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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

Prefer staying inside regex to exiting it

github.com/BioJulia/Automa.jl - jakobnissen opened this issue over 1 year ago
Remove dependency on Printf

github.com/BioJulia/Automa.jl - jakobnissen opened this pull request over 1 year ago
Issues with Tokenizer

github.com/BioJulia/Automa.jl - jakobnissen opened this issue over 1 year ago
Fix iterator constructor and other failing tests

github.com/BioJulia/Kmers.jl - cjprybol opened this pull request over 1 year ago
Fix behavior of iterate on indices <= 0

github.com/BioJulia/BioSequences.jl - cjprybol opened this pull request over 1 year ago
Looping regex can be given a final action

github.com/BioJulia/Automa.jl - jakobnissen opened this issue over 1 year ago
tweak1

github.com/BioJulia/BioMakie.jl - kool7d opened this pull request over 1 year ago
Kmers.jl is unable to comply with `BioSequences.has_interface` as currently implemented

github.com/BioJulia/Kmers.jl - cjprybol opened this issue over 1 year ago
consider removing kmer/sequence type inference from strings in favor of generalized version in BioSequences

github.com/BioJulia/Kmers.jl - cjprybol opened this issue over 1 year ago
Add guessparse function

github.com/BioJulia/BioSequences.jl - jakobnissen opened this pull request over 1 year ago
CompatHelper: add new compat entry for Aqua at version 0.6, (keep existing compat)

github.com/BioJulia/BioMakie.jl - github-actions[bot] opened this pull request over 1 year ago
Add eachoverlap(reader::Reader, refname::String)

github.com/BioJulia/XAM.jl - apraga opened this issue over 1 year ago
Dev

github.com/BioJulia/BioMakie.jl - kool7d opened this pull request over 1 year ago
Add docstrings and update docs

github.com/BioJulia/Kmers.jl - cjprybol opened this pull request over 1 year ago
Record type inference

github.com/BioJulia/BioSequences.jl - cjprybol opened this issue over 1 year ago
CompatHelper: bump compat for Meshes to 0.28, (keep existing compat)

github.com/BioJulia/BioMakie.jl - github-actions[bot] opened this pull request over 1 year ago
Update hardware post

github.com/BioJulia/biojulia.github.io - jakobnissen opened this pull request over 1 year ago
Domain name expired

github.com/BioJulia/biojulia.github.io - jakobnissen opened this issue over 1 year ago
CompatHelper: add new compat entry for Reexport at version 1, (keep existing compat)

github.com/BioJulia/BioMakie.jl - github-actions[bot] opened this pull request over 1 year ago
Fails to parse metadata with hypen in the key

github.com/BioJulia/GeneticVariation.jl - apraga opened this issue over 1 year ago
devup

github.com/BioJulia/BioMakie.jl - kool7d opened this pull request over 1 year ago
better docstrings and struc update

github.com/BioJulia/BioMakie.jl - kool7d opened this pull request over 1 year ago
CompatHelper: bump compat for BioAlignments to 3, (keep existing compat)

github.com/BioJulia/BioMakie.jl - github-actions[bot] opened this pull request over 1 year ago
CompatHelper: add new compat entry for Meshes at version 0.27, (keep existing compat)

github.com/BioJulia/BioMakie.jl - github-actions[bot] opened this pull request over 1 year ago
Improve error on predefined convert(::BioSymbol, ::Char)

github.com/BioJulia/BioSymbols.jl - jakobnissen opened this pull request over 1 year ago
Improve error when mis-encoding LongDNA from byte-like inputs

github.com/BioJulia/BioSequences.jl - jakobnissen opened this pull request over 1 year ago
Improve error message on encoding error

github.com/BioJulia/BioSequences.jl - jakobnissen opened this issue over 1 year ago
Fix Base.read!(::Reader, ::Record) and add tests

github.com/BioJulia/FASTX.jl - jakobnissen opened this pull request over 1 year ago
read! doesn't work in v2.0.0?

github.com/BioJulia/FASTX.jl - banhbio opened this issue over 1 year ago
CompatHelper: bump compat for Term to 2, (keep existing compat)

github.com/BioJulia/PopGen.jl - github-actions[bot] opened this pull request over 1 year ago
Remove references to Random.GLOBAL_RNG

github.com/BioJulia/BioSequences.jl - jakobnissen opened this pull request over 1 year ago
Update BioAlignments and BioSequences compat. Change LongAminoAcidSeq to LongSequence{AminoAcidAlphabet}

github.com/BioJulia/BioStructures.jl - kool7d opened this pull request over 1 year ago
Correctly finding matching double quotes when Unicode characters are present

github.com/BioJulia/Automa.jl - jagot opened this issue over 1 year ago
Fix outdated tests

github.com/BioJulia/BioServices.jl - kescobo opened this issue over 1 year ago
Release for expanding HTTP compat

github.com/BioJulia/BioServices.jl - kescobo opened this pull request over 1 year ago
Document `read!(::Reader, ::Record)`

github.com/BioJulia/FASTX.jl - jonathanBieler opened this issue over 1 year ago
TagBot trigger issue

github.com/BioJulia/SingleCellProjections.jl - JuliaTagBot opened this issue over 1 year ago
Allow translation of sequence views

github.com/BioJulia/BioSequences.jl - jakobnissen opened this pull request over 1 year ago
Release v0.2.2

github.com/BioJulia/SequenceVariation.jl - MillironX opened this pull request over 1 year ago
CompatHelper: add new compat entry for NamedArrays at version 0.9, (keep existing compat)

github.com/BioJulia/BioMakie.jl - github-actions[bot] opened this pull request over 1 year ago
CompatHelper: add new compat entry for Graphs at version 1, (keep existing compat)

github.com/BioJulia/BioMakie.jl - github-actions[bot] opened this pull request over 1 year ago
CompatHelper: add new compat entry for Meshes at version 0.27, (keep existing compat)

github.com/BioJulia/BioMakie.jl - github-actions[bot] opened this pull request over 1 year ago
Fix validation for Haplotypes

github.com/BioJulia/SequenceVariation.jl - MillironX opened this pull request over 1 year ago
Translate subsequence

github.com/BioJulia/BioSequences.jl - jakobnissen opened this issue over 1 year ago
CompatHelper: bump compat for MultivariateStats to 0.10, (keep existing compat)

github.com/BioJulia/PopGen.jl - github-actions[bot] opened this pull request over 1 year ago
Multiple `Substitution`s doesn't invalidate `Haplotype`

github.com/BioJulia/SequenceVariation.jl - MillironX opened this issue almost 2 years ago
New Feature: Molecular weight calculations for BioSequences

github.com/BioJulia/BioSequences.jl - benjaminlozanow opened this issue almost 2 years ago
Release v0.2.1

github.com/BioJulia/SequenceVariation.jl - MillironX opened this pull request almost 2 years ago
Better error descriptions

github.com/BioJulia/SequenceVariation.jl - MillironX opened this pull request almost 2 years ago
Release v0.2.0

github.com/BioJulia/SequenceVariation.jl - MillironX opened this pull request almost 2 years ago
Add `isless` for `Edit` and `Variation`

github.com/BioJulia/SequenceVariation.jl - MillironX opened this pull request almost 2 years ago
Add `translate` functionality for haplotypes

github.com/BioJulia/SequenceVariation.jl - MillironX opened this pull request almost 2 years ago
Refactor `reconstruct` function

github.com/BioJulia/SequenceVariation.jl - MillironX opened this pull request almost 2 years ago
Rename `Variant` to `Haplotype`

github.com/BioJulia/SequenceVariation.jl - MillironX opened this pull request almost 2 years ago
Organize/stylize code and docs

github.com/BioJulia/SequenceVariation.jl - MillironX opened this pull request almost 2 years ago
Release v3.1.0

github.com/BioJulia/BioAlignments.jl - MillironX opened this pull request almost 2 years ago
Make BioSequences a weak dependency

github.com/BioJulia/FASTX.jl - jakobnissen opened this pull request almost 2 years ago
Improve precompilation

github.com/BioJulia/FASTX.jl - jakobnissen opened this pull request almost 2 years ago
(Optionally) despecialize generated code on its IO

github.com/BioJulia/Automa.jl - jakobnissen opened this issue almost 2 years ago
Consider despecializing AbstractFormattedIOs

github.com/BioJulia/FASTX.jl - jakobnissen opened this issue almost 2 years ago
Correct way to add records to an array

github.com/BioJulia/XAM.jl - krishvishal opened this issue almost 2 years ago
Release v0.1.4

github.com/BioJulia/SequenceVariation.jl - MillironX opened this pull request almost 2 years ago
Reading whole file or FileIO integration ?

github.com/BioJulia/BED.jl - jonathanBieler opened this issue almost 2 years ago
Make BioSequences an optional dependency

github.com/BioJulia/FASTX.jl - jakobnissen opened this issue almost 2 years ago
Fix softclips causing Variant construction errors

github.com/BioJulia/SequenceVariation.jl - MillironX opened this pull request almost 2 years ago
Soft clips cause invalid Variants

github.com/BioJulia/SequenceVariation.jl - MillironX opened this issue almost 2 years ago
Grantham's substitution matrix

github.com/BioJulia/BioAlignments.jl - KaparaNewbie opened this pull request almost 2 years ago
Fix bug in zero_offset! called when materializing seqview

github.com/BioJulia/BioSequences.jl - jakobnissen opened this pull request almost 2 years ago
Converting a LongSubSeq to LongSequence can give weird results

github.com/BioJulia/BioSequences.jl - ian-small opened this issue almost 2 years ago
Release v0.1.3

github.com/BioJulia/SequenceVariation.jl - MillironX opened this pull request almost 2 years ago
Add type parameterization to variations getter

github.com/BioJulia/SequenceVariation.jl - MillironX opened this pull request almost 2 years ago
How to write the function called findoverlaps with minoverlap>=1?

github.com/BioJulia/GenomicFeatures.jl - zhangchunyong999 opened this issue almost 2 years ago
convert pdb to mol

github.com/BioJulia/BioStructures.jl - Nick-Mul opened this issue almost 2 years ago
Stop pirating BioSymbols

github.com/BioJulia/BioSequences.jl - jakobnissen opened this pull request almost 2 years ago
Add `gap(::Type{Char})` to prevent piracy from BioSequences.

github.com/BioJulia/BioSymbols.jl - jakobnissen opened this pull request almost 2 years ago
subset FASTX.FASTQ.Record

github.com/BioJulia/FASTX.jl - Liripo opened this issue almost 2 years ago
bugfix for delete!(genes)

github.com/BioJulia/GenomicAnnotations.jl - hsianktin opened this pull request almost 2 years ago
[feature] Merge all PopGen_.jl packages under PopGen.jl monorepo

github.com/BioJulia/PopGen.jl - pdimens opened this issue about 2 years ago
Add a `cigar` method and `BioAlignments.Alignment` constructor for XAM.jl optimisation

github.com/BioJulia/BioAlignments.jl - CiaranOMara opened this issue about 2 years ago
Release 0.3.1

github.com/BioJulia/XAM.jl - MillironX opened this pull request about 2 years ago
Fix typo

github.com/BioJulia/BioSequences.jl - cossio opened this pull request about 2 years ago
added method for handling different bam index types

github.com/BioJulia/XAM.jl - jonathanBieler opened this pull request about 2 years ago
Upgrade to BioAlignments v3

github.com/BioJulia/XAM.jl - MillironX opened this pull request about 2 years ago
GeneticVariation.VCF.Reader does not like output from the gatk tool: funcotator

github.com/BioJulia/GeneticVariation.jl - jackmo375 opened this issue about 2 years ago
Switch to Oneflow

github.com/BioJulia/XAM.jl - MillironX opened this issue about 2 years ago
Release v0.3.0

github.com/BioJulia/XAM.jl - MillironX opened this pull request about 2 years ago
`Base.parse` and `Base.tryparse` for `DNA` and `RNA`

github.com/BioJulia/BioSymbols.jl - warrenalphonso opened this pull request about 2 years ago
Release v0.1.2

github.com/BioJulia/SequenceVariation.jl - MillironX opened this pull request about 2 years ago
Update dependencies

github.com/BioJulia/SequenceVariation.jl - MillironX opened this pull request about 2 years ago
Release v3.0.0

github.com/BioJulia/BioAlignments.jl - MillironX opened this pull request about 2 years ago
Release v2.3.0

github.com/BioJulia/BioAlignments.jl - MillironX opened this pull request about 2 years ago
Can GenomicAnnotations.jl deal with multi-exon genes?

github.com/BioJulia/GenomicAnnotations.jl - Xiao-Zhong opened this issue about 2 years ago
Do you have the plan to add the pileup functions?

github.com/BioJulia/XAM.jl - panxiaoguang opened this issue about 2 years ago
Unambiguate type nomenclature

github.com/BioJulia/SequenceVariation.jl - MillironX opened this issue about 2 years ago
Better conversion from 2 to 4 bit nucleic kmers

github.com/BioJulia/Kmers.jl - SabrinaJaye opened this pull request about 2 years ago
Fix hashing

github.com/BioJulia/Kmers.jl - SabrinaJaye opened this issue about 2 years ago
Improve type stability slightly

github.com/BioJulia/FASTX.jl - jakobnissen opened this pull request about 2 years ago
Write to treemix allele count format

github.com/BioJulia/PopGenCore.jl - pdimens opened this issue about 2 years ago
Add SnoopPrecompile

github.com/BioJulia/BioSymbols.jl - jakobnissen opened this pull request about 2 years ago
Add SnoopPrecompile

github.com/BioJulia/BioSequences.jl - jakobnissen opened this pull request about 2 years ago