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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

switch testing to Julia 1.1 until dependencies resolved

github.com/BioJulia/BioStructures.jl - 59ea559fc354ab13dc3bb4b74524bd6f27f04e0a authored over 4 years ago by Joe Greener <[email protected]>
support newer BioSequences/BioAlignments, add threeletter_to_aa

github.com/BioJulia/BioStructures.jl - 19813c7f3860ec1292fab0ad65f3abb9217eaad4 authored over 4 years ago by Joe Greener <[email protected]>
Add docstring for type and add kmertype method

github.com/BioJulia/NTupleKmers.jl - c5e9bb8e653a043cbc903b0342db4ad0b31b0e52 authored over 4 years ago by Ben J. Ward <[email protected]>
Implement inbounds_getindex for the kmer type

github.com/BioJulia/NTupleKmers.jl - c873ef23574c3f256fc635d3b4ef20c273967fb1 authored over 4 years ago by Ben J. Ward <[email protected]>
First commit just to splurge some code on paper.

github.com/BioJulia/NTupleKmers.jl - 9d2d2b3d0f69554ddc8db69c62b3cceaab3024c6 authored over 4 years ago by Ben J. Ward <[email protected]>
Update Project.toml

github.com/BioJulia/BioSymbols.jl - 04ee588e51c65dd0beb5c56900569c9e829f6731 authored over 4 years ago by Ben J. Ward <[email protected]>
LTS support (#37)

* Support LTS

* Update .gitignore

* Update CI

github.com/BioJulia/BioSymbols.jl - e19b13cc609c1e5a040103d269448453aa25ce7b authored over 4 years ago by Ciarán O'Mara <[email protected]>
Create BenchmarkPlots.jl

github.com/BioJulia/PopGen.jl_archive - 602d0ead4c0d393b8528fb8796380042c5d0eaad authored over 4 years ago by Pavel Dimens <[email protected]>
Create BenchmarkPlots.jl

github.com/BioJulia/PopGen.jl - 602d0ead4c0d393b8528fb8796380042c5d0eaad authored over 4 years ago by Pavel Dimens <[email protected]>
Initial commit

github.com/BioJulia/NTupleKmers.jl - e98924bf75ec93ccca207f5cea4a91c21248618c authored over 4 years ago by Ben J. Ward <[email protected]>
move docs to separate branch

github.com/BioJulia/PopGen.jl - 87631784f91b3d00c55a4abe06fd22312bde85be authored over 4 years ago by Pavel Dimens <[email protected]>
move docs to separate branch

github.com/BioJulia/PopGen.jl_archive - 87631784f91b3d00c55a4abe06fd22312bde85be authored over 4 years ago by Pavel Dimens <[email protected]>
update docs

github.com/BioJulia/PopGen.jl_archive - f61ac5eae62a83f5d2a063afbd596b95ef944294 authored over 4 years ago by Pavel Dimens <[email protected]>
update docs

github.com/BioJulia/PopGen.jl - f61ac5eae62a83f5d2a063afbd596b95ef944294 authored over 4 years ago by Pavel Dimens <[email protected]>
update docs and by =

github.com/BioJulia/PopGen.jl - 599eb21b62ddb6268c89d49b12b22fc55b2fc888 authored over 4 years ago by Pavel Dimens <[email protected]>
update docs and by =

github.com/BioJulia/PopGen.jl_archive - 599eb21b62ddb6268c89d49b12b22fc55b2fc888 authored over 4 years ago by Pavel Dimens <[email protected]>
replace mode= with by=

github.com/BioJulia/PopGen.jl_archive - 3c339b98a52aff8d7f576f1a7854147eaa4bc29f authored over 4 years ago by Pavel Dimens <[email protected]>
replace mode= with by=

github.com/BioJulia/PopGen.jl - 3c339b98a52aff8d7f576f1a7854147eaa4bc29f authored over 4 years ago by Pavel Dimens <[email protected]>
update docs more

github.com/BioJulia/PopGen.jl - 518c980ee040deab583257dffc806e24e2e707c0 authored over 4 years ago by Pavel Dimens <[email protected]>
update docs more

github.com/BioJulia/PopGen.jl_archive - 518c980ee040deab583257dffc806e24e2e707c0 authored over 4 years ago by Pavel Dimens <[email protected]>
update docs

github.com/BioJulia/PopGen.jl_archive - 85441b868cb8c24278676ddac5b881e41ece9042 authored over 4 years ago by Pavel Dimens <[email protected]>
update docs

github.com/BioJulia/PopGen.jl - 85441b868cb8c24278676ddac5b881e41ece9042 authored over 4 years ago by Pavel Dimens <[email protected]>
Update ioUtils.jl

github.com/BioJulia/PopGen.jl - 19784f45aa92914f9cb7e24d49018acba9093465 authored over 4 years ago by Pavel Dimens <[email protected]>
Update ioUtils.jl

github.com/BioJulia/PopGen.jl_archive - 19784f45aa92914f9cb7e24d49018acba9093465 authored over 4 years ago by Pavel Dimens <[email protected]>
Update ioUtils.jl

github.com/BioJulia/PopGen.jl_archive - 95e8acc89e648f09766f04f409c188ec1dd1c4b9 authored over 4 years ago by Pavel Dimens <[email protected]>
Update ioUtils.jl

github.com/BioJulia/PopGen.jl - 95e8acc89e648f09766f04f409c188ec1dd1c4b9 authored over 4 years ago by Pavel Dimens <[email protected]>
Update .travis.yml

github.com/BioJulia/FASTX.jl - 2729dc00f4346672edef381e5248c8aa19d07541 authored over 4 years ago by Ben J. Ward <[email protected]>
Make ambiguity check optional

github.com/BioJulia/Automa.jl - bc71c6eabe70b0dfed1f72edf796321a93e55211 authored over 4 years ago by Jakob Nybo Nissen <[email protected]>
Update docs.yml

github.com/BioJulia/ReadDatastores.jl - eda468b11494199d18f58b698d7ad619bcf33cdd authored over 4 years ago by Ben J. Ward <[email protected]>
Update testing.yml

github.com/BioJulia/ReadDatastores.jl - 2eba10c47ff3a00226c30709228c5f622782745d authored over 4 years ago by Ben J. Ward <[email protected]>
Delete ci_prep.jl

github.com/BioJulia/ReadDatastores.jl - e96bb24440ae0a21da3084dd2dd2ddd4c9e8174e authored over 4 years ago by Ben J. Ward <[email protected]>
Update .travis.yml

github.com/BioJulia/ReadDatastores.jl - 7247ca48d9b125889d33b6ae27e5465b9081dad7 authored over 4 years ago by Ben J. Ward <[email protected]>
Update appveyor.yml

github.com/BioJulia/FASTX.jl - 400bf6dcc14216b3c56c5db48ccd7a48bc790cd6 authored over 4 years ago by Ben J. Ward <[email protected]>
add notes on reading gzipped files (#17)

github.com/BioJulia/FASTX.jl - 31061cdf3749baf62b40ef50cdc99a07672c1701 authored over 4 years ago by Kevin Bonham <[email protected]>
Update CompatHelper.yml

github.com/BioJulia/FASTX.jl - 4c99e033bbfdf7db0bb745fa9232b1256aa1fb6d authored over 4 years ago by Ben J. Ward <[email protected]>
Update Project.toml

github.com/BioJulia/PopGen.jl - d121bc3932451f1567b0a014ad27476b8fe56394 authored over 4 years ago by Pavel Dimens <[email protected]>
Update Project.toml

github.com/BioJulia/PopGen.jl_archive - d121bc3932451f1567b0a014ad27476b8fe56394 authored over 4 years ago by Pavel Dimens <[email protected]>
Delete genos.txt

github.com/BioJulia/PopGen.jl_archive - 23874bb54ae144dbb8caa64c7ebf260c270f78be authored over 4 years ago by Pavel V. Dimens <[email protected]>
Delete genos.txt

github.com/BioJulia/PopGen.jl - 23874bb54ae144dbb8caa64c7ebf260c270f78be authored over 4 years ago by Pavel V. Dimens <[email protected]>
Merge branch 'df_unstable' into dev

github.com/BioJulia/PopGen.jl - 78a2c5828ebdc9dce578ce9aa076fdd028641ec3 authored over 4 years ago by Pavel Dimens <[email protected]>
Merge branch 'df_unstable' into dev

github.com/BioJulia/PopGen.jl_archive - 78a2c5828ebdc9dce578ce9aa076fdd028641ec3 authored over 4 years ago by Pavel Dimens <[email protected]>
complete vcf and bcf importers

github.com/BioJulia/PopGen.jl_archive - 6d192f5b60243622b12a4ac169328994f1fd9440 authored over 4 years ago by Pavel Dimens <[email protected]>
complete vcf and bcf importers

github.com/BioJulia/PopGen.jl - 6d192f5b60243622b12a4ac169328994f1fd9440 authored over 4 years ago by Pavel Dimens <[email protected]>
rename GenotypeArray to GenoArray

also add PoolGenoArray alias

github.com/BioJulia/PopGen.jl - 6652ecd18fe94aaa5d8150ddd50bf22dd9ebe770 authored over 4 years ago by Pavel Dimens <[email protected]>
rename GenotypeArray to GenoArray

also add PoolGenoArray alias

github.com/BioJulia/PopGen.jl_archive - 6652ecd18fe94aaa5d8150ddd50bf22dd9ebe770 authored over 4 years ago by Pavel Dimens <[email protected]>
Merge pull request #2 from BioJulia/compathelper/new_version/2020-05-28-18-09-34-281-2821743422

CompatHelper: add new compat entry for "KmerAnalysis" at version "0.1"

github.com/BioJulia/KmerAnalysisMakie.jl - 98675166e57d7c1f93a4579f6832ba5b85cefa90 authored over 4 years ago by Ben J. Ward <[email protected]>
CompatHelper: add new compat entry for "KmerAnalysis" at version "0.1"

github.com/BioJulia/KmerAnalysisMakie.jl - 478ce764f085b17e102f19e6a7cd2de2cffd0df9 authored over 4 years ago by github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
finish updates to delimited

github.com/BioJulia/PopGen.jl_archive - fe1238a36898bf113b93a31a55253d4a10e94571 authored over 4 years ago by Pavel Dimens <[email protected]>
finish updates to delimited

github.com/BioJulia/PopGen.jl - fe1238a36898bf113b93a31a55253d4a10e94571 authored over 4 years ago by Pavel Dimens <[email protected]>
Optimize reduce_nodes

github.com/BioJulia/Automa.jl - 76c941f7cd74e1696288c947066ce42fffb649cd authored over 4 years ago by Jakob Nybo Nissen <[email protected]>
Merge remote-tracking branch 'origin/master'

github.com/BioJulia/KmerAnalysisMakie.jl - 56c143a46b1736a7ee49123e5abc603cbe1c0ab7 authored over 4 years ago by Ben J. Ward <[email protected]>
Add KmerAnalysis dependecy

github.com/BioJulia/KmerAnalysisMakie.jl - 1eae3ed13b0856b714de874a190e0ca761ccb0fa authored over 4 years ago by Ben J. Ward <[email protected]>
Update CompatHelper.yml

github.com/BioJulia/ReadDatastores.jl - 13de9b5c89bd0e87402de8fb084760369880c76d authored over 4 years ago by Ben J. Ward <[email protected]>
Update CompatHelper.yml

github.com/BioJulia/KmerAnalysisMakie.jl - 14131edf55dfde5a3b662135ab68a7504b5acc4e authored over 4 years ago by Ben J. Ward <[email protected]>
Update CompatHelper.yml

github.com/BioJulia/KmerAnalysis.jl - 5839e1b8b5059970c6d3080f9cba1e3cf73fe484 authored over 4 years ago by Ben J. Ward <[email protected]>
Update CompatHelper.yml

github.com/BioJulia/BioSequences.jl - 902f8bbd92d3805eb8741dda0717939f19fe4a3f authored over 4 years ago by Ben J. Ward <[email protected]>
Fixup README.md

github.com/BioJulia/KmerAnalysis.jl - f5ad9de4ecab044f863d17d8a2b95295046e5fa3 authored over 4 years ago by Ben J. Ward <[email protected]>
update hwe chisq to DataFrames API

github.com/BioJulia/PopGen.jl - cec77b7bdb08168a47de24c8d848301a38e59973 authored over 4 years ago by Pavel Dimens <[email protected]>
update hwe chisq to DataFrames API

github.com/BioJulia/PopGen.jl_archive - cec77b7bdb08168a47de24c8d848301a38e59973 authored over 4 years ago by Pavel Dimens <[email protected]>
Deprecate Package

github.com/BioJulia/MicrobiomePlots.jl - d10d47db20a1ebe15570e9b0987458d67191d3a8 authored over 4 years ago by Kevin Bonham <[email protected]>
Merge branch 'master' into compats

github.com/BioJulia/MicrobiomePlots.jl - 8bad6c8044244e6be7698e44128a33bc097be701 authored over 4 years ago by Kevin Bonham <[email protected]>
Update Heterozygosity.jl

github.com/BioJulia/PopGen.jl - fa2ff1e7e68c19b7948038cfa5f8187e5633a12c authored over 4 years ago by Pavel Dimens <[email protected]>
Update Heterozygosity.jl

github.com/BioJulia/PopGen.jl_archive - fa2ff1e7e68c19b7948038cfa5f8187e5633a12c authored over 4 years ago by Pavel Dimens <[email protected]>
Update PopGen.jl

github.com/BioJulia/PopGen.jl_archive - 6bfddcf4951a1407467bb8765ac15ee434fc8fcd authored over 4 years ago by Pavel Dimens <[email protected]>
Update PopGen.jl

github.com/BioJulia/PopGen.jl - 6bfddcf4951a1407467bb8765ac15ee434fc8fcd authored over 4 years ago by Pavel Dimens <[email protected]>
why 1.5?

github.com/BioJulia/MicrobiomePlots.jl - 9fccf76bcd0d8a7d71c448d731c7c9319d359f09 authored over 4 years ago by Kevin Bonham <[email protected]>
remove compat helper

github.com/BioJulia/MicrobiomePlots.jl - 337dc5089ac532638a381a565e9460eb2232cfbf authored over 4 years ago by Kevin Bonham <[email protected]>
Compatibility with earlier Julia versions

github.com/BioJulia/Automa.jl - c897d67484296df20b8c8e7e439c2e2247620b3f authored over 4 years ago by Jakob Nybo Nissen <[email protected]>
Restore julia 0.7 compat

github.com/BioJulia/Bio.jl - a0a871ab90fcf98874142dce2e732d7649b01f92 authored over 4 years ago by Ben J. Ward <[email protected]>
Add julia compat

github.com/BioJulia/Bio.jl - 6f2e0cef33e8aca1d0f0b257dd182f16fcd70235 authored over 4 years ago by Ben J. Ward <[email protected]>
Update tagbot

github.com/BioJulia/Bio.jl - 4e98a6c684850242a41a0b64da569dbcce5afa4d authored over 4 years ago by Ben J. Ward <[email protected]>
Update patch number

github.com/BioJulia/Bio.jl - 562a073641fcbf9c6aec6841590dc32a92152ce0 authored over 4 years ago by Ben J. Ward <[email protected]>
Add deprecation warning on init

github.com/BioJulia/Bio.jl - 49f100201bcf89f13565a584ac45bb8a31c918d2 authored over 4 years ago by Ben J. Ward <[email protected]>
Undo manual

github.com/BioJulia/Bio.jl - 30d7e5dd88f52cfe24aa5d2e2e90a98ef102aec6 authored over 4 years ago by Ben J. Ward <[email protected]>
Update manual

github.com/BioJulia/Bio.jl - 573c65a38e67ed7bd477eef66a24200d56eef312 authored over 4 years ago by Ben J. Ward <[email protected]>
Add workflow files

github.com/BioJulia/Bio.jl - 216cc333d1cfb6ad3f242d2d04868042ca073428 authored over 4 years ago by Ben J. Ward <[email protected]>
Update the documentation

github.com/BioJulia/Bio.jl - c2a3d955191efbf0a814be4dfd350fb8a9065865 authored over 4 years ago by Ben J. Ward <[email protected]>
Update README with deprecation message

github.com/BioJulia/Bio.jl - caf93a55afca8d6616f981260561f52151e69e74 authored over 4 years ago by Ben J. Ward <[email protected]>
Delete Registry.toml

github.com/BioJulia/BioJuliaRegistry - bb0f92f09d53099c8cdbad312812d4f5005f65a8 authored over 4 years ago by Ben J. Ward <[email protected]>
Delete .travis.yml

github.com/BioJulia/BioJuliaRegistry - 72a66f79dbf320145be388fa60ff5a46d75b59d3 authored over 4 years ago by Ben J. Ward <[email protected]>
Delete Project.toml

github.com/BioJulia/BioJuliaRegistry - 30c3b84f438d5782d379a3fd68b4c4a42071c7ef authored over 4 years ago by Ben J. Ward <[email protected]>
Delete automerge.yml

github.com/BioJulia/BioJuliaRegistry - 125698dddda895fbe5b19294da405c35fa2f0465 authored over 4 years ago by Ben J. Ward <[email protected]>
Update README.md

github.com/BioJulia/BioJuliaRegistry - 48035017d83435927d91c4f688c33531eb60450e authored over 4 years ago by Ben J. Ward <[email protected]>
Update SummaryInfo.jl

github.com/BioJulia/PopGen.jl_archive - fb73c706f46aaf94cca362ce5cbbe49379b81a96 authored over 4 years ago by Pavel Dimens <[email protected]>
Update SummaryInfo.jl

github.com/BioJulia/PopGen.jl - fb73c706f46aaf94cca362ce5cbbe49379b81a96 authored over 4 years ago by Pavel Dimens <[email protected]>
Update README.md

github.com/BioJulia/BioJuliaRegistry - 3b091f83206bdd29966c063c24a6e0ddf4124514 authored over 4 years ago by Ben J. Ward <[email protected]>
Update SummaryInfo.jl

github.com/BioJulia/PopGen.jl_archive - 75ac90b6959c676f4cd3e92036f53d59ea91cab3 authored over 4 years ago by Pavel Dimens <[email protected]>
Update SummaryInfo.jl

github.com/BioJulia/PopGen.jl - 75ac90b6959c676f4cd3e92036f53d59ea91cab3 authored over 4 years ago by Pavel Dimens <[email protected]>
Update SummaryInfo.jl

github.com/BioJulia/PopGen.jl - adfc9ece241d31ebfd3e270f0a609b52c074369b authored over 4 years ago by Pavel Dimens <[email protected]>
Update SummaryInfo.jl

github.com/BioJulia/PopGen.jl_archive - adfc9ece241d31ebfd3e270f0a609b52c074369b authored over 4 years ago by Pavel Dimens <[email protected]>
Update Heterozygosity.jl

github.com/BioJulia/PopGen.jl_archive - 4293fa35b2d1b43d6e716646739567466ccfb876 authored over 4 years ago by Pavel Dimens <[email protected]>
Update Heterozygosity.jl

github.com/BioJulia/PopGen.jl - 4293fa35b2d1b43d6e716646739567466ccfb876 authored over 4 years ago by Pavel Dimens <[email protected]>
migrations to DataFrames API

github.com/BioJulia/PopGen.jl - cc4835a5a746f72a9d4700b091ff3dcb2cd729f6 authored over 4 years ago by Pavel Dimens <[email protected]>
migrations to DataFrames API

github.com/BioJulia/PopGen.jl_archive - cc4835a5a746f72a9d4700b091ff3dcb2cd729f6 authored over 4 years ago by Pavel Dimens <[email protected]>
add abandoned repo status badge

github.com/BioJulia/MicrobiomePlots.jl - bcad97941e508e25fae6cdea7e05e4c7968349c5 authored over 4 years ago by Kevin Bonham <[email protected]>
convert AlleleFreq.jl to DataFrames

github.com/BioJulia/PopGen.jl - 895fcc27c2ff21218bf67d61cf3cce1a6902f420 authored over 4 years ago by Pavel Dimens <[email protected]>
convert AlleleFreq.jl to DataFrames

github.com/BioJulia/PopGen.jl_archive - 895fcc27c2ff21218bf67d61cf3cce1a6902f420 authored over 4 years ago by Pavel Dimens <[email protected]>
start Delim update

and remove old determine_markers, fix type signature

github.com/BioJulia/PopGen.jl_archive - 07b38233d03fcb1a339c3f50594b79508808c469 authored over 4 years ago by Pavel Dimens <[email protected]>
start Delim update

and remove old determine_markers, fix type signature

github.com/BioJulia/PopGen.jl - 07b38233d03fcb1a339c3f50594b79508808c469 authored over 4 years ago by Pavel Dimens <[email protected]>
finish Manipulate.jl conversion to DataFrames

github.com/BioJulia/PopGen.jl - 1ae0215800f64fa6fc4e34d30fbb50d25a063a03 authored over 4 years ago by Pavel Dimens <[email protected]>