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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

Fix issues from v3/master merge

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

github.com/BioJulia/BioSequences.jl - SabrinaJaye opened this pull request about 3 years ago
Deal better with missingness

github.com/BioJulia/FASTX.jl - jakobnissen opened this issue about 3 years ago
Return header, identifier and desc as string views

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

github.com/BioJulia/FASTX.jl - jakobnissen opened this pull request about 3 years ago
Loading order of `TwoBit` and `BioSequences` seems to matter.

github.com/BioJulia/TwoBit.jl - CiaranOMara opened this issue about 3 years ago
GzipDecompressorStream not defined

github.com/BioJulia/GenomicAnnotations.jl - jowch opened this issue about 3 years ago
Generic state machine library?

github.com/BioJulia/Automa.jl - jtrakk opened this issue about 3 years ago
GFF3 Record Encode Error in Attributes like ";product=xxx (a; b) xxx"

github.com/BioJulia/GFF3.jl - cihga39871 opened this issue about 3 years ago
Disallow record construction from anything

github.com/BioJulia/FASTX.jl - jakobnissen opened this pull request about 3 years ago
how to use @threads to use multithreads when reading BAM file

github.com/BioJulia/XAM.jl - panxiaoguang opened this issue about 3 years ago
Update the alignment figure

github.com/BioJulia/BioAlignments.jl - alyst opened this pull request about 3 years ago
Update docs with alignment position

github.com/BioJulia/BioAlignments.jl - alyst opened this pull request about 3 years ago
Release/v2.0.5

github.com/BioJulia/GenomicFeatures.jl - CiaranOMara opened this pull request about 3 years ago
More conservative autodetection of sequence type

github.com/BioJulia/FASTX.jl - jakobnissen opened this issue about 3 years ago
Add more SubstitutionMatrix operations

github.com/BioJulia/BioAlignments.jl - timholy opened this pull request about 3 years ago
CompatHelper: add new compat entry for SuffixArrays at version 1, (keep existing compat)

github.com/BioJulia/FMIndexes.jl - github-actions[bot] opened this pull request about 3 years ago
CompatHelper: add new compat entry for IndexableBitVectors at version 1, (keep existing compat)

github.com/BioJulia/FMIndexes.jl - github-actions[bot] opened this pull request about 3 years ago
CompatHelper: add new compat entry for Humanize at version 1, (keep existing compat)

github.com/BioJulia/FMIndexes.jl - github-actions[bot] opened this pull request about 3 years ago
Add CI

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

github.com/BioJulia/FMIndexes.jl - jakobnissen opened this issue about 3 years ago
Fix constructor for String

github.com/BioJulia/FMIndexes.jl - jakobnissen opened this pull request about 3 years ago
Handling of chromosomes not in index

github.com/BioJulia/Indexes.jl - rulixxx opened this issue about 3 years ago
Running past the end of a BED

github.com/BioJulia/Indexes.jl - rulixxx opened this issue about 3 years ago
custom ordering of chromosomes

github.com/BioJulia/GenomicFeatures.jl - rulixxx opened this issue about 3 years ago
Bug in `OverlapAlignment`

github.com/BioJulia/BioAlignments.jl - jakobnissen opened this issue about 3 years ago
multiple allele separated by semicolon in ALT field

github.com/BioJulia/GeneticVariation.jl - marbeno opened this issue about 3 years ago
Ordering of genomic intervals only works as expected when parameterised by the same type

github.com/BioJulia/GenomicFeatures.jl - owensnick opened this issue about 3 years ago
[feature] PCA and DAPC

github.com/BioJulia/PopGen.jl - pdimens opened this issue about 3 years ago
permutations for fst shuffle indices and return views

github.com/BioJulia/PopGen.jl - pdimens opened this issue about 3 years ago
CompatHelper: bump compat for BioSymbols to 5, (keep existing compat)

github.com/BioJulia/BioSequences.jl - github-actions[bot] opened this pull request about 3 years ago
CompatHelper: bump compat for BioSymbols to 5, (keep existing compat)

github.com/BioJulia/BioSequences.jl - github-actions[bot] opened this pull request about 3 years ago
Add workflow for downstream tests

github.com/BioJulia/BioSymbols.jl - CiaranOMara opened this pull request about 3 years ago
WIP: Test bonanza for v3

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

github.com/BioJulia/BioSequences.jl - jakobnissen opened this pull request about 3 years ago
Clarify comparison to sequences in docs

github.com/BioJulia/BioSequences.jl - jakobnissen opened this pull request about 3 years ago
Rename stringbyte and avoid pirating BioSymbols

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

github.com/BioJulia/BioSymbols.jl - jakobnissen opened this pull request about 3 years ago
The API of accessing fields of BioAlignments

github.com/BioJulia/BioAlignments.jl - jakobnissen opened this issue about 3 years ago
[feature] standardize function names

github.com/BioJulia/PopGen.jl - pdimens opened this issue about 3 years ago
Include comparison example

github.com/BioJulia/BioSequences.jl - CiaranOMara opened this issue about 3 years ago
Don't recommend users engage in type piracy with `stringbyte`

github.com/BioJulia/BioSequences.jl - jakobnissen opened this issue about 3 years ago
Fix REPL blocks in docs

github.com/BioJulia/BioSequences.jl - jakobnissen opened this pull request about 3 years ago
Remove sequence conversion to/from String and Vector

github.com/BioJulia/BioSequences.jl - jakobnissen opened this pull request about 3 years ago
errors in docs: random kmers

github.com/BioJulia/BioSequences.jl - EvoArt opened this issue about 3 years ago
Add parsing of BioSequence, simplify some printing

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

github.com/BioJulia/BioSequences.jl - jakobnissen opened this pull request about 3 years ago
Improve documentation of flag function

github.com/BioJulia/XAM.jl - jakobnissen opened this pull request about 3 years ago
Export all user-facing functions

github.com/BioJulia/FASTX.jl - jakobnissen opened this pull request about 3 years ago
Why export only a few names?

github.com/BioJulia/FASTX.jl - jakobnissen opened this issue about 3 years ago
Allow chain id to be assigned with chainid!()

github.com/BioJulia/BioStructures.jl - gusennan opened this pull request about 3 years ago
Add docstring to describe functionality

github.com/BioJulia/BioSymbols.jl - jamiecm17 opened this pull request about 3 years ago
Test status check

github.com/BioJulia/GenomicFeatures.jl - CiaranOMara opened this pull request about 3 years ago
Test downstream error handling

github.com/BioJulia/GenomicFeatures.jl - CiaranOMara opened this pull request about 3 years ago
Request: Explain populations!(::Vector) better

github.com/BioJulia/PopGen.jl - jakobnissen opened this issue about 3 years ago
Have accesor functions return views?

github.com/BioJulia/FASTX.jl - jakobnissen opened this issue about 3 years ago
Add workflow for downstream tests

github.com/BioJulia/BioSequences.jl - CiaranOMara opened this pull request about 3 years ago
Improve docstrings and changelog slightly

github.com/BioJulia/BioSequences.jl - jakobnissen opened this pull request about 3 years ago
Add workflow for downstream tests

github.com/BioJulia/Automa.jl - CiaranOMara opened this pull request about 3 years ago
CompatHelper: bump compat for MetaGraphs to 0.7, (keep existing compat)

github.com/BioJulia/BioStructures.jl - github-actions[bot] opened this pull request about 3 years ago
Make `seqname` consistent with BioJulia ecosystem

github.com/BioJulia/XAM.jl - CiaranOMara opened this issue about 3 years ago
Add an eof block check

github.com/BioJulia/BGZFStreams.jl - CiaranOMara opened this pull request about 3 years ago
Search API redo

github.com/BioJulia/BioSequences.jl - TransGirlCodes opened this pull request about 3 years ago
What does the two integer fields in `Alignment` do?

github.com/BioJulia/BioAlignments.jl - jakobnissen opened this issue about 3 years ago
CompatHelper: add new compat entry for PopGenCore at version 0.2, (keep existing compat)

github.com/BioJulia/PopGen.jl - github-actions[bot] opened this pull request about 3 years ago
CompatHelper: add new compat entry for Reexport at version 1, (keep existing compat)

github.com/BioJulia/PopGen.jl - github-actions[bot] opened this pull request about 3 years ago
CompatHelper: add new compat entry for BioSequences at version 2, (keep existing compat)

github.com/BioJulia/Kmers.jl - github-actions[bot] opened this pull request about 3 years ago
Add `findall` methods

github.com/BioJulia/BioSequences.jl - CiaranOMara opened this pull request about 3 years ago
Allow parsing FASTA record with no sequence

github.com/BioJulia/FASTX.jl - jakobnissen opened this pull request over 3 years ago
CompatHelper: bump compat for PopGenCore to 0.2, (keep existing compat)

github.com/BioJulia/PopGen.jl - github-actions[bot] opened this pull request over 3 years ago
CompatHelper: add new compat entry for PopGenCore at version 0.2, (keep existing compat)

github.com/BioJulia/PopGen.jl - github-actions[bot] opened this pull request over 3 years ago
Remove dependency on StableRNGs

github.com/BioJulia/BioSequences.jl - jakobnissen opened this pull request over 3 years ago
Stop shipping with StableRNGs?

github.com/BioJulia/BioSequences.jl - jakobnissen opened this issue over 3 years ago
No version for Julia 1.6.1

github.com/BioJulia/BioSequences.jl - ammonite opened this issue over 3 years ago
No version for Julia 1.6.1

github.com/BioJulia/BioSequences.jl - ammonite opened this issue over 3 years ago
Secondary Structure Information

github.com/BioJulia/BioStructures.jl - emrekuecuek opened this issue over 3 years ago
[feature] locus-by-locus pairwise FST

github.com/BioJulia/PopGen.jl - pdimens opened this issue over 3 years ago
CompatHelper: bump compat for CSV to 0.9, (keep existing compat)

github.com/BioJulia/PopGenCore.jl - github-actions[bot] opened this pull request over 3 years ago
overload getindex to allow PopData filtering like a normal dataframe

github.com/BioJulia/PopGenCore.jl - pdimens opened this issue over 3 years ago
CompatHelper: add new compat entry for CodecZlib at version 0.7, (keep existing compat)

github.com/BioJulia/PopGenCore.jl - github-actions[bot] opened this pull request over 3 years ago
CompatHelper: add new compat entry for VariantCallFormat at version 0.5, (keep existing compat)

github.com/BioJulia/PopGenCore.jl - github-actions[bot] opened this pull request over 3 years ago
CompatHelper: add new compat entry for Reexport at version 1, (keep existing compat)

github.com/BioJulia/PopGen.jl - github-actions[bot] opened this pull request over 3 years ago
CompatHelper: add new compat entry for PopGenCore at version 0.1, (keep existing compat)

github.com/BioJulia/PopGen.jl - github-actions[bot] opened this pull request over 3 years ago
TagBot trigger issue

github.com/BioJulia/SubstitutionModels.jl - JuliaTagBot opened this issue over 3 years ago
Constructor consistency/documentation fix

github.com/BioJulia/SubstitutionModels.jl - jangevaare opened this pull request over 3 years ago
Fix package CI/update actions, and update [compat]

github.com/BioJulia/SubstitutionModels.jl - jangevaare opened this pull request over 3 years ago
CompatHelper: bump compat for BioSymbols to 5, (keep existing compat)

github.com/BioJulia/SubstitutionModels.jl - github-actions[bot] opened this pull request over 3 years ago
CompatHelper: bump compat for StaticArrays to 1, (keep existing compat)

github.com/BioJulia/SubstitutionModels.jl - github-actions[bot] opened this pull request over 3 years ago
[feature] speed up fst permutations

github.com/BioJulia/PopGen.jl - pdimens opened this issue over 3 years ago
Is there any function available in Phylogenies.jl to read phylogenetic trees from xml file?

github.com/BioJulia/Phylogenies.jl - efmanu opened this issue over 3 years ago
[bug] write_to for structure format "filename" kwarg error

github.com/BioJulia/PopGenCore.jl - pdimens opened this issue over 3 years ago
Optimize away dict lookup when possible

github.com/BioJulia/Automa.jl - jakobnissen opened this pull request over 3 years ago
Optimize away dict lookup at machine exit

github.com/BioJulia/Automa.jl - jakobnissen opened this issue over 3 years ago
Allow construction of `RegExp` from invalid UTF-8 strings

github.com/BioJulia/Automa.jl - jakobnissen opened this issue over 3 years ago
Factor out transcoding streams dependency

github.com/BioJulia/Automa.jl - jakobnissen opened this issue over 3 years ago
Shift-based tables for small machines

github.com/BioJulia/Automa.jl - jakobnissen opened this issue over 3 years ago
CompatHelper: bump compat for BioSymbols to 5, (keep existing compat)

github.com/BioJulia/BioSequences.jl - github-actions[bot] opened this pull request over 3 years ago
[bug] structure IO extremely slow for larger data

github.com/BioJulia/PopGenCore.jl - pdimens opened this issue over 3 years ago
`ref2seq` returns a position outside of the sequence length

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

github.com/BioJulia/PopGenCore.jl - JuliaTagBot opened this issue over 3 years ago