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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

TagBot trigger issue

github.com/BioJulia/Kmers.jl - JuliaTagBot opened this issue over 2 years ago
Proposal: Allow zero-length kmers

github.com/BioJulia/Kmers.jl - jakobnissen opened this issue over 2 years ago
Add iterate method for Alphabets

github.com/BioJulia/BioSequences.jl - SabrinaJaye opened this pull request over 2 years ago
Feature request: Include in GeneticVariation or register as standalone package

github.com/BioJulia/SequenceVariation.jl - MillironX opened this issue over 2 years ago
Kmer Slicing

github.com/BioJulia/Kmers.jl - SabrinaJaye opened this pull request over 2 years ago
Feature request: Add a function to create `Variations` from edit strings

github.com/BioJulia/SequenceVariation.jl - MillironX opened this issue over 2 years ago
Feature request: Add equality functions for `Variation`

github.com/BioJulia/SequenceVariation.jl - MillironX opened this issue over 2 years ago
Feature request: Add method to extract `Variation`s from `Variant`s

github.com/BioJulia/SequenceVariation.jl - MillironX opened this issue over 2 years ago
`Base.eltype(::Type{<:Alphabet})` violates `eltype` docstring

github.com/BioJulia/BioSequences.jl - jakobnissen opened this issue over 2 years ago
Various small issues

github.com/BioJulia/Kmers.jl - jakobnissen opened this issue over 2 years ago
Missing contructors

github.com/BioJulia/Kmers.jl - jakobnissen opened this issue over 2 years ago
`join(LongRNA{2}, (RNA_A,))` should work

github.com/BioJulia/BioSequences.jl - jakobnissen opened this issue over 2 years ago
Clean-up, tests

github.com/BioJulia/BioTutorials - kescobo opened this pull request over 2 years ago
Build website

github.com/BioJulia/BioTutorials - kescobo opened this issue over 2 years ago
Update RNAseq tutorial

github.com/BioJulia/BioTutorials - kescobo opened this issue over 2 years ago
Should EveryKmer and SpacedKmers be merged?

github.com/BioJulia/Kmers.jl - TransGirlCodes opened this issue over 2 years ago
Doctests

github.com/BioJulia/BioAlignments.jl - CiaranOMara opened this pull request over 2 years ago
Housekeeping

github.com/BioJulia/BioAlignments.jl - CiaranOMara opened this pull request over 2 years ago
Sequence hashing: Bugfix and slight simplification

github.com/BioJulia/BioSequences.jl - jakobnissen opened this pull request over 2 years ago
CompatHelper: add new compat entry for TSne at version 1, (keep existing compat)

github.com/BioJulia/PopGen.jl - github-actions[bot] opened this pull request over 2 years ago
Hotfix/2.2.0

github.com/BioJulia/BioAlignments.jl - CiaranOMara opened this pull request over 2 years ago
Fix small errors

github.com/BioJulia/BioSequences.jl - jakobnissen opened this pull request over 2 years ago
🐛-fix iscanonical

github.com/BioJulia/BioSequences.jl - SabrinaJaye opened this pull request over 2 years ago
🐛 in iscanonical / canonical

github.com/BioJulia/BioSequences.jl - SabrinaJaye opened this pull request over 2 years ago
🐛 in iscanonical / canonical

github.com/BioJulia/BioSequences.jl - SabrinaJaye opened this issue over 2 years ago
Alignment of 2 LongAminoAcidSeq with AffineGapScoreModel from docs goes out of bounds

github.com/BioJulia/BioAlignments.jl - kool7d opened this issue over 2 years ago
CompatHelper: add new compat entry for StatsBase at version 0.33, (keep existing compat)

github.com/BioJulia/PopGen.jl - github-actions[bot] opened this pull request over 2 years ago
CompatHelper: add new compat entry for Term at version 0.3, (keep existing compat)

github.com/BioJulia/PopGen.jl - github-actions[bot] opened this pull request over 2 years ago
CompatHelper: add new compat entry for OnlineStats at version 1, (keep existing compat)

github.com/BioJulia/PopGen.jl - github-actions[bot] opened this pull request over 2 years ago
Update CHANGELOG.md

github.com/BioJulia/BioGenerics.jl - CiaranOMara opened this pull request over 2 years ago
Fix inconsistent Variation positions

github.com/BioJulia/SequenceVariation.jl - MillironX opened this pull request over 2 years ago
Fix show function for Variations with Insertion edits

github.com/BioJulia/SequenceVariation.jl - MillironX opened this pull request over 2 years ago
[Bug]: `Variation`s from different starting places give incorrect positions

github.com/BioJulia/SequenceVariation.jl - MillironX opened this issue over 2 years ago
[Bug]: Cannot `show` `Variation` of `Insertion`

github.com/BioJulia/SequenceVariation.jl - MillironX opened this issue over 2 years ago
Add tryparse(::BioSequence, s::AbstractString) or similar

github.com/BioJulia/BioSequences.jl - jakobnissen opened this issue over 2 years ago
Add parse for DNA/RNA and Char/String

github.com/BioJulia/BioSymbols.jl - jakobnissen opened this issue over 2 years ago
EOFError: read end of file

github.com/BioJulia/GFF3.jl - junjunlab opened this issue over 2 years ago
Small cleanup of Automa codegen

github.com/BioJulia/Automa.jl - jakobnissen opened this pull request over 2 years ago
Automa has too many code generators

github.com/BioJulia/Automa.jl - jakobnissen opened this issue over 2 years ago
Small tweaks to Tokenizer internals

github.com/BioJulia/Automa.jl - jakobnissen opened this pull request over 2 years ago
Have Tokenizer check if in accept state when EOF

github.com/BioJulia/Automa.jl - jakobnissen opened this pull request over 2 years ago
Do these methods work and are they tested?

github.com/BioJulia/BioAlignments.jl - CiaranOMara opened this issue over 2 years ago
Tokenisation fails to produce an error

github.com/BioJulia/Automa.jl - andreypopp opened this issue over 2 years ago
CompatHelper: add new compat entry for NamedArrays at version 0.9, (keep existing compat)

github.com/BioJulia/PopGen.jl - github-actions[bot] opened this pull request almost 3 years ago
add cluster() wrapper

github.com/BioJulia/PopGen.jl - pdimens opened this pull request almost 3 years ago
add more clustering methods

github.com/BioJulia/PopGen.jl - pdimens opened this pull request almost 3 years ago
CompatHelper: add new compat entry for Clustering at version 0.14, (keep existing compat)

github.com/BioJulia/PopGen.jl - github-actions[bot] opened this pull request almost 3 years ago
Pca

github.com/BioJulia/PopGen.jl - pdimens opened this pull request almost 3 years ago
samplenames() to return sample names in order of appearance in genodata

github.com/BioJulia/PopGenCore.jl - pdimens opened this issue almost 3 years ago
Finding a map between observed bases and positions in the reference genome

github.com/BioJulia/XAM.jl - scikal opened this issue almost 3 years ago
v0.3.0

github.com/BioJulia/BED.jl - CiaranOMara opened this pull request almost 3 years ago
CompatHelper: bump compat for Indexes to 0.2, (keep existing compat)

github.com/BioJulia/BED.jl - github-actions[bot] opened this pull request almost 3 years ago
Skip blank lines and comment lines

github.com/BioJulia/BED.jl - CiaranOMara opened this pull request almost 3 years ago
Extract start and end positions from a PairwiseAlignment

github.com/BioJulia/BioAlignments.jl - rohanmaddamsetti opened this issue almost 3 years ago
[FR] add `Query` versions for `Base.count`

github.com/BioJulia/BioSequences.jl - BeastyBlacksmith opened this issue almost 3 years ago
BioSequences v3 and BioSymbols v5

github.com/BioJulia/BioAlignments.jl - CiaranOMara opened this pull request almost 3 years ago
[feature] replace ProgressMeter with Term.jl ProgressBar

github.com/BioJulia/PopGen.jl - pdimens opened this issue almost 3 years ago
What happened to DNAMer?

github.com/BioJulia/BioSequences.jl - JokingHero opened this issue almost 3 years ago
Skip comments in BED files

github.com/BioJulia/BED.jl - Emiller88 opened this issue almost 3 years ago
TagBot trigger issue

github.com/BioJulia/BGZFStreams.jl - JuliaTagBot opened this issue almost 3 years ago
[RFC]: Broaden characters allowed in FASTA sequences

github.com/BioJulia/FASTX.jl - jakobnissen opened this pull request almost 3 years ago
Fix missing character in docs example

github.com/BioJulia/FASTX.jl - jakobnissen opened this pull request almost 3 years ago
Include period (.) in valid letters

github.com/BioJulia/FASTX.jl - suyang-nju opened this issue almost 3 years ago
Clarify that streams take ownership of IO

github.com/BioJulia/FASTX.jl - jakobnissen opened this pull request almost 3 years ago
Erratum in documentation

github.com/BioJulia/FASTX.jl - reganbaucke opened this issue almost 3 years ago
Documenter clearer that writers/readers take ownership of underlying IO

github.com/BioJulia/FASTX.jl - spragud2 opened this issue almost 3 years ago
Add the more abstract `groupname` and `hasgroupname`.

github.com/BioJulia/BioGenerics.jl - CiaranOMara opened this pull request almost 3 years ago
Change fileld field of records to Int

github.com/BioJulia/FASTX.jl - jakobnissen opened this pull request almost 3 years ago
Rewrite for v2

github.com/BioJulia/FASTX.jl - jakobnissen opened this pull request almost 3 years ago
Update TagBot.yml

github.com/BioJulia/FASTX.jl - CiaranOMara opened this pull request almost 3 years ago
Bump BioSequences/BioSymbols to v3/v5

github.com/BioJulia/FASTX.jl - jakobnissen opened this pull request almost 3 years ago
bump compatibility for BioSymbols v5 and BioSequences v3?

github.com/BioJulia/FASTX.jl - cecileane opened this issue almost 3 years ago
TagBot trigger issue

github.com/BioJulia/TwoBit.jl - JuliaTagBot opened this issue almost 3 years ago
Update Project.toml so this package can run in downstream tests

github.com/BioJulia/BioTools.jl - CiaranOMara opened this pull request almost 3 years ago
Add ssh key to TagBot workflow

github.com/BioJulia/BioAlignments.jl - CiaranOMara opened this pull request almost 3 years ago
Add downstream tests

github.com/BioJulia/BioAlignments.jl - CiaranOMara opened this pull request almost 3 years ago
`AlignmentAnchor` method signature

github.com/BioJulia/BioAlignments.jl - CiaranOMara opened this issue almost 3 years ago
TagBot trigger issue

github.com/BioJulia/BioAlignments.jl - JuliaTagBot opened this issue almost 3 years ago
TagBot not triggering.

github.com/BioJulia/BioAlignments.jl - kescobo opened this issue almost 3 years ago
Zenodo Prep

github.com/BioJulia/BioAlignments.jl - kescobo opened this pull request almost 3 years ago
Lack of an article to cite BioAlignments.jl

github.com/BioJulia/BioAlignments.jl - Hugemiler opened this issue almost 3 years ago
Loosen search iterator

github.com/BioJulia/BioSequences.jl - CiaranOMara opened this pull request almost 3 years ago
Add `findall` method

github.com/BioJulia/BioSequences.jl - CiaranOMara opened this pull request almost 3 years ago
Add support for 'meta' alignment operations (`OP_PAD` and `OP_HARD_CLIP`)

github.com/BioJulia/BioAlignments.jl - MillironX opened this pull request almost 3 years ago
OP_BACK has no use?

github.com/BioJulia/BioAlignments.jl - jakobnissen opened this issue almost 3 years ago
Fix Kabsch Algorithm to Prevent Reflections

github.com/BioJulia/BioStructures.jl - nhz2 opened this pull request almost 3 years ago
Micro-optimise the hell out of this package.

github.com/BioJulia/Kmers.jl - TransGirlCodes opened this issue about 3 years ago
add an `ispermitted` for Alphabets?

github.com/BioJulia/BioSequences.jl - TransGirlCodes opened this issue about 3 years ago
CompatHelper: bump compat for CSV to 0.10, (keep existing compat)

github.com/BioJulia/PopGenCore.jl - github-actions[bot] opened this pull request about 3 years ago
Feature Request: Conversion from `BioAlignments` to `SAM.Record`

github.com/BioJulia/XAM.jl - MillironX opened this issue about 3 years ago
Should gaps be permitted in Kmers?

github.com/BioJulia/Kmers.jl - SabrinaJaye opened this issue about 3 years ago
Add `findall` method

github.com/BioJulia/BioSequences.jl - CiaranOMara opened this pull request about 3 years ago
Implement `findall`

github.com/BioJulia/BioSequences.jl - jakobnissen opened this issue about 3 years ago
LongDNA, LongRNA "not defined"

github.com/BioJulia/BioSequences.jl - fpmenninger opened this issue about 3 years ago
findnext, findprev broken ... possible to add findall?

github.com/BioJulia/BioSequences.jl - fpmenninger opened this issue about 3 years ago
Correct Julia compatibility entry

github.com/BioJulia/BioSequences.jl - CiaranOMara opened this pull request about 3 years ago
Update Julia requirement to 1.6

github.com/BioJulia/FASTX.jl - jakobnissen opened this pull request about 3 years ago
CompatHelper: bump compat for BioSequences to 3, (keep existing compat)

github.com/BioJulia/BioStructures.jl - github-actions[bot] opened this pull request about 3 years ago
Migrate CI to GitHub workflows and upgrade to BioSequences v3

github.com/BioJulia/TwoBit.jl - CiaranOMara opened this pull request about 3 years ago
Small internal refactors

github.com/BioJulia/BioSequences.jl - jakobnissen opened this pull request about 3 years ago