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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

Bump compat for MemoryViews

github.com/BioJulia/XAMAuxData.jl - jakobnissen opened this pull request 9 days ago
Add compat with MemoryViews 0.3

github.com/BioJulia/PairwiseMappingFormat.jl - jakobnissen opened this pull request 9 days ago
Bump version

github.com/BioJulia/MemoryViews.jl - jakobnissen opened this pull request 9 days ago
Fix some bugs

github.com/BioJulia/MemoryViews.jl - jakobnissen opened this pull request 10 days ago
Add optimised findfirst etc

github.com/BioJulia/MemoryViews.jl - jakobnissen opened this pull request 12 days ago
Add split functions

github.com/BioJulia/MemoryViews.jl - jakobnissen opened this pull request 14 days ago
Compat update?

github.com/BioJulia/BioMakie.jl - dgleich opened this issue 18 days ago
little typo fix

github.com/BioJulia/Automa.jl - denshd opened this pull request 20 days ago
[feature] Tag a new release?

github.com/BioJulia/PopGen.jl - dgleich opened this issue 26 days ago
parse query on Select object creation

github.com/BioJulia/BioStructures.jl - lmiq opened this pull request 30 days ago
Sequence section of .gbk output is non-standard?

github.com/BioJulia/GenomicAnnotations.jl - ian-small opened this issue 30 days ago
CompatHelper: bump compat for GeometryBasics to 0.5, (keep existing compat)

github.com/BioJulia/BioMakie.jl - github-actions[bot] opened this pull request about 1 month ago
Update ci workflows

github.com/BioJulia/ProteinSecondaryStructures.jl - lmiq opened this pull request about 1 month ago
Bump codecov/codecov-action from 4 to 5

github.com/BioJulia/BioMarkovChains.jl - dependabot[bot] opened this pull request about 1 month ago
Fix small errors in examples/ code

github.com/BioJulia/MemoryViews.jl - jakobnissen opened this pull request about 1 month ago
Bump codecov/codecov-action from 4 to 5

github.com/BioJulia/BioStructures.jl - dependabot[bot] opened this pull request about 1 month ago
Add constructor that allows specifying type

github.com/BioJulia/MemoryViews.jl - jakobnissen opened this pull request about 1 month ago
minor issues with headers

github.com/BioJulia/GenomicAnnotations.jl - ian-small opened this issue about 1 month ago
gffstring mishandles transpliced genes

github.com/BioJulia/GenomicAnnotations.jl - ian-small opened this issue about 1 month ago
gffstring can still merge reverse strand multi-position loci

github.com/BioJulia/GenomicAnnotations.jl - ian-small opened this issue about 1 month ago
gffstring merges multi-position features

github.com/BioJulia/GenomicAnnotations.jl - ian-small opened this issue about 1 month ago
memory usage when reading (really large) files

github.com/BioJulia/BioStructures.jl - lmiq opened this issue about 1 month ago
Post for ubioinfie

github.com/BioJulia/biojulia.github.io - kescobo opened this issue about 2 months ago
Document BioSequence interface(s)

github.com/BioJulia/BioSequences.jl - kescobo opened this issue about 2 months ago
Lazy dep on Muon.jl for loading h5ad files

github.com/BioJulia/SingleCellProjections.jl - rasmushenningsson opened this pull request about 2 months ago
Unroll == and some search functions

github.com/BioJulia/BioSequences.jl - jakobnissen opened this pull request about 2 months ago
Use part when counting over chunk iterators

github.com/BioJulia/BioSequences.jl - jakobnissen opened this pull request about 2 months ago
Speed up search operations for SeqOrView

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

github.com/BioJulia/BioSequences.jl - jakobnissen opened this pull request about 2 months ago
Implement Iterators.reverse for MemoryView

github.com/BioJulia/MemoryViews.jl - jakobnissen opened this pull request about 2 months ago
Various internal code cleanup

github.com/BioJulia/BioSequences.jl - jakobnissen opened this pull request about 2 months ago
Optimise findnext for SeqOrView

github.com/BioJulia/BioSequences.jl - jakobnissen opened this issue about 2 months ago
Remove `convert` for biosequences

github.com/BioJulia/BioSequences.jl - jakobnissen opened this issue 2 months ago
CompatHelper: bump compat for Colors to 0.13, (keep existing compat)

github.com/BioJulia/BioMakie.jl - github-actions[bot] opened this pull request 2 months ago
Optimise some LongSequence constructors

github.com/BioJulia/BioSequences.jl - jakobnissen opened this pull request 2 months ago
Internals: Use QualityScores iterator

github.com/BioJulia/FASTX.jl - jakobnissen opened this pull request 2 months ago
Add tests for record functions

github.com/BioJulia/PairwiseMappingFormat.jl - jakobnissen opened this pull request 2 months ago
More consistently throw EncodeError

github.com/BioJulia/BioSequences.jl - jakobnissen opened this pull request 2 months ago
Prepare for release

github.com/BioJulia/PairwiseMappingFormat.jl - jakobnissen opened this pull request 2 months ago
Hide inner constructors of objects in this package

github.com/BioJulia/BioSequences.jl - jakobnissen opened this issue 2 months ago
WIP Make LongSequence and LongSubSeq use Memory [DO NOT MERGE]

github.com/BioJulia/BioSequences.jl - jakobnissen opened this pull request 2 months ago
CompatHelper: bump compat for MetaGraphs in [weakdeps] to 0.8, (keep existing compat)

github.com/BioJulia/BioStructures.jl - github-actions[bot] opened this pull request 2 months ago
CompatHelper: bump compat for ColorTypes to 0.12, (keep existing compat)

github.com/BioJulia/BioMakie.jl - github-actions[bot] opened this pull request 2 months ago
Rewrite counting of BioSequence

github.com/BioJulia/BioSequences.jl - jakobnissen opened this pull request 2 months ago
Rewrite bitpar compiler

github.com/BioJulia/BioSequences.jl - jakobnissen opened this issue 2 months ago
What's up with the strange two-argument counting methods?

github.com/BioJulia/BioSequences.jl - jakobnissen opened this issue 2 months ago
Document bitpar counting

github.com/BioJulia/BioSequences.jl - jakobnissen opened this pull request 2 months ago
Bump version

github.com/BioJulia/Automa.jl - jakobnissen opened this pull request 2 months ago
Re-enable SIMD

github.com/BioJulia/Automa.jl - jakobnissen opened this pull request 2 months ago
Test for AuxException cases

github.com/BioJulia/XAMAuxData.jl - jakobnissen opened this pull request 2 months ago
Redefine validity for records

github.com/BioJulia/XAMAuxData.jl - jakobnissen opened this pull request 2 months ago
CompatHelper: bump compat for Meshes to 0.52, (keep existing compat)

github.com/BioJulia/BioMakie.jl - github-actions[bot] opened this pull request 2 months ago
Update README.md

github.com/BioJulia/NCBIBlast.jl - jonalm opened this pull request 2 months ago
Delete workaround for compat with extensions

github.com/BioJulia/FASTX.jl - jakobnissen opened this pull request 2 months ago
Annotate const fields as const

github.com/BioJulia/BioSequences.jl - jakobnissen opened this pull request 2 months ago
Type piracy of Base breaks package in 1.11

github.com/BioJulia/GenomicAnnotations.jl - jakobnissen opened this issue 2 months ago
Drop pre-LTS Julia support

github.com/BioJulia/BioSequences.jl - jakobnissen opened this pull request 2 months ago
Mark const fields as const

github.com/BioJulia/FASTX.jl - jakobnissen opened this pull request 2 months ago
Drop support for Julia <1.10

github.com/BioJulia/FASTX.jl - jakobnissen opened this pull request 2 months ago
Decoupling the alphabet field as BMC type parameter

github.com/BioJulia/BioMarkovChains.jl - camilogarciabotero opened this pull request 2 months ago
TagBot trigger issue

github.com/BioJulia/NCBIBlast.jl - JuliaTagBot opened this issue 2 months ago
Consider using NCBI artifacts directly

github.com/BioJulia/NCBIBlast.jl - jonalm opened this issue 2 months ago
use artifacts from NCBI directly

github.com/BioJulia/NCBIBlast.jl - jonalm opened this pull request 2 months ago
Add tblastx

github.com/BioJulia/NCBIBlast.jl - jakobnissen opened this pull request 2 months ago
Deprecate Package

github.com/BioJulia/BioTools.jl - kescobo opened this pull request 2 months ago
File types (inputs and outputs)

github.com/BioJulia/NCBIBlast.jl - kescobo opened this issue 2 months ago
Bike-shedding the name

github.com/BioJulia/NCBIBlast.jl - kescobo opened this issue 2 months ago
Mothball this package, re-write, and register a separate BLAST.jl package

github.com/BioJulia/BioTools.jl - kescobo opened this issue 3 months ago
Dependency and compatibility issues installing BioTools

github.com/BioJulia/BioTools.jl - hodgensc opened this issue 3 months ago
Add compat for TS 0.11

github.com/BioJulia/Automa.jl - jakobnissen opened this pull request 3 months ago
Remove unused parameter in (==) extended method

github.com/BioJulia/GenomicFeatures.jl - camilogarciabotero opened this pull request 4 months ago
CompatHelper: bump compat for Meshes to 0.51, (keep existing compat)

github.com/BioJulia/BioMakie.jl - github-actions[bot] opened this pull request 4 months ago
CompatHelper: bump compat for Meshes to 0.50, (keep existing compat)

github.com/BioJulia/BioMakie.jl - github-actions[bot] opened this pull request 4 months ago
1 warning in loading data and 1 error in cell annotation

github.com/BioJulia/SingleCellProjections.jl - pywugate opened this issue 4 months ago
biojulep: iterators or fold for structures

github.com/BioJulia/BioStructures.jl - timholy opened this issue 4 months ago
Add recursive copy for structures

github.com/BioJulia/BioStructures.jl - timholy opened this pull request 4 months ago
3-vector for coordinates?

github.com/BioJulia/BioStructures.jl - timholy opened this issue 4 months ago
Read error on TabulaSapients 10X data

github.com/BioJulia/SingleCellProjections.jl - rasmushenningsson opened this issue 4 months ago
CompatHelper: bump compat for Meshes to 0.49, (keep existing compat)

github.com/BioJulia/BioMakie.jl - github-actions[bot] opened this pull request 4 months ago
Concrete fields for `Transformation`

github.com/BioJulia/BioStructures.jl - timholy opened this pull request 4 months ago
Support for Concurrent Access with XAM.jl: Reader/Writer Safety and Locking Considerations

github.com/BioJulia/XAM.jl - abhinavsns opened this issue 4 months ago
PFM just accepts vectors?

github.com/BioJulia/BioSequences.jl - felipe-mansoldo opened this issue 4 months ago
Flat file -> DataMatrix?

github.com/BioJulia/SingleCellProjections.jl - kescobo opened this issue 5 months ago
CompatHelper: bump compat for Meshes to 0.48, (keep existing compat)

github.com/BioJulia/BioMakie.jl - github-actions[bot] opened this pull request 5 months ago
Last Bed entry not being read

github.com/BioJulia/BED.jl - abhinavsns opened this issue 5 months ago
Read sequences don't have overlapping with gene, but eachoverlap() reported there're.

github.com/BioJulia/XAM.jl - Xiao-Zhong opened this issue 5 months ago
Cross compatibility with XAM.jl?

github.com/BioJulia/BED.jl - abhinavsns opened this issue 5 months ago
Update docs

github.com/BioJulia/BED.jl - jakobnissen opened this pull request 5 months ago
Update docs

github.com/BioJulia/BED.jl - jakobnissen opened this pull request 5 months ago
Rebase changes from develop branch

github.com/BioJulia/BED.jl - jakobnissen opened this pull request 5 months ago
Bump version to 0.3.1

github.com/BioJulia/BED.jl - jakobnissen opened this pull request 5 months ago
Migrate to Automa v1

github.com/BioJulia/BED.jl - jakobnissen opened this pull request 5 months ago
Making BED.jl compatible with Automa v1

github.com/BioJulia/BED.jl - abhinavsns opened this pull request 5 months ago
CompatHelper: bump compat for Makie to 0.21, (keep existing compat)

github.com/BioJulia/BioMakie.jl - github-actions[bot] opened this pull request 5 months ago
CompatHelper: bump compat for GLMakie to 0.10, (keep existing compat)

github.com/BioJulia/BioMakie.jl - github-actions[bot] opened this pull request 5 months ago
CompatHelper: bump compat for Meshes to 0.47, (keep existing compat)

github.com/BioJulia/BioMakie.jl - github-actions[bot] opened this pull request 5 months ago
CompatHelper: bump compat for MolecularGraph to 0.17, (keep existing compat)

github.com/BioJulia/BioMakie.jl - github-actions[bot] opened this pull request 5 months ago
fix meshes compile

github.com/BioJulia/BioMakie.jl - kool7d opened this pull request 5 months ago
Use MIToS v3

github.com/BioJulia/BioMakie.jl - diegozea opened this pull request 5 months ago
Update TranscodingStreams compat to 0.11

github.com/BioJulia/FASTX.jl - jakobnissen opened this pull request 5 months ago