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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

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github.com/BioJulia/BioSequences.jl - de8981366f8f3541f85545abec9de10ec035cbdf authored over 2 years ago by Ciarán O’Mara <[email protected]>
Extract `ExactSearchQuery` query for consistency with other examples

github.com/BioJulia/BioSequences.jl - 465a8c66ee0e4d81edde1d2f533bb0e752a2164d authored over 2 years ago by Ciarán O’Mara <[email protected]>
Add doctests to CI

github.com/BioJulia/BioSequences.jl - a1a6b04d3e63952df7b019d4c00efd002f50d944 authored over 2 years ago by Ciarán O’Mara <[email protected]>
Add symbol search section

github.com/BioJulia/BioSequences.jl - 853da8f67acfc224fd662f5ec301227bece5f7fb authored over 2 years ago by Ciarán O’Mara <[email protected]>
Increment `Documenter` compat

github.com/BioJulia/BioSequences.jl - ad9193cb4fecb8b89e0aef2a3935fb453976cd01 authored over 2 years ago by Ciarán O’Mara <[email protected]>
Doctest corrections

github.com/BioJulia/BioSequences.jl - 7385c1b9a26f2f6fefe2066e483ef11f1abf2465 authored over 2 years ago by Ciarán O’Mara <[email protected]>
Add tests for Variation parsing

github.com/BioJulia/SequenceVariation.jl - 6bc1528d18ac2bbda9f48c2ebffe2cb51201e9a0 authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Add accessor functions for Variation properties

github.com/BioJulia/SequenceVariation.jl - 2d05b233a9222c925aadcd2b1b2155d5612904ee authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Add accessor functions for Edit properties

github.com/BioJulia/SequenceVariation.jl - 1e6f6ea0756ad73d04da5c018e1939ff2af3cdb6 authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Add BioGenerics dependency

github.com/BioJulia/SequenceVariation.jl - 101f4016353ea4e47a7e36d85695e6adfbcfe05b authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Add test dependencies to project file

github.com/BioJulia/SequenceVariation.jl - 9967ff4df26f2639a7815536f62dbe2b2aaac0de authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Add Variation constructor based on edit parsing

github.com/BioJulia/SequenceVariation.jl - 76d5b6059e922dc80f68ee0aca7fa384242576b4 authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Merge pull request #105 from BioJulia/compathelper/new_version/2022-06-07-01-53-48-361-04287279668

CompatHelper: add new compat entry for TSne at version 1, (keep existing compat)

github.com/BioJulia/PopGen.jl - 808da81a3a116b4b219acf9f282c891d9c58eaa9 authored over 2 years ago by Pavel V. Dimens <[email protected]>
Fix ambiguity errors (#235)

Fix ambiguity errors

Julia 1.8 introduces LazyString, which is useful in error throwing code....

github.com/BioJulia/BioSequences.jl - bf4aac5ada8d7cbbd2020c85113ebbd19620aa6b authored over 2 years ago by Jakob Nybo Nissen <[email protected]>
Fix minor bugs (#22)

github.com/BioJulia/Kmers.jl - a3348abcce0d55137d116d89b1ecdf0cd336dfc8 authored over 2 years ago by Jakob Nybo Nissen <[email protected]>
Allow join to work with BioSymbol (#234)

Previously, it was only possible to join BioSequences. Now, one can call
join(LongRNA{2}, (RNA_...

github.com/BioJulia/BioSequences.jl - f12d64bcae4b65598076216945c0fa5393052653 authored over 2 years ago by Jakob Nybo Nissen <[email protected]>
Kmer Slicing (#16)

github.com/BioJulia/Kmers.jl - 5ab500b725f89521e23d57541ca8658124b3338d authored over 2 years ago by Sabrina Jaye Ward <[email protected]>
Clean-up, tests (#7)

* add binder badge to readme

* change name in readme

* try to make module

* try adding ...

github.com/BioJulia/BioTutorials - f24f37186a74ed1b9558e8e6e11bb98367462254 authored over 2 years ago by Kevin Bonham <[email protected]>
[WIP] Updates (#4)

* begin updates

* rename folders

* let's use literate rather than pluto

* update pairwi...

github.com/BioJulia/BioTutorials - aa355e06b47f6d700dafb7a36b25353a9dbe9870 authored over 2 years ago by Kevin Bonham <[email protected]>
Merge pull request #72 from CiaranOMara/develop

- Increments BioSequences compatibility to v3.
- Increments BioSymbols compatibility to v5.
- ...

github.com/BioJulia/BioAlignments.jl - 25602e1f5834b2749dd17df291200c572b1e3a10 authored over 2 years ago by Ciarán O'Mara <[email protected]>
Merge pull request #72 from CiaranOMara/develop

- Increments BioSequences compatibility to v3.
- Increments BioSymbols compatibility to v5.
- ...

github.com/BioJulia/BioAlignments.jl - ed087374d3dc199f35fc02a45a974d1e67f01898 authored over 2 years ago by Ciarán O'Mara <[email protected]>
CHANGELOG entries

github.com/BioJulia/BioAlignments.jl - 8125f960dc85b34a001d46d3c6b948d4bad315ca authored over 2 years ago by Ciarán O’Mara <[email protected]>
Merge pull request #78 from CiaranOMara/doctests

- Include doctests as part of the unit tests.
- Doctest corrections.

github.com/BioJulia/BioAlignments.jl - a5bba8e5833ea4ac8b10d12c78e43bdae727108a authored over 2 years ago by Ciarán O'Mara <[email protected]>
Merge pull request #77 from CiaranOMara/housekeeping

- Backfill CHANGELOG entries.
- Updates CI.

github.com/BioJulia/BioAlignments.jl - af441d326499924d026ba257d548e3fa491656a1 authored over 2 years ago by Ciarán O'Mara <[email protected]>
Doctest corrections

github.com/BioJulia/BioAlignments.jl - 7e6d24b20de7438ec4997022afead486ef1bd9fd authored over 2 years ago by Ciarán O’Mara <[email protected]>
Adjust test matrix for minimum compatibility

BioSequences v3 requires julia v1.6.

github.com/BioJulia/BioAlignments.jl - 9a61761d841c3131e43b74b42818dab0f7248dc3 authored over 2 years ago by Ciarán O’Mara <[email protected]>
Remove doctest version adjustments

github.com/BioJulia/BioAlignments.jl - 6e1a5484ea5b01c180f40435a8f080d299217edd authored over 2 years ago by Ciarán O’Mara <[email protected]>
Increment compatibilities for BioSequences v3

github.com/BioJulia/BioAlignments.jl - ff57108c89b779908ed9b1e2a400a45affbf68ce authored over 2 years ago by Ciarán O’Mara <[email protected]>
Merge pull request #78 from CiaranOMara/doctests

- Include doctests as part of the unit tests.
- Doctest corrections.

github.com/BioJulia/BioAlignments.jl - 4045711665388a66d5ba5b2efead361569a7d371 authored over 2 years ago by Ciarán O'Mara <[email protected]>
CHANGELOG entries

github.com/BioJulia/BioAlignments.jl - 30e34fc41b93d85e1aca0fea440bf4f271e31928 authored over 2 years ago by Ciarán O’Mara <[email protected]>
Include doctests as part of the unit tests

github.com/BioJulia/BioAlignments.jl - fceeeaf5939621daf03307f8d1664fd0632cb08b authored over 2 years ago by Ciarán O’Mara <[email protected]>
Doctest corrections

github.com/BioJulia/BioAlignments.jl - fd633913ee242545a6a4bec4bda414742348e6ee authored over 2 years ago by Ciarán O’Mara <[email protected]>
Merge pull request #77 from CiaranOMara/housekeeping

- Backfill CHANGELOG entries.
- Updates CI.

github.com/BioJulia/BioAlignments.jl - 84b0d903e80c288a81c9f671c7e8216633ebe49d authored over 2 years ago by Ciarán O'Mara <[email protected]>
Merge pull request #1 from BioJulia/rollout-contributing

Contributing files rollout

github.com/BioJulia/BioTutorials - f3be56c349f899e956b49986fe34e8b13bd66860 authored over 2 years ago by Kevin Bonham <[email protected]>
CHANGELOG entries

github.com/BioJulia/BioAlignments.jl - 8f97073c82934d9fd39d4981f0f9fa002d889faa authored over 2 years ago by Ciarán O’Mara <[email protected]>
Add julia v1.6 to test matrix

github.com/BioJulia/BioAlignments.jl - 9c7f286cca53cc9d9e8b875f36c9c00193c89c59 authored over 2 years ago by Ciarán O’Mara <[email protected]>
Update workflows

- Update CompatHelper workflow.
- Update TagBot workflow.
- Update docs job in CI workflow.
- Lo...

github.com/BioJulia/BioAlignments.jl - 4a5af007cd189b4436c474960788e7862923c93c authored over 2 years ago by Ciarán O’Mara <[email protected]>
Sequence hashing: Bugfix and slight simplification (#229)

* Sequence hashing: Bugfix and slight simplification

Slightly simplify hashing code and fix a...

github.com/BioJulia/BioSequences.jl - fe5aabd193ffacfc1f9fdfc5f4bef8f991f17165 authored over 2 years ago by Jakob Nybo Nissen <[email protected]>
CompatHelper: add new compat entry for TSne at version 1, (keep existing compat)

github.com/BioJulia/PopGen.jl - 7b85048da1142d0d22e7bd1a6b667af14de0fa66 authored over 2 years ago by CompatHelper Julia <[email protected]>
Fixup docs

github.com/BioJulia/Kmers.jl - f8ea398015fa384728c611b900d639ba46f73036 authored over 2 years ago by Ben J. Ward <[email protected]>
Fixup iterator constructors

github.com/BioJulia/Kmers.jl - 014b50323670956bae61bdff42bd62c1a63a5920 authored over 2 years ago by Ben J. Ward <[email protected]>
update authors

github.com/BioJulia/BioAlignments.jl - 8c978d29b95ce3eb036cf7ed1c65b2967c354e04 authored over 2 years ago by Kevin Bonham <[email protected]>
Merge pull request #71 from CiaranOMara/tagbot

Add ssh key to TagBot workflow

github.com/BioJulia/BioAlignments.jl - e578e83fb5327491dacb788cc44087d810e93fe7 authored over 2 years ago by Ciarán O'Mara <[email protected]>
Add Zenodo badge

github.com/BioJulia/BioAlignments.jl - c3b9052f9174266ab8e9a33d6e3c66deadbfbd01 authored over 2 years ago by Kevin Bonham <[email protected]>
Remove Gitter chat links

github.com/BioJulia/BioAlignments.jl - e9b5c578347c45540cabb9d02db59649881a2840 authored over 2 years ago by Ciarán O’Mara <[email protected]>
Merge pull request #70 from CiaranOMara/develop

Add downstream tests

github.com/BioJulia/BioAlignments.jl - f9a84fe6493c497fd75c85f32e375064f48a7dd0 authored over 2 years ago by Ciarán O'Mara <[email protected]>
Merge pull request #53 from jakobnissen/master

Allow compact printing of alignments

github.com/BioJulia/BioAlignments.jl - cdfa4529fd2d8a5a399c69efb56279a9bef67ac3 authored over 2 years ago by Jakob Nybo Nissen <[email protected]>
Update documentation

github.com/BioJulia/Kmers.jl - fb14c7adaf51196766a87c1c9ca35f41a5ece93c authored over 2 years ago by Ben J. Ward <[email protected]>
Merge pull request #50 from alyst/reinstate_master

Prepare for minor release

github.com/BioJulia/BioAlignments.jl - 0c54bfe14ed9acd93e7a8a7757b4b747a03fe898 authored over 2 years ago by Jakob Nybo Nissen <[email protected]>
add t-sne

github.com/BioJulia/PopGen.jl - b1b932131cc3d2da3f45b6a53b147f98ef1bbf28 authored over 2 years ago by Pavel Dimens <[email protected]>
Enable SpacedKmers to mix nucleic acid alphabets

github.com/BioJulia/Kmers.jl - d0341e03debcf723e8bc595fc2ec79eb54f6a71c authored over 2 years ago by Ben J. Ward <[email protected]>
Enable SpacedCanonicalKmers to mix nucleic acid alphabets

github.com/BioJulia/Kmers.jl - 5867c3695289e77472ef84b4eaa53ab8ed326b2c authored over 2 years ago by Ben J. Ward <[email protected]>
Fix small errors (#228)

github.com/BioJulia/BioSequences.jl - 26e05f723040bd6726ec1e9be37332fec1c4abab authored over 2 years ago by Jakob Nybo Nissen <[email protected]>
ishom logic more succinct

haploids as heterozygotes

github.com/BioJulia/PopGenCore.jl - b16bcead76c8392f063f4644680026e2a0d33c2b authored over 2 years ago by Pavel Dimens <[email protected]>
Merge branch 'canonical-bugfix'

github.com/BioJulia/BioSequences.jl - 40222aca06f24f0ac450185642718ad1b30d8e53 authored over 2 years ago by Ben J. Ward <[email protected]>
🐛 in iscanonical / canonical

Fixes #225

Add tests for edge case

Fixup

Fiixup

🐛 in iscanonical / canonical
Fixes #225

🐛 in...

github.com/BioJulia/BioSequences.jl - 41ff95257fe7b072fc7f824cc675759b64b32cea authored over 2 years ago by Ben J. Ward <[email protected]>
add bugs where not consistent with Coancestry

github.com/BioJulia/PopGen.jl - 16e2553e3d18939fd715029ef066fab90626f732 authored over 2 years ago by Pavel Dimens <[email protected]>
fixed LynchLi math

github.com/BioJulia/PopGen.jl - d806f94c10fb615932d382d2844871038310a14d authored over 2 years ago by Pavel Dimens <[email protected]>
add coancestry results for validation

github.com/BioJulia/PopGen.jl - b17f559967d361b1bd3b03edd9fc0aef07183ccc authored over 2 years ago by Pavel Dimens <[email protected]>
fix moran

github.com/BioJulia/PopGen.jl - 564327e90c42f68b2ecc8dac489b18b4a37d33d2 authored over 2 years ago by Pavel Dimens <[email protected]>
add simple test function

github.com/BioJulia/PopGen.jl - 6a83bdf4e9ff093d79d087e5a2058d79550e0941 authored over 2 years ago by Pavel Dimens <[email protected]>
tidy

github.com/BioJulia/PopGen.jl - 0ff7770399f125979fb3435bcc9dd1577304547f authored over 2 years ago by Pavel Dimens <[email protected]>
Add SpacedCanonicalKmers iterator

github.com/BioJulia/Kmers.jl - 33ac95a26b6ee1368b7f945dd340b7d7701dd3de authored over 2 years ago by Ben J. Ward <[email protected]>
split out

github.com/BioJulia/PopGen.jl - 58d6119cd5911118fd97efe58352972e6ef06cc7 authored over 2 years ago by Pavel Dimens <[email protected]>
split out estimators

github.com/BioJulia/PopGen.jl - 0698227b946e0f74465ab98a40a8375d32423aaf authored over 2 years ago by Pavel Dimens <[email protected]>
rm progressbar b/c its getting deprecated

github.com/BioJulia/PopGen.jl - 062034f786a8d35f0d406044638212e37c23efd7 authored over 2 years ago by Pavel Dimens <[email protected]>
add todo

github.com/BioJulia/PopGen.jl - c0c4d84d8344cd4cf9cc50e7594bc081120d8553 authored over 2 years ago by Pavel Dimens <[email protected]>
add kinship for specific samples

github.com/BioJulia/PopGen.jl - 1dcbefc31672674ef80f4801e7b880859b8c7e40 authored over 2 years ago by Pavel Dimens <[email protected]>
updates

github.com/BioJulia/PopGenCore.jl - 409c847e0e113a546b16e4938ed32c1007b035ae authored over 2 years ago by Pavel Dimens <[email protected]>
Merge pull request #104 from BioJulia/compathelper/new_version/2022-05-21-01-28-29-680-00083884516

CompatHelper: add new compat entry for StatsBase at version 0.33, (keep existing compat)

github.com/BioJulia/PopGen.jl - d04e18cf12d30bae0372bc1e5289594ddc9810d4 authored over 2 years ago by Pavel V. Dimens <[email protected]>
CompatHelper: add new compat entry for StatsBase at version 0.33, (keep existing compat)

github.com/BioJulia/PopGen.jl - 839d67d62fd94895bcc6a5b4e552d45dc2b1ee86 authored over 2 years ago by CompatHelper Julia <[email protected]>
fix test

github.com/BioJulia/PopGenCore.jl - f9261630e47ee8a03f575222bbf8065deb3dd00a authored over 2 years ago by Pavel Dimens <[email protected]>
add ZScoreTransform (oops)

github.com/BioJulia/PopGenCore.jl - b914682122aea70566ac0398c2ed622d319b996c authored over 2 years ago by Pavel Dimens <[email protected]>
add correct StatsBase deps

github.com/BioJulia/PopGenCore.jl - b29bd6f55eaa45a2cd220047477588c7ee8862b9 authored over 2 years ago by Pavel Dimens <[email protected]>
remove PopGen. prefix

github.com/BioJulia/PopGenCore.jl - 012d0c0eedae27851f9e828a9b340cd20f39e9a4 authored over 2 years ago by Pavel Dimens <[email protected]>
move allelematrix* operations to Core

github.com/BioJulia/PopGen.jl - c1fcbe44d95d4184763c7fc11eaf8e124fa708f8 authored over 2 years ago by Pavel Dimens <[email protected]>
move allelematrix* methods to Core

github.com/BioJulia/PopGenCore.jl - 8330caad482bb2a338046e3e9e4e9381dd4a8b6d authored over 2 years ago by Pavel Dimens <[email protected]>
promote type to include missing

github.com/BioJulia/PopGen.jl - 20877ca2ed1dad016b8bb140c6c4494a67c81048 authored over 2 years ago by Pavel Dimens <[email protected]>
slighty more sane

github.com/BioJulia/PopGen.jl - af2c3a73180a6b3f24fe4aaf35141d19c078588d authored over 2 years ago by Pavel Dimens <[email protected]>
fix test

github.com/BioJulia/PopGen.jl - a191f3a154dfcfcd43811ff22950475dc62832d0 authored over 2 years ago by Pavel Dimens <[email protected]>
minor formatting

github.com/BioJulia/PopGen.jl - cad87d3d4264f9e645e3d48994bed9c9f65768e6 authored over 2 years ago by Pavel Dimens <[email protected]>
fix pairwiseidential(PopData, samplenames)

github.com/BioJulia/PopGen.jl - 871a85ca5cc399d54f41657ab0a1a8c5a3da799a authored over 2 years ago by Pavel Dimens <[email protected]>
fix project.toml

github.com/BioJulia/PopGen.jl - 1ef1d450fba6fb6beb9fc1ffec72c7f1aba014c8 authored over 2 years ago by Pavel Dimens <[email protected]>
make nei fst loop-based

github.com/BioJulia/PopGen.jl - f86dbe57f19cc336216229470779ec6f78caf67f authored over 2 years ago by Pavel Dimens <[email protected]>
pairwise FST improvements

github.com/BioJulia/PopGen.jl - 3468fec09c52ccdd4ee53c8c94705dd88ecf0b8d authored over 2 years ago by Pavel Dimens <[email protected]>
Merge pull request #103 from BioJulia/compathelper/new_version/2022-05-18-01-47-58-672-01729527574

CompatHelper: add new compat entry for Term at version 0.3, (keep existing compat)

github.com/BioJulia/PopGen.jl - 664534bf0d206fc6c66fe6851929bd6becdaf3e7 authored over 2 years ago by Pavel V. Dimens <[email protected]>
Merge pull request #102 from BioJulia/compathelper/new_version/2022-05-18-01-47-43-394-02241188886

CompatHelper: add new compat entry for OnlineStats at version 1, (keep existing compat)

github.com/BioJulia/PopGen.jl - c5944f70c5d3ebf464c6ef4c212a8b5038c390ba authored over 2 years ago by Pavel V. Dimens <[email protected]>
CompatHelper: add new compat entry for Term at version 0.3, (keep existing compat)

github.com/BioJulia/PopGen.jl - 31b9272cc104cabd43ad941479bd33e49827168e authored over 2 years ago by CompatHelper Julia <[email protected]>
CompatHelper: add new compat entry for OnlineStats at version 1, (keep existing compat)

github.com/BioJulia/PopGen.jl - 28654c558e731e3e5a1492547595b14321684262 authored over 2 years ago by CompatHelper Julia <[email protected]>
Update downstream.yml

github.com/BioJulia/PopGenCore.jl - 2e9746ccf784e0617c9ad8b1921341a3cb56fd94 authored over 2 years ago by Pavel V. Dimens <[email protected]>
Somehow PopGen doesnt use statsbase anymore

github.com/BioJulia/PopGen.jl - 2cf0cc8ef8b1b43d92d388e7a070e2f97def37a0 authored over 2 years ago by Pavel Dimens <[email protected]>
fix more pkgtests

github.com/BioJulia/PopGenCore.jl - 050f69e5510941bcead427ce4076ae2482a76b1e authored over 2 years ago by Pavel Dimens <[email protected]>
few extra type assertions

github.com/BioJulia/PopGenCore.jl - a97dc186aadfd4971ddecc996c010c734c6821fb authored over 2 years ago by Pavel Dimens <[email protected]>
update functoin defintitions and tests

github.com/BioJulia/PopGenCore.jl - 6332b77f52919411e6e5c478e4bd57dca2138ac2 authored over 2 years ago by Pavel Dimens <[email protected]>
update FST api to be consistent with new kinship API

github.com/BioJulia/PopGen.jl - 2b1ade0c2a59135f49c64ba34900ea485d246de4 authored over 2 years ago by Pavel Dimens <[email protected]>
change progressmeter to term.jl progress

github.com/BioJulia/PopGen.jl - 12f03ca52816b4d15c44abee0bd4928057bdb092 authored over 2 years ago by Pavel Dimens <[email protected]>
new kinship api

github.com/BioJulia/PopGen.jl - 7fd504333bfffd4f2ac489c98b05bb800ce5c491 authored over 2 years ago by Pavel Dimens <[email protected]>
add upper/lowertri2vec

github.com/BioJulia/PopGenCore.jl - 60a331c2f7c4cff1fd30c974a2897e18b5567171 authored over 2 years ago by Pavel Dimens <[email protected]>
experiment with onlinestats.jl

github.com/BioJulia/PopGen.jl - ae5eee11ac7f8718fb605e026d914124914f26e9 authored over 2 years ago by Pavel Dimens <[email protected]>
Add 4 to 2 bit nuc iteration for EveryCanonicalKmer

github.com/BioJulia/Kmers.jl - 9b90ad7970375f666aa81a96d0af5fda59c549d9 authored over 2 years ago by Ben J. Ward <[email protected]>