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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

Update TS dep to 0.11

github.com/BioJulia/BioGenerics.jl - jakobnissen opened this pull request 5 months ago
CompatHelper: bump compat for MIToS to 3, (keep existing compat)

github.com/BioJulia/BioMakie.jl - github-actions[bot] opened this pull request 6 months ago
Fix MemoryView on empty SubString{String}

github.com/BioJulia/MemoryViews.jl - jakobnissen opened this pull request 6 months ago
Bump TranscodingStreams to 0.11

github.com/BioJulia/Automa.jl - nhz2 opened this pull request 6 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 6 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 6 months ago
Upgrade CI

github.com/BioJulia/BioSequences.jl - jakobnissen opened this pull request 6 months ago
Upgrade CI

github.com/BioJulia/FASTX.jl - jakobnissen opened this pull request 6 months ago
Disable CI for x86 macOS-latest

github.com/BioJulia/FASTX.jl - jakobnissen opened this pull request 6 months ago
Import missing symbol in FASTQ

github.com/BioJulia/FASTX.jl - jakobnissen opened this pull request 6 months ago
Mark f003.fasta as invalid

github.com/BioJulia/FormatSpecimens.jl - jakobnissen opened this pull request 6 months ago
Flip sticker

github.com/BioJulia/BioSequences.jl - jakobnissen opened this pull request 6 months ago
Flip sticker

github.com/BioJulia/BioSymbols.jl - jakobnissen opened this pull request 6 months ago
Flip sticker

github.com/BioJulia/BioAlignments.jl - jakobnissen opened this pull request 6 months ago
Flip sticker

github.com/BioJulia/BioGenerics.jl - jakobnissen opened this pull request 6 months ago
Flip sticker

github.com/BioJulia/FASTX.jl - jakobnissen opened this pull request 6 months ago
Switch mutability to types, and hide inner constructor

github.com/BioJulia/MemoryViews.jl - jakobnissen opened this pull request 6 months ago
the `MemView` design around the mutability parameter could be better

github.com/BioJulia/MemoryViews.jl - nsajko opened this issue 6 months ago
BioStructures.jl compat

github.com/BioJulia/BioMakie.jl - jgreener64 opened this pull request 6 months ago
Fix error in PAF file

github.com/BioJulia/FormatSpecimens.jl - jakobnissen opened this pull request 6 months ago
CompatHelper: bump compat for BioStructures to 4, (keep existing compat)

github.com/BioJulia/BioMakie.jl - github-actions[bot] opened this pull request 6 months ago
Add new ncbi translation code

github.com/BioJulia/BioSequences.jl - camilogarciabotero opened this pull request 6 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 6 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 6 months ago
Bump to version 1.2.0

github.com/BioJulia/FormatSpecimens.jl - jakobnissen opened this pull request 6 months ago
update docs

github.com/BioJulia/ProteinSecondaryStructures.jl - lmiq opened this pull request 6 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 6 months ago
Add PAF specimens

github.com/BioJulia/FormatSpecimens.jl - jakobnissen opened this pull request 6 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 6 months ago
Intersection doesn't give back correct result

github.com/BioJulia/IntervalTrees.jl - Wikunia opened this issue 6 months ago
long time no up

github.com/BioJulia/BioMakie.jl - kool7d opened this pull request 6 months ago
Update the log_odds_ratio_score and log_odds_ratio_matrix

github.com/BioJulia/BioMarkovChains.jl - camilogarciabotero opened this pull request 7 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 7 months ago
fix compat note

github.com/BioJulia/BioStructures.jl - lmiq opened this pull request 7 months ago
Drop CI for MacOS Julia 1.5

github.com/BioJulia/BioSequences.jl - jakobnissen opened this pull request 7 months ago
Precompute ExactSearchQuery faster

github.com/BioJulia/BioSequences.jl - jakobnissen opened this pull request 7 months ago
selection syntax

github.com/BioJulia/BioStructures.jl - lmiq opened this pull request 7 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 7 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 7 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 7 months ago
fix typo: run_strude -> run_stride

github.com/BioJulia/BioStructures.jl - lmiq opened this pull request 7 months ago
Speed up parsing of PDB line

github.com/BioJulia/BioStructures.jl - timholy opened this pull request 7 months ago
x, y, z seem too generic to export

github.com/BioJulia/BioStructures.jl - timholy opened this issue 7 months ago
failing to read PDB files generated by VMD

github.com/BioJulia/BioStructures.jl - lmiq opened this issue 7 months ago
Precompile `read(filename, PDB)`

github.com/BioJulia/BioStructures.jl - timholy opened this pull request 7 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 7 months ago
Has flag() renamed to flags()?

github.com/BioJulia/XAM.jl - egoecho opened this issue 7 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 8 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 8 months ago
Bump julia-actions/cache from 1 to 2

github.com/BioJulia/BioMarkovChains.jl - dependabot[bot] opened this pull request 8 months ago
Bump julia-actions/cache from 1 to 2

github.com/BioJulia/BioStructures.jl - dependabot[bot] opened this pull request 8 months ago
error when using SAM.auxdata(record)

github.com/BioJulia/XAM.jl - yr-neurospace opened this issue 8 months ago
plotstruct fail on non standard atoms

github.com/BioJulia/BioMakie.jl - hack-hard opened this issue 8 months ago
Update index.md: Add "Get Started" section and update package installation instructions

github.com/BioJulia/BioMarkovChains.jl - camilogarciabotero opened this pull request 8 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 9 months ago
Bump julia-actions/setup-julia from 1 to 2

github.com/BioJulia/BioMarkovChains.jl - dependabot[bot] opened this pull request 9 months ago
Do not reach into TranscodingSteams internals

github.com/BioJulia/FASTX.jl - jakobnissen opened this pull request 9 months ago
Next release of TranscodingStreams will likely break this package

github.com/BioJulia/FASTX.jl - nhz2 opened this issue 9 months ago
Update `ispalindromic`

github.com/BioJulia/BioSequences.jl - jakobnissen opened this pull request 9 months ago
`ispalindromic` with respect to `reverse` or `reverse_complement`?

github.com/BioJulia/BioSequences.jl - Seelengrab opened this issue 9 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 9 months ago
Update tcm methods to new VK version

github.com/BioJulia/BioMarkovChains.jl - camilogarciabotero opened this pull request 9 months ago
Do not allow unused trailing bytes in BAM records

github.com/BioJulia/XAM.jl - jakobnissen opened this pull request 10 months ago
Rewrite BAM auxiliary data

github.com/BioJulia/XAM.jl - jakobnissen opened this pull request 10 months ago
CompatHelper: bump compat for VectorizedKmers to 0.9, (keep existing compat)

github.com/BioJulia/BioMarkovChains.jl - github-actions[bot] opened this pull request 10 months ago
A strange behavior in approximate searches

github.com/BioJulia/BioSequences.jl - panxiaoguang opened this issue 10 months ago
Attempts at multithreading lead to various errors

github.com/BioJulia/BGZFStreams.jl - adkinsrs opened this issue 11 months ago
Bump codecov/codecov-action from 3 to 4

github.com/BioJulia/BioMarkovChains.jl - dependabot[bot] opened this pull request 11 months ago
CompatHelper: bump compat for GenomicFeatures to 3, (keep existing compat)

github.com/BioJulia/XAM.jl - github-actions[bot] opened this pull request 11 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 11 months ago
Correct YML whitespace

github.com/BioJulia/XAM.jl - CiaranOMara opened this pull request 11 months ago
Feature suggestion: support BinaryCIF file format

github.com/BioJulia/BioStructures.jl - marcom opened this issue 11 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 11 months ago
Refine tests and some refactors

github.com/BioJulia/BioMarkovChains.jl - camilogarciabotero opened this pull request 11 months ago
Release/v0.4.0

github.com/BioJulia/XAM.jl - CiaranOMara opened this pull request 11 months ago
Bugfix: Escape reference to Automa in error function

github.com/BioJulia/Automa.jl - jakobnissen opened this pull request 11 months ago
Correct typos in documentation

github.com/BioJulia/Automa.jl - jakobnissen opened this pull request 11 months ago
Update docs with recipes pages

github.com/BioJulia/BioSequences.jl - jakobnissen opened this pull request 11 months ago
Expand on documentation for `compatbits`

github.com/BioJulia/BioSymbols.jl - jakobnissen opened this pull request 11 months ago
XAM compatibilty for Automa very old, please update?

github.com/BioJulia/XAM.jl - mashu opened this issue 12 months ago
CompatHelper: bump compat for MolecularGraph to 0.16, (keep existing compat)

github.com/BioJulia/BioMakie.jl - github-actions[bot] opened this pull request 12 months ago
Document string literal macro

github.com/BioJulia/BioSequences.jl - jakobnissen opened this pull request 12 months ago
Correct some small typos in the docs

github.com/BioJulia/Kmers.jl - camilogarciabotero opened this pull request 12 months ago
CompatHelper: bump compat for BioStructures to 3, (keep existing compat)

github.com/BioJulia/BioMakie.jl - github-actions[bot] opened this pull request 12 months ago
Breaking changes for v1

github.com/BioJulia/Kmers.jl - jakobnissen opened this pull request 12 months ago
Optimise complementation of nucleotides

github.com/BioJulia/BioSymbols.jl - jakobnissen opened this pull request 12 months ago
CompatHelper: bump compat for Meshes to 0.39, (keep existing compat)

github.com/BioJulia/BioMakie.jl - github-actions[bot] opened this pull request 12 months ago
Refactor BioMarkovChain struct to be BioJulia compliant using correct alphabet types

github.com/BioJulia/BioMarkovChains.jl - camilogarciabotero opened this pull request 12 months ago
CompatHelper: bump compat for Meshes to 0.38, (keep existing compat)

github.com/BioJulia/BioMakie.jl - github-actions[bot] opened this pull request about 1 year ago
Local Outlier Factor

github.com/BioJulia/SingleCellProjections.jl - rasmushenningsson opened this pull request about 1 year ago
Reason behind not using Muon/AnnData

github.com/BioJulia/SingleCellProjections.jl - aadimator opened this issue about 1 year ago
MethodError: no method matching

github.com/BioJulia/SingleCellProjections.jl - akhst7 opened this issue about 1 year ago
CompatHelper: bump compat for Hyperscript to 0.0.5, (keep existing compat)

github.com/BioJulia/BioMakie.jl - github-actions[bot] opened this pull request about 1 year ago
CompatHelper: bump compat for Meshes to 0.37, (keep existing compat)

github.com/BioJulia/BioMakie.jl - github-actions[bot] opened this pull request about 1 year ago
Clicking on protein plot does nothing with WGLMakie

github.com/BioJulia/BioMakie.jl - PGimenez opened this issue about 1 year ago
CompatHelper: bump compat for Makie to 0.20, (keep existing compat)

github.com/BioJulia/BioMakie.jl - github-actions[bot] opened this pull request about 1 year ago
CompatHelper: bump compat for GLMakie to 0.9, (keep existing compat)

github.com/BioJulia/BioMakie.jl - github-actions[bot] opened this pull request about 1 year ago
CompatHelper: bump compat for Meshes to 0.36, (keep existing compat)

github.com/BioJulia/BioMakie.jl - github-actions[bot] opened this pull request about 1 year ago
Update index.md

github.com/BioJulia/BioMakie.jl - kool7d opened this pull request about 1 year ago
fix doc links

github.com/BioJulia/BioMakie.jl - kool7d opened this pull request about 1 year ago