From 4f80f44412cdfe4c6f9322c88ac62eef726cf56e Mon Sep 17 00:00:00 2001 From: Danielle Pinto Date: Thu, 22 Jan 2026 21:57:42 -0500 Subject: [PATCH 1/4] fixing broken links --- docs/src/index.md | 26 +++++++++++++------------- 1 file changed, 13 insertions(+), 13 deletions(-) diff --git a/docs/src/index.md b/docs/src/index.md index 2e07572..4b22b09 100644 --- a/docs/src/index.md +++ b/docs/src/index.md @@ -22,7 +22,7 @@ hero:
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BioTutorials

These are still a work in progress

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2Bit.jl Files

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TwoBit.jl Files

Read and write 2bit sequence files

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WaveletMatrices.jl Other

Wavelet matrix data structure for fast queries

From 00a21ed98af61c5bdeb5e18133224f4cc6c96d8f Mon Sep 17 00:00:00 2001 From: Danielle Pinto Date: Fri, 23 Jan 2026 21:47:04 -0500 Subject: [PATCH 2/4] add rel='external' to all links --- docs/src/index.md | 70 +++++++++++++++++++++++------------------------ 1 file changed, 35 insertions(+), 35 deletions(-) diff --git a/docs/src/index.md b/docs/src/index.md index bdf96c3..e3429c4 100644 --- a/docs/src/index.md +++ b/docs/src/index.md @@ -22,7 +22,7 @@ hero:
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BioTutorials

These are still a work in progress

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XAMAuxData.jl Files

Auxiliary data handling for SAM/BAM files

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BioJulia Blog

Stay up to date with the latest news, tutorials, and community updates

From 626d85eaafcc483cc706db2cba604b5f509fa8bf Mon Sep 17 00:00:00 2001 From: Danielle Pinto Date: Sat, 24 Jan 2026 21:42:45 -0500 Subject: [PATCH 3/4] remove contributing.md, add link to contributing on github --- docs/src/index.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/src/index.md b/docs/src/index.md index e3429c4..59f36f5 100644 --- a/docs/src/index.md +++ b/docs/src/index.md @@ -425,7 +425,7 @@ hero:
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Contributing to BioJulia

Learn how to contribute to BioJulia packages

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TwoBit.jl Files

Read and write 2bit sequence files

+
@@ -56,6 +57,7 @@ hero:

Automa.jl Files

Efficient state-machine generation to quickly and correctly parse bespoke file formats

+
@@ -64,6 +66,7 @@ hero:

BED.jl Files

Read and write BED format files

+
@@ -72,6 +75,7 @@ hero:

BGZFLib.jl Files

Low-level BGZF compression library

+
@@ -80,6 +84,7 @@ hero:

BGZFStreams.jl Files

Read and write BGZF compressed files

+
@@ -88,6 +93,7 @@ hero:

BigWig.jl Files

Read and write BigWig format files

+
@@ -96,6 +102,7 @@ hero:

BioAlignments.jl Bioinformatics

Sequence alignment algorithms and data structures

+
@@ -104,6 +111,7 @@ hero:

BioGenerics.jl Other

Generic interface definitions for BioJulia packages

+
@@ -112,6 +120,7 @@ hero:

BioMakie.jl Bioinformatics

Visualize sequences and 3D proteins with ease

+
@@ -120,6 +129,7 @@ hero:

BioMarkovChains.jl Bioinformatics

Markov chain models for biological sequences

+
@@ -128,6 +138,7 @@ hero:

BioSequences.jl Bioinformatics

Optimized types for working with biological sequences (eg DNA, RNA, proteins)

+
@@ -136,6 +147,7 @@ hero:

BioServices.jl Other

Interface to biological web services and databases

+
@@ -144,6 +156,7 @@ hero:

BioStructures.jl Bioinformatics

Read, write, and manipulate macromolecular structures (PDB, mmCIF)

+
@@ -152,6 +165,7 @@ hero:

BioSymbols.jl Bioinformatics

Primitive types for nucleotides and amino acids

+
@@ -160,6 +174,7 @@ hero:

BufferIO.jl I/O

IO interface for buffer operations

+
@@ -168,6 +183,7 @@ hero:

CIGARStrings.jl Bioinformatics

Parse and manipulate CIGAR strings for sequence alignments

+
@@ -184,6 +200,7 @@ hero:

FASTX.jl Files

Read and write FASTA and FASTQ files

+
@@ -192,6 +209,7 @@ hero:

FormatSpecimens.jl Other

Test specimens for biological file formats

+
@@ -200,6 +218,7 @@ hero:

GeneticVariation.jl Bioinformatics

Types and methods for working with genetic variation data

+
@@ -208,6 +227,7 @@ hero:

GenomicAnnotations.jl Bioinformatics

Read and write genomic annotations (GFF3, GenBank, EMBL)

+
@@ -216,6 +236,7 @@ hero:

GenomicFeatures.jl Bioinformatics

Genomic interval operations and data structures

+
@@ -224,6 +245,7 @@ hero:

GFF3.jl Files

Read and write GFF3 format files

+
@@ -232,6 +254,7 @@ hero:

GraphicalFragmentAssembly.jl Files

Read and write GFA format for sequence graphs

+
@@ -240,6 +263,7 @@ hero:

IntervalTrees.jl Other

Efficient interval tree data structures

+
@@ -256,6 +280,7 @@ hero:

KmerAnalysis.jl Bioinformatics

K-mer counting and analysis tools

+
@@ -264,6 +289,7 @@ hero:

Kmers.jl Bioinformatics

Efficient k-mer representation and operations

+
@@ -272,6 +298,7 @@ hero:

KWayMerges.jl Other

K-way merge algorithms for sorted iterators

+
@@ -280,6 +307,7 @@ hero:

MemoryViews.jl I/O

Efficient memory views for IO operations

+
@@ -288,6 +316,7 @@ hero:

MMTF.jl Files

Read and write MMTF macromolecular structure files

+
@@ -296,6 +325,7 @@ hero:

NCBIBlast.jl Bioinformatics

Interface to NCBI BLAST+ for sequence similarity searches

+
@@ -312,6 +342,7 @@ hero:

PairwiseMappingFormat.jl Files

Read and write PAF alignment format

+
@@ -320,6 +351,7 @@ hero:

PopGen.jl Bioinformatics

Population genetics analysis and simulation

+
@@ -328,6 +360,7 @@ hero:

PopGenCore.jl Bioinformatics

Core types and functions for population genetics

+
@@ -336,6 +369,7 @@ hero:

ProteinSecondaryStructures.jl Bioinformatics

Analyze and predict protein secondary structures

+
@@ -344,6 +378,7 @@ hero:

ReadDatastores.jl Bioinformatics

Efficient storage and access for sequencing read data

+
@@ -352,6 +387,7 @@ hero:

SequenceVariation.jl Bioinformatics

Represent and manipulate sequence variations (mutations, variants)

+
@@ -360,6 +396,7 @@ hero:

SingleCellProjections.jl Bioinformatics

More cells? No Problem! Get UMAPs and other projections of your single cell data using the power of Sparse Matrices

+
@@ -368,6 +405,7 @@ hero:

SubstitutionModels.jl Bioinformatics

Nucleotide and amino acid substitution models for phylogenetics

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WaveletMatrices.jl Other

Wavelet matrix data structure for fast queries

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XAM.jl Files

Read and write SAM and BAM files

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XAMAuxData.jl Files

Auxiliary data handling for SAM/BAM files

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