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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

Deprecate Package

github.com/BioJulia/BioTools.jl - kescobo opened this pull request 10 days ago
Mothball this package, re-write, and register a separate BLAST.jl package

github.com/BioJulia/BioTools.jl - kescobo opened this issue 22 days ago
Dependency and compatibility issues installing BioTools

github.com/BioJulia/BioTools.jl - hodgensc opened this issue 22 days ago
Add compat for TS 0.11

github.com/BioJulia/Automa.jl - jakobnissen opened this pull request about 1 month ago
Remove unused parameter in (==) extended method

github.com/BioJulia/GenomicFeatures.jl - camilogarciabotero opened this pull request about 1 month ago
CompatHelper: bump compat for Meshes to 0.51, (keep existing compat)

github.com/BioJulia/BioMakie.jl - github-actions[bot] opened this pull request about 1 month ago
CompatHelper: bump compat for Meshes to 0.50, (keep existing compat)

github.com/BioJulia/BioMakie.jl - github-actions[bot] opened this pull request about 2 months ago
1 warning in loading data and 1 error in cell annotation

github.com/BioJulia/SingleCellProjections.jl - pywugate opened this issue about 2 months ago
biojulep: iterators or fold for structures

github.com/BioJulia/BioStructures.jl - timholy opened this issue about 2 months ago
Add recursive copy for structures

github.com/BioJulia/BioStructures.jl - timholy opened this pull request about 2 months ago
3-vector for coordinates?

github.com/BioJulia/BioStructures.jl - timholy opened this issue 2 months ago
Read error on TabulaSapients 10X data

github.com/BioJulia/SingleCellProjections.jl - rasmushenningsson opened this issue 2 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 2 months ago
Concrete fields for `Transformation`

github.com/BioJulia/BioStructures.jl - timholy opened this pull request 2 months ago
Support for Concurrent Access with XAM.jl: Reader/Writer Safety and Locking Considerations

github.com/BioJulia/XAM.jl - abhinavsns opened this issue 2 months ago
PFM just accepts vectors?

github.com/BioJulia/BioSequences.jl - felipe-mansoldo opened this issue 2 months ago
Flat file -> DataMatrix?

github.com/BioJulia/SingleCellProjections.jl - kescobo opened this issue 2 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 2 months ago
Last Bed entry not being read

github.com/BioJulia/BED.jl - abhinavsns opened this issue 2 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 2 months ago
Cross compatibility with XAM.jl?

github.com/BioJulia/BED.jl - abhinavsns opened this issue 3 months ago
Update docs

github.com/BioJulia/BED.jl - jakobnissen opened this pull request 3 months ago
Update docs

github.com/BioJulia/BED.jl - jakobnissen opened this pull request 3 months ago
Rebase changes from develop branch

github.com/BioJulia/BED.jl - jakobnissen opened this pull request 3 months ago
Bump version to 0.3.1

github.com/BioJulia/BED.jl - jakobnissen opened this pull request 3 months ago
Migrate to Automa v1

github.com/BioJulia/BED.jl - jakobnissen opened this pull request 3 months ago
Making BED.jl compatible with Automa v1

github.com/BioJulia/BED.jl - abhinavsns opened this pull request 3 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 3 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 3 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 3 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 3 months ago
fix meshes compile

github.com/BioJulia/BioMakie.jl - kool7d opened this pull request 3 months ago
Use MIToS v3

github.com/BioJulia/BioMakie.jl - diegozea opened this pull request 3 months ago
Update TranscodingStreams compat to 0.11

github.com/BioJulia/FASTX.jl - jakobnissen opened this pull request 3 months ago
Update TS dep to 0.11

github.com/BioJulia/BioGenerics.jl - jakobnissen opened this pull request 3 months ago
CompatHelper: bump compat for MIToS to 3, (keep existing compat)

github.com/BioJulia/BioMakie.jl - github-actions[bot] opened this pull request 3 months ago
Fix MemoryView on empty SubString{String}

github.com/BioJulia/MemoryViews.jl - jakobnissen opened this pull request 4 months ago
Bump TranscodingStreams to 0.11

github.com/BioJulia/Automa.jl - nhz2 opened this pull request 4 months ago
CompatHelper: bump compat for TranscodingStreams to 0.11, (keep existing compat)

github.com/BioJulia/XAM.jl - github-actions[bot] opened this pull request 4 months ago
CompatHelper: bump compat for Meshes to 0.46, (keep existing compat)

github.com/BioJulia/BioMakie.jl - github-actions[bot] opened this pull request 4 months ago
Upgrade CI

github.com/BioJulia/BioSequences.jl - jakobnissen opened this pull request 4 months ago
Upgrade CI

github.com/BioJulia/FASTX.jl - jakobnissen opened this pull request 4 months ago
Disable CI for x86 macOS-latest

github.com/BioJulia/FASTX.jl - jakobnissen opened this pull request 4 months ago
Import missing symbol in FASTQ

github.com/BioJulia/FASTX.jl - jakobnissen opened this pull request 4 months ago
Mark f003.fasta as invalid

github.com/BioJulia/FormatSpecimens.jl - jakobnissen opened this pull request 4 months ago
Flip sticker

github.com/BioJulia/BioSequences.jl - jakobnissen opened this pull request 4 months ago
Flip sticker

github.com/BioJulia/BioSymbols.jl - jakobnissen opened this pull request 4 months ago
Flip sticker

github.com/BioJulia/BioAlignments.jl - jakobnissen opened this pull request 4 months ago
Flip sticker

github.com/BioJulia/BioGenerics.jl - jakobnissen opened this pull request 4 months ago
Flip sticker

github.com/BioJulia/FASTX.jl - jakobnissen opened this pull request 4 months ago
Switch mutability to types, and hide inner constructor

github.com/BioJulia/MemoryViews.jl - jakobnissen opened this pull request 4 months ago
the `MemView` design around the mutability parameter could be better

github.com/BioJulia/MemoryViews.jl - nsajko opened this issue 4 months ago
BioStructures.jl compat

github.com/BioJulia/BioMakie.jl - jgreener64 opened this pull request 4 months ago
Fix error in PAF file

github.com/BioJulia/FormatSpecimens.jl - jakobnissen opened this pull request 4 months ago
CompatHelper: bump compat for BioStructures to 4, (keep existing compat)

github.com/BioJulia/BioMakie.jl - github-actions[bot] opened this pull request 4 months ago
Add new ncbi translation code

github.com/BioJulia/BioSequences.jl - camilogarciabotero opened this pull request 4 months ago
Breaking changes for 0.4 - simplified IDs, support for external annotations and SCTransform update

github.com/BioJulia/SingleCellProjections.jl - rasmushenningsson opened this pull request 4 months ago
CompatHelper: bump compat for SCTransform to 0.2, (keep existing compat)

github.com/BioJulia/SingleCellProjections.jl - github-actions[bot] opened this pull request 4 months ago
Bump to version 1.2.0

github.com/BioJulia/FormatSpecimens.jl - jakobnissen opened this pull request 4 months ago
update docs

github.com/BioJulia/ProteinSecondaryStructures.jl - lmiq opened this pull request 4 months ago
CompatHelper: bump compat for Meshes to 0.45, (keep existing compat)

github.com/BioJulia/BioMakie.jl - github-actions[bot] opened this pull request 4 months ago
Add PAF specimens

github.com/BioJulia/FormatSpecimens.jl - jakobnissen opened this pull request 4 months ago
CompatHelper: bump compat for Meshes to 0.44, (keep existing compat)

github.com/BioJulia/BioMakie.jl - github-actions[bot] opened this pull request 4 months ago
Intersection doesn't give back correct result

github.com/BioJulia/IntervalTrees.jl - Wikunia opened this issue 4 months ago
long time no up

github.com/BioJulia/BioMakie.jl - kool7d opened this pull request 4 months ago
CompatHelper: bump compat for Meshes to 0.44, (keep existing compat)

github.com/BioJulia/BioMakie.jl - github-actions[bot] opened this pull request 4 months ago
fix compat note

github.com/BioJulia/BioStructures.jl - lmiq opened this pull request 5 months ago
Drop CI for MacOS Julia 1.5

github.com/BioJulia/BioSequences.jl - jakobnissen opened this pull request 5 months ago
Precompute ExactSearchQuery faster

github.com/BioJulia/BioSequences.jl - jakobnissen opened this pull request 5 months ago
selection syntax

github.com/BioJulia/BioStructures.jl - lmiq opened this pull request 5 months ago
CompatHelper: add new compat entry for TSne in [weakdeps] at version 1, (keep existing compat)

github.com/BioJulia/SingleCellProjections.jl - github-actions[bot] opened this pull request 5 months ago
CompatHelper: add new compat entry for PrincipalMomentAnalysis in [weakdeps] at version 0.2, (keep existing compat)

github.com/BioJulia/SingleCellProjections.jl - github-actions[bot] opened this pull request 5 months ago
CompatHelper: add new compat entry for UMAP in [weakdeps] at version 0.1, (keep existing compat)

github.com/BioJulia/SingleCellProjections.jl - github-actions[bot] opened this pull request 5 months ago
fix typo: run_strude -> run_stride

github.com/BioJulia/BioStructures.jl - lmiq opened this pull request 5 months ago
Speed up parsing of PDB line

github.com/BioJulia/BioStructures.jl - timholy opened this pull request 5 months ago
x, y, z seem too generic to export

github.com/BioJulia/BioStructures.jl - timholy opened this issue 5 months ago
failing to read PDB files generated by VMD

github.com/BioJulia/BioStructures.jl - lmiq opened this issue 5 months ago
Precompile `read(filename, PDB)`

github.com/BioJulia/BioStructures.jl - timholy opened this pull request 5 months ago
CompatHelper: bump compat for Meshes to 0.43, (keep existing compat)

github.com/BioJulia/BioMakie.jl - github-actions[bot] opened this pull request 5 months ago
Has flag() renamed to flags()?

github.com/BioJulia/XAM.jl - egoecho opened this issue 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
Bump julia-actions/cache from 1 to 2

github.com/BioJulia/BioStructures.jl - dependabot[bot] opened this pull request 6 months ago
error when using SAM.auxdata(record)

github.com/BioJulia/XAM.jl - yr-neurospace opened this issue 6 months ago
plotstruct fail on non standard atoms

github.com/BioJulia/BioMakie.jl - hack-hard opened this issue 6 months ago
CompatHelper: bump compat for Meshes to 0.42, (keep existing compat)

github.com/BioJulia/BioMakie.jl - github-actions[bot] opened this pull request 6 months ago
Do not reach into TranscodingSteams internals

github.com/BioJulia/FASTX.jl - jakobnissen opened this pull request 7 months ago
Next release of TranscodingStreams will likely break this package

github.com/BioJulia/FASTX.jl - nhz2 opened this issue 7 months ago
Update `ispalindromic`

github.com/BioJulia/BioSequences.jl - jakobnissen opened this pull request 7 months ago
`ispalindromic` with respect to `reverse` or `reverse_complement`?

github.com/BioJulia/BioSequences.jl - Seelengrab opened this issue 7 months ago
CompatHelper: bump compat for Meshes to 0.41, (keep existing compat)

github.com/BioJulia/BioMakie.jl - github-actions[bot] opened this pull request 7 months ago
Do not allow unused trailing bytes in BAM records

github.com/BioJulia/XAM.jl - jakobnissen opened this pull request 7 months ago
Rewrite BAM auxiliary data

github.com/BioJulia/XAM.jl - jakobnissen opened this pull request 7 months ago
A strange behavior in approximate searches

github.com/BioJulia/BioSequences.jl - panxiaoguang opened this issue 8 months ago
Attempts at multithreading lead to various errors

github.com/BioJulia/BGZFStreams.jl - adkinsrs opened this issue 9 months ago
CompatHelper: bump compat for GenomicFeatures to 3, (keep existing compat)

github.com/BioJulia/XAM.jl - github-actions[bot] opened this pull request 9 months ago
CompatHelper: bump compat for Indexes to 0.2, (keep existing compat)

github.com/BioJulia/XAM.jl - github-actions[bot] opened this pull request 9 months ago
Correct YML whitespace

github.com/BioJulia/XAM.jl - CiaranOMara opened this pull request 9 months ago
Feature suggestion: support BinaryCIF file format

github.com/BioJulia/BioStructures.jl - marcom opened this issue 9 months ago
CompatHelper: bump compat for Meshes to 0.40, (keep existing compat)

github.com/BioJulia/BioMakie.jl - github-actions[bot] opened this pull request 9 months ago