constructors

github.com/BioJulia/IntervalTrees.jl - bicycle1885 opened this pull request over 7 years ago
Checking whether or not an Interval overlaps with an Interval Collection

github.com/BioJulia/Bio.jl - phbromley opened this issue over 7 years ago
check gap existence before making a kmer

github.com/BioJulia/Bio.jl - bicycle1885 opened this pull request over 7 years ago
WIP: Foundational code from Bio.jl

github.com/BioJulia/Kmers.jl - kdm9 opened this pull request over 7 years ago
Update CI URLs to point to new caching infrastructure

github.com/BioJulia/Phylogenies.jl - staticfloat opened this pull request over 7 years ago
Renaming of BioCore.Ragel

github.com/BioJulia/BioCore.jl - SabrinaJaye opened this issue over 7 years ago
Basic project setup

github.com/BioJulia/BioCore.jl - SabrinaJaye opened this pull request over 7 years ago
.

github.com/BioJulia/Libz.jl - hpoit opened this issue over 7 years ago
implement a faster and simpler eachkmer

github.com/BioJulia/Bio.jl - bicycle1885 opened this pull request over 7 years ago
add isprimary for SAM.Record and BAM.Record

github.com/BioJulia/Bio.jl - bicycle1885 opened this pull request over 7 years ago
Fix wrong use of reinterpret in tests

github.com/BioJulia/Codecs.jl - yuyichao opened this pull request over 7 years ago
define Base.nb_available

github.com/BioJulia/Libz.jl - tpapp opened this issue over 7 years ago
Update CI URLs to point to new caching infrastructure

github.com/BioJulia/Libz.jl - staticfloat opened this pull request over 7 years ago
Update CI URLs to point to new caching infrastructure

github.com/BioJulia/FMIndexes.jl - staticfloat opened this pull request over 7 years ago
Update CI URLs to point to new caching infrastructure

github.com/BioJulia/Codecs.jl - staticfloat opened this pull request over 7 years ago
Update CI URLs to point to new caching infrastructure

github.com/BioJulia/BioSymbols.jl - staticfloat opened this pull request over 7 years ago
Update CI URLs to point to new caching infrastructure

github.com/BioJulia/Bio.jl - staticfloat opened this pull request over 7 years ago
Update CI URLs to point to new caching infrastructure

github.com/BioJulia/BGZFStreams.jl - staticfloat opened this pull request over 7 years ago
Implement a Cuckoo filter

github.com/BioJulia/Kmers.jl - kdm9 opened this issue over 7 years ago
License choices

github.com/BioJulia/Community-Issues - kdm9 opened this issue over 7 years ago
Implement a Counting Quotient Filter

github.com/BioJulia/Kmers.jl - kdm9 opened this issue over 7 years ago
Added kmer types and aliases.

github.com/BioJulia/Kmers.jl - SabrinaJaye opened this pull request over 7 years ago
Inexact error when inflating

github.com/BioJulia/Libz.jl - pwl opened this issue over 7 years ago
Short and/or long k-mer types.

github.com/BioJulia/Kmers.jl - bicycle1885 opened this issue over 7 years ago
add Interval(seqname, range) constructor

github.com/BioJulia/Bio.jl - bicycle1885 opened this pull request over 7 years ago
add BigWig.values

github.com/BioJulia/Bio.jl - bicycle1885 opened this pull request over 7 years ago
Create Libz, Gzip, and Raw stream types

github.com/BioJulia/Libz.jl - Hydrotoast opened this pull request over 7 years ago
add BBI (bigWig and bigBed) files

github.com/BioJulia/BioFmtSpecimens - bicycle1885 opened this pull request over 7 years ago
How to get kmer counts of a particular kmer?

github.com/BioJulia/Bio.jl - CorySimon opened this issue over 7 years ago
Mutually exclusive stream types

github.com/BioJulia/Libz.jl - Hydrotoast opened this issue over 7 years ago
Optimization

github.com/BioJulia/IntervalTrees.jl - dcjones opened this pull request over 7 years ago
add BigWig and BigBed modules

github.com/BioJulia/Bio.jl - bicycle1885 opened this pull request over 7 years ago
add linewrap tags in FASTQ

github.com/BioJulia/BioFmtSpecimens - bicycle1885 opened this pull request over 7 years ago
Split Seq.Demultiplexer off to BioSeqDemuxers.jl

github.com/BioJulia/Bio.jl - kdm9 opened this issue over 7 years ago
update docs

github.com/BioJulia/BioSymbols.jl - bicycle1885 opened this pull request over 7 years ago
fix package name in docs

github.com/BioJulia/BioSymbols.jl - bicycle1885 opened this pull request over 7 years ago