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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

CompatHelper: bump compat for "DataFrames" to "0.22"

github.com/BioJulia/PopGen.jl - github-actions[bot] opened this pull request about 4 years ago
Fix FASTQ line counting bug

github.com/BioJulia/FASTX.jl - jakobnissen opened this pull request about 4 years ago
CompatHelper: bump compat for "CSV" to "0.8"

github.com/BioJulia/PopGen.jl - github-actions[bot] opened this pull request about 4 years ago
docs pages not loading

github.com/BioJulia/PopGen.jl - pdimens opened this issue about 4 years ago
TagBot trigger issue

github.com/BioJulia/PopGen.jl - JuliaTagBot opened this issue about 4 years ago
stage 0.1.0 release

github.com/BioJulia/PopGen.jl - pdimens opened this pull request about 4 years ago
Fix description newline bug

github.com/BioJulia/FASTX.jl - jakobnissen opened this pull request about 4 years ago
Fix escape \f

github.com/BioJulia/Automa.jl - jakobnissen opened this pull request about 4 years ago
SIMD code generator

github.com/BioJulia/Automa.jl - jakobnissen opened this pull request about 4 years ago
Pushdown automata

github.com/BioJulia/Automa.jl - jakobnissen opened this issue about 4 years ago
Simplify membership codegen

github.com/BioJulia/Automa.jl - jakobnissen opened this pull request about 4 years ago
Improve DFA edge reduction

github.com/BioJulia/Automa.jl - jakobnissen opened this pull request about 4 years ago
Suboptimal DFA construction when epsilon loop in NFA

github.com/BioJulia/Automa.jl - jakobnissen opened this issue about 4 years ago
Allow no actions in generate exec code

github.com/BioJulia/Automa.jl - jakobnissen opened this pull request about 4 years ago
eachoverlap running past end of stream

github.com/BioJulia/XAM.jl - rulixxx opened this issue about 4 years ago
CompatHelper: bump compat for "AbstractPlotting" to "0.13"

github.com/BioJulia/KmerAnalysisMakie.jl - github-actions[bot] opened this pull request about 4 years ago
CompatHelper: add new compat entry for "ProgressMeter" at version "1.4"

github.com/BioJulia/PopGen.jl - github-actions[bot] opened this pull request about 4 years ago
CompatHelper: add new compat entry for "PooledArrays" at version "0.5"

github.com/BioJulia/PopGen.jl - github-actions[bot] opened this pull request about 4 years ago
CompatHelper: add new compat entry for "StaticArrays" at version "0.12"

github.com/BioJulia/PopGen.jl - github-actions[bot] opened this pull request about 4 years ago
CompatHelper: add new compat entry for "GZip" at version "0.5"

github.com/BioJulia/PopGen.jl - github-actions[bot] opened this pull request about 4 years ago
CompatHelper: add new compat entry for "Requires" at version "1.1"

github.com/BioJulia/PopGen.jl - github-actions[bot] opened this pull request about 4 years ago
merge Kinship into dev for release staging

github.com/BioJulia/PopGen.jl - pdimens opened this pull request about 4 years ago
Cannot install this package

github.com/BioJulia/GeneticVariation.jl - yuehhua opened this issue about 4 years ago
Refactor tests

github.com/BioJulia/FASTX.jl - jakobnissen opened this issue about 4 years ago
CompatHelper: bump compat for "Distributions" to "0.24"

github.com/BioJulia/PopGen.jl - github-actions[bot] opened this pull request over 4 years ago
Avoid copying data when extracting sequence

github.com/BioJulia/FASTX.jl - jakobnissen opened this pull request over 4 years ago
Subset fastq record using string syntax

github.com/BioJulia/FASTX.jl - tp2750 opened this pull request over 4 years ago
Subsetting a FASTQ record

github.com/BioJulia/FASTX.jl - tp2750 opened this issue over 4 years ago
Add readmultimmcif, writemultimmcif functions

github.com/BioJulia/BioStructures.jl - marcom opened this pull request over 4 years ago
Tab completion in the REPL for MMCIFDict and MMTFDict

github.com/BioJulia/BioStructures.jl - marcom opened this pull request over 4 years ago
Add header function

github.com/BioJulia/FASTX.jl - jakobnissen opened this pull request over 4 years ago
Is our FASTA format idiosyncratic?

github.com/BioJulia/FASTX.jl - jakobnissen opened this issue over 4 years ago
Add ProteinStructure constructors from MMCIFDict and MMTFDict

github.com/BioJulia/BioStructures.jl - marcom opened this pull request over 4 years ago
Add MMCIF reading and writing with gzip compression

github.com/BioJulia/BioStructures.jl - marcom opened this pull request over 4 years ago
Add get(mmcif, key, default) method for MMCIFDict.

github.com/BioJulia/BioStructures.jl - marcom opened this pull request over 4 years ago
MMCIF reader parsing mistakes, some keys are missing / corrupted

github.com/BioJulia/BioStructures.jl - marcom opened this issue over 4 years ago
Add alignment string position support

github.com/BioJulia/BioAlignments.jl - alyst opened this pull request over 4 years ago
BoundsError in eachoverlap()

github.com/BioJulia/XAM.jl - yuifu opened this issue over 4 years ago
How to get the score of two alignments?

github.com/BioJulia/BioAlignments.jl - aadimator opened this issue over 4 years ago
CompatHelper: bump compat for "JLD2" to "0.2"

github.com/BioJulia/PopGen.jl - github-actions[bot] opened this pull request over 4 years ago
CompatHelper: add new compat entry for "JuMP" at version "0.21"

github.com/BioJulia/PopGen.jl - github-actions[bot] opened this pull request over 4 years ago
CompatHelper: add new compat entry for "ECOS" at version "0.12"

github.com/BioJulia/PopGen.jl - github-actions[bot] opened this pull request over 4 years ago
Add constant time fasta index seeking [NEED REVIEW]

github.com/BioJulia/FASTX.jl - jakobnissen opened this pull request over 4 years ago
Simplify seekrecord

github.com/BioJulia/FASTX.jl - jakobnissen opened this pull request over 4 years ago
so slowly of extract sequence by coord

github.com/BioJulia/FASTX.jl - panxiaoguang opened this issue over 4 years ago
Possible optimization: SIMD unrolled loops

github.com/BioJulia/Automa.jl - jakobnissen opened this issue over 4 years ago
Generated code is highly redundant

github.com/BioJulia/Automa.jl - jakobnissen opened this issue over 4 years ago
CompatHelper: bump compat for "JLD2" to "0.2"

github.com/BioJulia/PopGen.jl - github-actions[bot] opened this pull request over 4 years ago
Migrate from BGZFStreams to CodecBGZF

github.com/BioJulia/XAM.jl - jakobnissen opened this issue over 4 years ago
Add Project.toml

github.com/BioJulia/GeneticVariation.jl - rasmushenningsson opened this pull request over 4 years ago
CompatHelper: bump compat for "DataStructures" to "0.18"

github.com/BioJulia/GenomicFeatures.jl - github-actions[bot] opened this pull request over 4 years ago
Fix windows newline bug (issue 25)

github.com/BioJulia/FASTX.jl - jakobnissen opened this pull request over 4 years ago
Natural sorter

github.com/BioJulia/BioGenerics.jl - CiaranOMara opened this pull request over 4 years ago
Bugfix: Make trailing FASTQ line optional

github.com/BioJulia/FASTX.jl - jakobnissen opened this pull request over 4 years ago
Switch to libdeflate [WIP - do not merge]

github.com/BioJulia/BGZFStreams.jl - jakobnissen opened this pull request over 4 years ago
Make writers parametric and buffered

github.com/BioJulia/FASTX.jl - jakobnissen opened this pull request over 4 years ago
Begin crosschecks

github.com/BioJulia/XAM.jl - CiaranOMara opened this pull request over 4 years ago
Rehaul BAM and SAM accessor functions

github.com/BioJulia/XAM.jl - jakobnissen opened this pull request over 4 years ago
Parsegff

github.com/BioJulia/GenomicAnnotations.jl - kdyrhage opened this pull request over 4 years ago
ERROR: EOFError: read end of file

github.com/BioJulia/FASTX.jl - godkin1211 opened this issue over 4 years ago
add recode flag to V/BCF importer

github.com/BioJulia/PopGen.jl - pdimens opened this issue over 4 years ago
inconsistent VCF importing

github.com/BioJulia/PopGen.jl - pdimens opened this issue over 4 years ago
Amend field access errors

github.com/BioJulia/XAM.jl - jakobnissen opened this pull request over 4 years ago
Make BAM record layout match BAM specs

github.com/BioJulia/XAM.jl - jakobnissen opened this pull request over 4 years ago
Converge SAM and BAM records

github.com/BioJulia/XAM.jl - jakobnissen opened this issue over 4 years ago
Various spec violations

github.com/BioJulia/XAM.jl - jakobnissen opened this issue over 4 years ago
CompatHelper: add new compat entry for "JuMP" at version "0.21"

github.com/BioJulia/PopGen.jl - github-actions[bot] opened this pull request over 4 years ago
CompatHelper: add new compat entry for "ECOS" at version "0.12"

github.com/BioJulia/PopGen.jl - github-actions[bot] opened this pull request over 4 years ago
Error when opening a BAM file generated by HISAT2 version 2.2.0

github.com/BioJulia/XAM.jl - yuifu opened this issue over 4 years ago
Fix zero-length copy

github.com/BioJulia/FASTX.jl - jakobnissen opened this pull request over 4 years ago
CompatHelper: add new compat entry for "FileIO" at version "1.3"

github.com/BioJulia/PopGen.jl - github-actions[bot] opened this pull request over 4 years ago
CompatHelper: add new compat entry for "MultipleTesting" at version "0.4"

github.com/BioJulia/PopGen.jl - github-actions[bot] opened this pull request over 4 years ago
CompatHelper: add new compat entry for "JLD2" at version "0.1"

github.com/BioJulia/PopGen.jl - github-actions[bot] opened this pull request over 4 years ago
CompatHelper: add new compat entry for "DataFrames" at version "0.21"

github.com/BioJulia/PopGen.jl - github-actions[bot] opened this pull request over 4 years ago
CompatHelper: add new compat entry for "GeneticVariation" at version "0.4"

github.com/BioJulia/PopGen.jl - github-actions[bot] opened this pull request over 4 years ago
CompatHelper: add new compat entry for "Distributions" at version "0.23"

github.com/BioJulia/PopGen.jl - github-actions[bot] opened this pull request over 4 years ago
CompatHelper: add new compat entry for "StatsBase" at version "0.33"

github.com/BioJulia/PopGen.jl - github-actions[bot] opened this pull request over 4 years ago
CompatHelper: add new compat entry for "LoopVectorization" at version "0.8"

github.com/BioJulia/PopGen.jl - github-actions[bot] opened this pull request over 4 years ago
CompatHelper: add new compat entry for "CSV" at version "0.7"

github.com/BioJulia/PopGen.jl - github-actions[bot] opened this pull request over 4 years ago
Fixes BAM.isnextmapped()

github.com/BioJulia/XAM.jl - dialvarezs opened this pull request over 4 years ago
CompatHelper: bump compat for "AbstractPlotting" to "0.12"

github.com/BioJulia/KmerAnalysisMakie.jl - github-actions[bot] opened this pull request over 4 years ago
Suggestion: Make structural elements mutable

github.com/BioJulia/BioStructures.jl - amaurypm opened this issue over 4 years ago
CompatHelper: add new compat entry for "Observables" at version "0.3"

github.com/BioJulia/KmerAnalysisMakie.jl - github-actions[bot] opened this pull request over 4 years ago
CompatHelper: bump compat for "KmerAnalysis" to "0.4"

github.com/BioJulia/KmerAnalysisMakie.jl - github-actions[bot] opened this pull request over 4 years ago
CompatHelper: bump compat for "KmerAnalysis" to "0.3"

github.com/BioJulia/KmerAnalysisMakie.jl - github-actions[bot] opened this pull request over 4 years ago
Benjward/backwards compat

github.com/BioJulia/KmerAnalysis.jl - SabrinaJaye opened this pull request over 4 years ago
Different slicing methods for FASTX.FASTA.sequences produces inconsistent behavior

github.com/BioJulia/FASTX.jl - cjprybol opened this issue over 4 years ago
release/v0.2.5

github.com/BioJulia/XAM.jl - CiaranOMara opened this pull request over 4 years ago
hotfix/encode_copy

github.com/BioJulia/XAM.jl - CiaranOMara opened this pull request over 4 years ago
release/v0.2.1

github.com/BioJulia/BBI.jl - CiaranOMara opened this pull request over 4 years ago
release/v0.1.1

github.com/BioJulia/Indexes.jl - CiaranOMara opened this pull request over 4 years ago
[Question] Practical example of how to use the `when` field in RE

github.com/BioJulia/Automa.jl - Azzaare opened this issue over 4 years ago
recommended limits on term length?

github.com/BioJulia/BioServices.jl - mkarikom opened this issue over 4 years ago
release/v2.0.3

github.com/BioJulia/GenomicFeatures.jl - CiaranOMara opened this pull request over 4 years ago
CompatHelper: bump compat for "KmerAnalysis" to "0.2"

github.com/BioJulia/KmerAnalysisMakie.jl - github-actions[bot] opened this pull request over 4 years ago
Remove manifest and bump compats

github.com/BioJulia/MMTF.jl - sethaxen opened this pull request over 4 years ago
cannot read vcf from Sanger

github.com/BioJulia/GeneticVariation.jl - pfarndt opened this issue over 4 years ago
CompatHelper: bump compat for "ReadDatastores" to "0.4"

github.com/BioJulia/KmerAnalysis.jl - github-actions[bot] opened this pull request over 4 years ago
Fixup addition with a BitIndex

github.com/BioJulia/BioSequences.jl - SabrinaJaye opened this pull request over 4 years ago
Support Julia LTS versions

github.com/BioJulia/ReadDatastores.jl - SabrinaJaye opened this pull request over 4 years ago