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kescobo merged 2 commits into from
Jan 23, 2026
Merged

Fix discussions link #33

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033ada3
Fix discussions link
danielle-pinto Jan 22, 2026
af0b48e
fix links
danielle-pinto Jan 23, 2026
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2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -46,7 +46,7 @@ detailed contributor and maintainer guidelines, and code of conduct.

## Questions?

Feel free to open a new discussion under the [BioJuliaDocs Discussions](https://github.com/BioJulia/discussions) section.
Feel free to open a new discussion under the [BioJuliaDocs Discussions](https://github.com/orgs/BioJulia/discussions) section.
Alternatively, one can chat with the community either via the [Slack](https://julialang.org/slack/) #biology workspace
or in the [forums](https://discourse.julialang.org/).

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84 changes: 42 additions & 42 deletions docs/src/index.md
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Expand Up @@ -22,7 +22,7 @@ hero:

<div class="VPFeatures">
<div class="VPFeature">
<a href="https://biojulia.dev/BioTutorials" class="feature-link">
<a href="https://biojulia.dev/BioTutorials/dev/" class="feature-link">
<article class="box">
<h3 class="title">BioTutorials</h3>
<p class="details">These are still a work in progress</p>
Expand All @@ -44,127 +44,127 @@ hero:

<div class="VPFeatures" id="packages-grid">
<div class="VPFeature" data-category="files">
<a href="https://biojulia.dev/2Bit.jl" class="feature-link">
<a href="https://biojulia.dev/TwoBit.jl/stable/" class="feature-link">
<article class="box">
<h3 class="title">2Bit.jl <span class="feature-badge badge-files">Files</span></h3>
<h3 class="title">TwoBit.jl <span class="feature-badge badge-files">Files</span></h3>
<p class="details">Read and write 2bit sequence files</p>
</article>
</a>
</div>
<div class="VPFeature" data-category="files">
<a href="https://biojulia.dev/Automa.jl" class="feature-link">
<a href="https://biojulia.dev/Automa.jl/stable/" class="feature-link">
<article class="box">
<h3 class="title">Automa.jl <span class="feature-badge badge-files">Files</span></h3>
<p class="details">Efficient state-machine generation to quickly and correctly parse bespoke file formats</p>
</article>
</a>
</div>
<div class="VPFeature" data-category="files">
<a href="https://biojulia.dev/BED.jl" class="feature-link">
<a href="https://biojulia.dev/BED.jl/stable/" class="feature-link">
<article class="box">
<h3 class="title">BED.jl <span class="feature-badge badge-files">Files</span></h3>
<p class="details">Read and write BED format files</p>
</article>
</a>
</div>
<div class="VPFeature" data-category="files">
<a href="https://biojulia.dev/BGZFLib.jl" class="feature-link">
<a href="https://biojulia.dev/BGZFLib.jl/stable/" class="feature-link">
<article class="box">
<h3 class="title">BGZFLib.jl <span class="feature-badge badge-files">Files</span></h3>
<p class="details">Low-level BGZF compression library</p>
</article>
</a>
</div>
<div class="VPFeature" data-category="files">
<a href="https://biojulia.dev/BGZFStreams.jl" class="feature-link">
<a href="https://github.com/BioJulia/BGZFStreams.jl" class="feature-link">
<article class="box">
<h3 class="title">BGZFStreams.jl <span class="feature-badge badge-files">Files</span></h3>
<p class="details">Read and write BGZF compressed files</p>
</article>
</a>
</div>
<div class="VPFeature" data-category="files">
<a href="https://biojulia.dev/BigWig.jl" class="feature-link">
<a href="https://biojulia.dev/BigWig.jl/dev/" class="feature-link">
<article class="box">
<h3 class="title">BigWig.jl <span class="feature-badge badge-files">Files</span></h3>
<p class="details">Read and write BigWig format files</p>
</article>
</a>
</div>
<div class="VPFeature" data-category="bioinformatics">
<a href="https://biojulia.dev/BioAlignments.jl" class="feature-link">
<a href="https://biojulia.dev/BioAlignments.jl/stable/" class="feature-link">
<article class="box">
<h3 class="title">BioAlignments.jl <span class="feature-badge badge-bioinformatics">Bioinformatics</span></h3>
<p class="details">Sequence alignment algorithms and data structures</p>
</article>
</a>
</div>
<div class="VPFeature" data-category="other">
<a href="https://biojulia.dev/BioGenerics.jl" class="feature-link">
<a href="https://biojulia.dev/BioGenerics.jl/stable/" class="feature-link">
<article class="box">
<h3 class="title">BioGenerics.jl <span class="feature-badge badge-other">Other</span></h3>
<p class="details">Generic interface definitions for BioJulia packages</p>
</article>
</a>
</div>
<div class="VPFeature" data-category="bioinformatics">
<a href="https://biojulia.dev/BioMakie.jl" class="feature-link">
<a href="https://biojulia.dev/BioMakie.jl/dev/" class="feature-link">
<article class="box">
<h3 class="title">BioMakie.jl <span class="feature-badge badge-bioinformatics">Bioinformatics</span></h3>
<p class="details">Visualize sequences and 3D proteins with ease</p>
</article>
</a>
</div>
<div class="VPFeature" data-category="bioinformatics">
<a href="https://biojulia.dev/BioMarkovChains.jl" class="feature-link">
<a href="https://biojulia.dev/BioMarkovChains.jl/stable/" class="feature-link">
<article class="box">
<h3 class="title">BioMarkovChains.jl <span class="feature-badge badge-bioinformatics">Bioinformatics</span></h3>
<p class="details">Markov chain models for biological sequences</p>
</article>
</a>
</div>
<div class="VPFeature" data-category="bioinformatics">
<a href="https://biojulia.dev/BioSequences.jl" class="feature-link">
<a href="https://biojulia.dev/BioSequences.jl/stable/" class="feature-link">
<article class="box">
<h3 class="title">BioSequences.jl <span class="feature-badge badge-bioinformatics">Bioinformatics</span></h3>
<p class="details">Optimized types for working with biological sequences (eg DNA, RNA, proteins)</p>
</article>
</a>
</div>
<div class="VPFeature" data-category="other">
<a href="https://biojulia.dev/BioServices.jl" class="feature-link">
<a href="https://biojulia.dev/BioServices.jl/stable/" class="feature-link">
<article class="box">
<h3 class="title">BioServices.jl <span class="feature-badge badge-other">Other</span></h3>
<p class="details">Interface to biological web services and databases</p>
</article>
</a>
</div>
<div class="VPFeature" data-category="bioinformatics">
<a href="https://biojulia.dev/BioStructures.jl" class="feature-link">
<a href="https://biojulia.dev/BioStructures.jl/stable/" class="feature-link">
<article class="box">
<h3 class="title">BioStructures.jl <span class="feature-badge badge-bioinformatics">Bioinformatics</span></h3>
<p class="details">Read, write, and manipulate macromolecular structures (PDB, mmCIF)</p>
</article>
</a>
</div>
<div class="VPFeature" data-category="bioinformatics">
<a href="https://biojulia.dev/BioSymbols.jl" class="feature-link">
<a href="https://biojulia.dev/BioSymbols.jl/stable/" class="feature-link">
<article class="box">
<h3 class="title">BioSymbols.jl <span class="feature-badge badge-bioinformatics">Bioinformatics</span></h3>
<p class="details">Primitive types for nucleotides and amino acids</p>
</article>
</a>
</div>
<div class="VPFeature" data-category="io">
<a href="https://biojulia.dev/BufferIO.jl" class="feature-link">
<a href="https://biojulia.dev/BufferIO.jl/stable/" class="feature-link">
<article class="box">
<h3 class="title">BufferIO.jl <span class="feature-badge badge-io">I/O</span></h3>
<p class="details">IO interface for buffer operations</p>
</article>
</a>
</div>
<div class="VPFeature" data-category="bioinformatics">
<a href="https://biojulia.dev/CIGARStrings.jl" class="feature-link">
<a href="https://biojulia.dev/CIGARStrings.jl/stable/" class="feature-link">
<article class="box">
<h3 class="title">CIGARStrings.jl <span class="feature-badge badge-bioinformatics">Bioinformatics</span></h3>
<p class="details">Parse and manipulate CIGAR strings for sequence alignments</p>
Expand All @@ -180,63 +180,63 @@ hero:
</a>
</div>
<div class="VPFeature" data-category="files">
<a href="https://biojulia.dev/FASTX.jl" class="feature-link">
<a href="https://biojulia.dev/FASTX.jl/stable/" class="feature-link">
<article class="box">
<h3 class="title">FASTX.jl <span class="feature-badge badge-files">Files</span></h3>
<p class="details">Read and write FASTA and FASTQ files</p>
</article>
</a>
</div>
<div class="VPFeature" data-category="other">
<a href="https://biojulia.dev/FormatSpecimens.jl" class="feature-link">
<a href="https://github.com/BioJulia/FormatSpecimens.jl" class="feature-link">
<article class="box">
<h3 class="title">FormatSpecimens.jl <span class="feature-badge badge-other">Other</span></h3>
<p class="details">Test specimens for biological file formats</p>
</article>
</a>
</div>
<div class="VPFeature" data-category="bioinformatics">
<a href="https://biojulia.dev/GeneticVariation.jl" class="feature-link">
<a href="https://biojulia.dev/GeneticVariation.jl/stable/" class="feature-link">
<article class="box">
<h3 class="title">GeneticVariation.jl <span class="feature-badge badge-bioinformatics">Bioinformatics</span></h3>
<p class="details">Types and methods for working with genetic variation data</p>
</article>
</a>
</div>
<div class="VPFeature" data-category="bioinformatics">
<a href="https://biojulia.dev/GenomicAnnotations.jl" class="feature-link">
<a href="https://biojulia.dev/GenomicAnnotations.jl/stable/" class="feature-link">
<article class="box">
<h3 class="title">GenomicAnnotations.jl <span class="feature-badge badge-bioinformatics">Bioinformatics</span></h3>
<p class="details">Read and write genomic annotations (GFF3, GenBank, EMBL)</p>
</article>
</a>
</div>
<div class="VPFeature" data-category="bioinformatics">
<a href="https://biojulia.dev/GenomicFeatures.jl" class="feature-link">
<a href="https://biojulia.dev/GenomicFeatures.jl/stable/" class="feature-link">
<article class="box">
<h3 class="title">GenomicFeatures.jl <span class="feature-badge badge-bioinformatics">Bioinformatics</span></h3>
<p class="details">Genomic interval operations and data structures</p>
</article>
</a>
</div>
<div class="VPFeature" data-category="files">
<a href="https://biojulia.dev/GFF3.jl" class="feature-link">
<a href="https://biojulia.dev/GFF3.jl/stable/" class="feature-link">
<article class="box">
<h3 class="title">GFF3.jl <span class="feature-badge badge-files">Files</span></h3>
<p class="details">Read and write GFF3 format files</p>
</article>
</a>
</div>
<div class="VPFeature" data-category="files">
<a href="https://biojulia.dev/GraphicalFragmentAssembly.jl" class="feature-link">
<a href="https://github.com/BioJulia/GraphicalFragmentAssembly.jl" class="feature-link">
<article class="box">
<h3 class="title">GraphicalFragmentAssembly.jl <span class="feature-badge badge-files">Files</span></h3>
<p class="details">Read and write GFA format for sequence graphs</p>
</article>
</a>
</div>
<div class="VPFeature" data-category="other">
<a href="https://biojulia.dev/IntervalTrees.jl" class="feature-link">
<a href="https://biojulia.dev/IntervalTrees.jl/stable/" class="feature-link">
<article class="box">
<h3 class="title">IntervalTrees.jl <span class="feature-badge badge-other">Other</span></h3>
<p class="details">Efficient interval tree data structures</p>
Expand All @@ -252,47 +252,47 @@ hero:
</a>
</div>
<div class="VPFeature" data-category="bioinformatics">
<a href="https://biojulia.dev/KmerAnalysis.jl" class="feature-link">
<a href="https://biojulia.dev/KmerAnalysis.jl/dev/" class="feature-link">
<article class="box">
<h3 class="title">KmerAnalysis.jl <span class="feature-badge badge-bioinformatics">Bioinformatics</span></h3>
<p class="details">K-mer counting and analysis tools</p>
</article>
</a>
</div>
<div class="VPFeature" data-category="bioinformatics">
<a href="https://biojulia.dev/Kmers.jl" class="feature-link">
<a href="https://biojulia.dev/Kmers.jl/stable/" class="feature-link">
<article class="box">
<h3 class="title">Kmers.jl <span class="feature-badge badge-bioinformatics">Bioinformatics</span></h3>
<p class="details">Efficient k-mer representation and operations</p>
</article>
</a>
</div>
<div class="VPFeature" data-category="other">
<a href="https://biojulia.dev/KWayMerges.jl" class="feature-link">
<a href="https://github.com/BioJulia/KWayMerges.jl" class="feature-link">
<article class="box">
<h3 class="title">KWayMerges.jl <span class="feature-badge badge-other">Other</span></h3>
<p class="details">K-way merge algorithms for sorted iterators</p>
</article>
</a>
</div>
<div class="VPFeature" data-category="io">
<a href="https://biojulia.dev/MemoryViews.jl" class="feature-link">
<a href="https://biojulia.dev/MemoryViews.jl/stable/" class="feature-link">
<article class="box">
<h3 class="title">MemoryViews.jl <span class="feature-badge badge-io">I/O</span></h3>
<p class="details">Efficient memory views for IO operations</p>
</article>
</a>
</div>
<div class="VPFeature" data-category="files">
<a href="https://biojulia.dev/MMTF.jl" class="feature-link">
<a href="https://github.com/BioJulia/MMTF.jl" class="feature-link">
<article class="box">
<h3 class="title">MMTF.jl <span class="feature-badge badge-files">Files</span></h3>
<p class="details">Read and write MMTF macromolecular structure files</p>
</article>
</a>
</div>
<div class="VPFeature" data-category="bioinformatics">
<a href="https://biojulia.dev/NCBIBlast.jl" class="feature-link">
<a href="https://github.com/BioJulia/NCBIBlast.jl" class="feature-link">
<article class="box">
<h3 class="title">NCBIBlast.jl <span class="feature-badge badge-bioinformatics">Bioinformatics</span></h3>
<p class="details">Interface to NCBI BLAST+ for sequence similarity searches</p>
Expand All @@ -308,7 +308,7 @@ hero:
</a>
</div>
<div class="VPFeature" data-category="files">
<a href="https://biojulia.dev/PairwiseMappingFormat.jl" class="feature-link">
<a href="https://biojulia.dev/PairwiseMappingFormat.jl/stable/" class="feature-link">
<article class="box">
<h3 class="title">PairwiseMappingFormat.jl <span class="feature-badge badge-files">Files</span></h3>
<p class="details">Read and write PAF alignment format</p>
Expand All @@ -324,71 +324,71 @@ hero:
</a>
</div>
<div class="VPFeature" data-category="bioinformatics">
<a href="https://biojulia.dev/PopGenCore.jl" class="feature-link">
<a href="https://github.com/BioJulia/PopGenCore.jl" class="feature-link">
<article class="box">
<h3 class="title">PopGenCore.jl <span class="feature-badge badge-bioinformatics">Bioinformatics</span></h3>
<p class="details">Core types and functions for population genetics</p>
</article>
</a>
</div>
<div class="VPFeature" data-category="bioinformatics">
<a href="https://biojulia.dev/ProteinSecondaryStructures.jl" class="feature-link">
<a href="https://biojulia.dev/ProteinSecondaryStructures.jl/stable/" class="feature-link">
<article class="box">
<h3 class="title">ProteinSecondaryStructures.jl <span class="feature-badge badge-bioinformatics">Bioinformatics</span></h3>
<p class="details">Analyze and predict protein secondary structures</p>
</article>
</a>
</div>
<div class="VPFeature" data-category="bioinformatics">
<a href="https://biojulia.dev/ReadDatastores.jl" class="feature-link">
<a href="https://biojulia.dev/ReadDatastores.jl/stable/" class="feature-link">
<article class="box">
<h3 class="title">ReadDatastores.jl <span class="feature-badge badge-bioinformatics">Bioinformatics</span></h3>
<p class="details">Efficient storage and access for sequencing read data</p>
</article>
</a>
</div>
<div class="VPFeature" data-category="bioinformatics">
<a href="https://biojulia.dev/SequenceVariation.jl" class="feature-link">
<a href="https://biojulia.dev/SequenceVariation.jl/stable/" class="feature-link">
<article class="box">
<h3 class="title">SequenceVariation.jl <span class="feature-badge badge-bioinformatics">Bioinformatics</span></h3>
<p class="details">Represent and manipulate sequence variations (mutations, variants)</p>
</article>
</a>
</div>
<div class="VPFeature" data-category="bioinformatics">
<a href="https://biojulia.dev/SingleCellProjections.jl" class="feature-link">
<a href="https://biojulia.dev/SingleCellProjections.jl/stable/" class="feature-link">
<article class="box">
<h3 class="title">SingleCellProjections.jl <span class="feature-badge badge-bioinformatics">Bioinformatics</span></h3>
<p class="details">More cells? No Problem! Get UMAPs and other projections of your single cell data using the power of Sparse Matrices</p>
</article>
</a>
</div>
<div class="VPFeature" data-category="bioinformatics">
<a href="https://biojulia.dev/SubstitutionModels.jl" class="feature-link">
<a href="https://biojulia.dev/SubstitutionModels.jl/stable/" class="feature-link">
<article class="box">
<h3 class="title">SubstitutionModels.jl <span class="feature-badge badge-bioinformatics">Bioinformatics</span></h3>
<p class="details">Nucleotide and amino acid substitution models for phylogenetics</p>
</article>
</a>
</div>
<div class="VPFeature" data-category="other">
<a href="https://biojulia.dev/WaveletMatrices.jl" class="feature-link">
<a href="https://github.com/BioJulia/WaveletMatrices.jl" class="feature-link">
<article class="box">
<h3 class="title">WaveletMatrices.jl <span class="feature-badge badge-other">Other</span></h3>
<p class="details">Wavelet matrix data structure for fast queries</p>
</article>
</a>
</div>
<div class="VPFeature" data-category="files">
<a href="https://biojulia.dev/XAM.jl" class="feature-link">
<a href="https://biojulia.dev/XAM.jl/stable/" class="feature-link">
<article class="box">
<h3 class="title">XAM.jl <span class="feature-badge badge-files">Files</span></h3>
<p class="details">Read and write SAM and BAM files</p>
</article>
</a>
</div>
<div class="VPFeature" data-category="files">
<a href="https://biojulia.dev/XAMAuxData.jl" class="feature-link">
<a href="https://biojulia.dev/XAMAuxData.jl/stable/" class="feature-link">
<article class="box">
<h3 class="title">XAMAuxData.jl <span class="feature-badge badge-files">Files</span></h3>
<p class="details">Auxiliary data handling for SAM/BAM files</p>
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