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github.com/BioJulia/BioSequences.jl

Biological sequences for the julia language
https://github.com/BioJulia/BioSequences.jl

PFM just accepts vectors?

felipe-mansoldo opened this issue 2 months ago
Upgrade CI

jakobnissen opened this pull request 4 months ago
Flip sticker

jakobnissen opened this pull request 4 months ago
Add new ncbi translation code

camilogarciabotero opened this pull request 4 months ago
Drop CI for MacOS Julia 1.5

jakobnissen opened this pull request 5 months ago
Precompute ExactSearchQuery faster

jakobnissen opened this pull request 5 months ago
Update `ispalindromic`

jakobnissen opened this pull request 7 months ago
`ispalindromic` with respect to `reverse` or `reverse_complement`?

Seelengrab opened this issue 7 months ago
A strange behavior in approximate searches

panxiaoguang opened this issue 8 months ago
Update docs with recipes pages

jakobnissen opened this pull request 9 months ago
Document string literal macro

jakobnissen opened this pull request 10 months ago
How should one search for ORFs?

jakobnissen opened this issue 12 months ago
Update issue and PR template to match BioJulia guidelines

jakobnissen opened this pull request 12 months ago
add predicate method and tests

camilogarciabotero opened this pull request 12 months ago
Create and export a generic test biosequence

jakobnissen opened this issue 12 months ago
Get this package back into PkgEval

jakobnissen opened this issue almost 1 year ago
Run CI on Julia 1.5

jakobnissen opened this pull request about 1 year ago
Bump Julia compat to 1.6

jakobnissen opened this pull request about 1 year ago
[RFC]: Add functions `guess_parse` and `guess_alphabet`

jakobnissen opened this pull request about 1 year ago
Do not fail CI if codecov falls

jakobnissen opened this pull request about 1 year ago
Define compat for Random

jakobnissen opened this pull request about 1 year ago
Consider making Random a weak dep

jakobnissen opened this issue about 1 year ago
Allow translation of LongSubSeq

jakobnissen opened this pull request about 1 year ago
Remove downstream BioMakie CI

jakobnissen opened this pull request about 1 year ago
Bump Documenter to 1.0

jakobnissen opened this pull request about 1 year ago
A few fixes for tests

jakobnissen opened this pull request about 1 year ago
Feature: concatenate bases with sequences

BioTurboNick opened this issue about 1 year ago
Fix tests

jakobnissen opened this pull request about 1 year ago
WIP: Kmers.jl compatibility

jakobnissen opened this pull request about 1 year ago
Decode nocheck

jakobnissen opened this pull request about 1 year ago
Improve heuristics of translating ambiguous nucs

jakobnissen opened this pull request about 1 year ago
Can we skip check in `decode`?

jakobnissen opened this issue about 1 year ago
Error when translating gaps

jakobnissen opened this pull request over 1 year ago
Translation Issue arising from `isambiguous(DNA_Gap) == false`

chelate opened this issue over 1 year ago
domain name of this repo should be updated

ctarn opened this issue over 1 year ago
Use lowercase in DNA sequences

ruysan opened this issue over 1 year ago
Bump version to v3.1.4

jakobnissen opened this pull request over 1 year ago
Migrate from SnoopPrecompile to PrecompileTools

timholy opened this pull request over 1 year ago
Update URLs from biojulia.net to biojulia.dev

kescobo opened this pull request over 1 year ago
Fix behavior of iterate on indices <= 0

cjprybol opened this pull request over 1 year ago
Add guessparse function

jakobnissen opened this pull request over 1 year ago
Record type inference

cjprybol opened this issue over 1 year ago
Improve error when mis-encoding LongDNA from byte-like inputs

jakobnissen opened this pull request over 1 year ago
Improve error message on encoding error

jakobnissen opened this issue over 1 year ago
Remove references to Random.GLOBAL_RNG

jakobnissen opened this pull request over 1 year ago
Allow translation of sequence views

jakobnissen opened this pull request over 1 year ago
Translate subsequence

jakobnissen opened this issue over 1 year ago
New Feature: Molecular weight calculations for BioSequences

benjaminlozanow opened this issue almost 2 years ago
Fix bug in zero_offset! called when materializing seqview

jakobnissen opened this pull request almost 2 years ago
Converting a LongSubSeq to LongSequence can give weird results

ian-small opened this issue almost 2 years ago
Stop pirating BioSymbols

jakobnissen opened this pull request almost 2 years ago
Fix typo

cossio opened this pull request about 2 years ago
Add SnoopPrecompile

jakobnissen opened this pull request about 2 years ago
Indexing with bool or integer vector does not work with seqview

jakobnissen opened this issue about 2 years ago
Improve robustness of rand tests

jakobnissen opened this pull request about 2 years ago
Vbump

jakobnissen opened this pull request about 2 years ago
Various small doc fixes

jakobnissen opened this pull request about 2 years ago
Add doctests to CI

jakobnissen opened this issue about 2 years ago
FASTA module not defined

dinesh110598 opened this issue about 2 years ago
Add rand!([::AbstractRNG], ::LongSequence, [::Sampler]) methods

jakobnissen opened this pull request over 2 years ago
Implement rand!

jakobnissen opened this issue over 2 years ago
Improve hasinterface(::Type{BioSequence})

jakobnissen opened this pull request over 2 years ago
CenteredSequence{A} type for comparing short reads padding with AA_Gap

gszep opened this issue over 2 years ago
Reset Julia compat to v1.5

jakobnissen opened this pull request over 2 years ago
Use naive hash fallback for BioSequence

jakobnissen opened this pull request over 2 years ago
Design of hash(::BioSequence). What to do?

jakobnissen opened this issue over 2 years ago
Schedule method for removal

CiaranOMara opened this pull request over 2 years ago
WIP: Add tryparse

jakobnissen opened this pull request over 2 years ago
Cosmetic changes in constructors

jakobnissen opened this pull request over 2 years ago
Use codeunits over unsafe_wrap

jakobnissen opened this pull request over 2 years ago
Add tryencode and trydecode

jakobnissen opened this pull request over 2 years ago
Doctests

CiaranOMara opened this pull request over 2 years ago
Documentation for `findall` method

CiaranOMara opened this pull request over 2 years ago
Fix ambiguity errors

jakobnissen opened this pull request over 2 years ago
Allow join to work with BioSymbol

jakobnissen opened this pull request over 2 years ago
Add iterate method for Alphabets

SabrinaJaye opened this pull request over 2 years ago
`Base.eltype(::Type{<:Alphabet})` violates `eltype` docstring

jakobnissen opened this issue over 2 years ago
`join(LongRNA{2}, (RNA_A,))` should work

jakobnissen opened this issue over 2 years ago
Sequence hashing: Bugfix and slight simplification

jakobnissen opened this pull request over 2 years ago
Fix small errors

jakobnissen opened this pull request over 2 years ago
🐛-fix iscanonical

SabrinaJaye opened this pull request over 2 years ago
🐛 in iscanonical / canonical

SabrinaJaye opened this pull request over 2 years ago
🐛 in iscanonical / canonical

SabrinaJaye opened this issue over 2 years ago
Add tryparse(::BioSequence, s::AbstractString) or similar

jakobnissen opened this issue over 2 years ago
[FR] add `Query` versions for `Base.count`

BeastyBlacksmith opened this issue over 2 years ago
What happened to DNAMer?

JokingHero opened this issue over 2 years ago
Loosen search iterator

CiaranOMara opened this pull request over 2 years ago
Add `findall` method

CiaranOMara opened this pull request over 2 years ago
add an `ispermitted` for Alphabets?

SabrinaJaye opened this issue over 2 years ago
Add `findall` method

CiaranOMara opened this pull request almost 3 years ago
Implement `findall`

jakobnissen opened this issue almost 3 years ago
LongDNA, LongRNA "not defined"

fpmenninger opened this issue almost 3 years ago
findnext, findprev broken ... possible to add findall?

fpmenninger opened this issue almost 3 years ago
Correct Julia compatibility entry

CiaranOMara opened this pull request almost 3 years ago
Small internal refactors

jakobnissen opened this pull request almost 3 years ago
TagBot trigger issue

JuliaTagBot opened this issue almost 3 years ago
Fix bugs in minimal Alphabet interface example

jakobnissen opened this pull request almost 3 years ago
Fix issues from v3/master merge

jakobnissen opened this pull request almost 3 years ago
Version 3 updates

SabrinaJaye opened this pull request almost 3 years ago
CompatHelper: bump compat for BioSymbols to 5, (keep existing compat)

github-actions[bot] opened this pull request almost 3 years ago