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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

CompatHelper: add new compat entry for Transducers at version 0.4, (keep existing compat)

github.com/BioJulia/BioMakie.jl - a4856003f4ada9580c824e88ecca6261e03923c2 authored over 2 years ago by CompatHelper Julia <[email protected]>
Merge pull request #11 from CiaranOMara/patch-3

Update CHANGELOG.md

github.com/BioJulia/BioGenerics.jl - 6edb58e4ccd4f8917afad1e96e54c226ab444a23 authored over 2 years ago by Kevin Bonham <[email protected]>
Update CHANGELOG.md

github.com/BioJulia/BioGenerics.jl - 23d55952bbdfaa3a9c3ce3667345e1da924f975b authored over 2 years ago by Ciarán O'Mara <[email protected]>
Merge pull request #10 from CiaranOMara/patch-1

Add the more abstract `groupname` and `hasgroupname`.

github.com/BioJulia/BioGenerics.jl - d750473988fcbeb308be96d34c6b1701708ee197 authored over 2 years ago by Kevin Bonham <[email protected]>
Add the more abstract `groupname` and `hasgroupname`.

github.com/BioJulia/BioGenerics.jl - a172d3f11a4178d0dafeea4564ea841edaa63b84 authored over 2 years ago by Ciarán O'Mara <[email protected]>
Merge pull request #457 from kool7d/dev

docs minor

github.com/BioJulia/BioMakie.jl - b58f957f1f8157998cf48d080c38b840d03c593a authored over 2 years ago by Dan Kool <[email protected]>
docs minor

github.com/BioJulia/BioMakie.jl - f906caaf7ec38bdcbae8c0f54ba74b297c6bf385 authored over 2 years ago by kool7d <[email protected]>
initial bootstrap rewrite

github.com/BioJulia/PopGen.jl - 341170265e3421791e74d74d9622675dadc50876 authored over 2 years ago by Pavel Dimens <[email protected]>
tidying up

github.com/BioJulia/PopGen.jl - b26338e90f8fb203cba50020b6a21120e7f42b80 authored over 2 years ago by Pavel Dimens <[email protected]>
optim

github.com/BioJulia/PopGen.jl - 0ded41d1907a679b60ee4cf51923b97f95357a31 authored over 2 years ago by Pavel Dimens <[email protected]>
substantial optimization

github.com/BioJulia/PopGenCore.jl - bcb08eebb4f06d640a453f26f210e58bc43193ba authored over 2 years ago by Pavel Dimens <[email protected]>
optimize

github.com/BioJulia/PopGen.jl - 37175c32127eae647955b5206bba0c6a90c35c01 authored over 2 years ago by Pavel Dimens <[email protected]>
optimize memory of genofreq

github.com/BioJulia/PopGenCore.jl - 0b0c25ac606a6f8d894ae82e86c7cea74dc8a576 authored over 2 years ago by Pavel Dimens <[email protected]>
optimize memory of allelefreq

github.com/BioJulia/PopGenCore.jl - 1b7408ded71875086a78f49664b8fb422d766dd0 authored over 2 years ago by Pavel Dimens <[email protected]>
trim the fat

github.com/BioJulia/PopGen.jl - 0f7374fbd40f331307e3d9c5bacc79f9835f7d69 authored over 2 years ago by Pavel Dimens <[email protected]>
update tests

github.com/BioJulia/PopGenCore.jl - 2bf13bd7f0dc47d662f8a41d019215f4415a54c0 authored over 2 years ago by Pavel Dimens <[email protected]>
Merge pull request #456 from kool7d/dev

Update LICENSE

github.com/BioJulia/BioMakie.jl - f17f93f4d4fb840d2a04c725f1638c91a81005e4 authored over 2 years ago by Dan Kool <[email protected]>
Update LICENSE

github.com/BioJulia/BioMakie.jl - 3f33bdc06eae34a98b56977b3830757b506c2f95 authored over 2 years ago by Dan Kool <[email protected]>
Merge pull request #455 from kool7d/dev

Dev

github.com/BioJulia/BioMakie.jl - 839afff4c8ad89b4125eb38338c32553620ce47e authored over 2 years ago by Dan Kool <[email protected]>
fixcompat

github.com/BioJulia/BioMakie.jl - d259319a3d280dd1271f81dea18283248048e32a authored over 2 years ago by kool7d <[email protected]>
Merge remote-tracking branch 'origin/compathelper/new_version/2022-05-09-01-41-09-617-00049041388' into dev

github.com/BioJulia/BioMakie.jl - 2c32fbf04605c1ca9bc7213457dc67093df82167 authored over 2 years ago by Daniel Kool <[email protected]>
Merge pull request #454 from kool7d/dev

Dev

github.com/BioJulia/BioMakie.jl - 3e76dc19c87f9e1e4e8c6335a1253ebdc69ea4ea authored over 2 years ago by Dan Kool <[email protected]>
Update README.md

github.com/BioJulia/BioMakie.jl - a8e93106baedf6944574386713bab64248f99539 authored over 2 years ago by Dan Kool <[email protected]>
update tests

github.com/BioJulia/PopGenCore.jl - ac3df443aa923241812a5b23ca645aa85e02f711 authored over 2 years ago by Pavel Dimens <[email protected]>
update HW logic

github.com/BioJulia/PopGen.jl - 39641c0d74d5a3182157638dce415852ea56ddca authored over 2 years ago by Pavel Dimens <[email protected]>
adjustments

github.com/BioJulia/PopGenCore.jl - b4055acbcc6434f63309dd880ccbba71c0ae4987 authored over 2 years ago by Pavel Dimens <[email protected]>
Add Skipping behaviour to EveryKmer

github.com/BioJulia/Kmers.jl - 91da92eb7a62761ddbc5473700a81f01bad7639d authored over 2 years ago by Ben J. Ward <[email protected]>
bump to next version 6.0

github.com/BioJulia/PopGenCore.jl - 65c46de72c86efbac562a3a83398bdbde59ee520 authored over 2 years ago by Pavel Dimens <[email protected]>
Merge branch 'dev' of https://github.com/BioJulia/PopGenCore.jl into dev

github.com/BioJulia/PopGenCore.jl - 33f694e4146f0261f0156935967ef5be5bd91734 authored over 2 years ago by Pavel Dimens <[email protected]>
update for new isallmissing

conditional in popgencore

github.com/BioJulia/PopGen.jl - 05563a6a631af767273e699e931412b17f829fca authored over 2 years ago by Pavel Dimens <[email protected]>
first pass of optimizations

github.com/BioJulia/PopGenCore.jl - 1e2c34e08f9c29d9907a891a7d9a5188e2b98b4d authored over 2 years ago by Pavel Dimens <[email protected]>
finish method optims

github.com/BioJulia/PopGen.jl - 02b038d1bbdd609ed8fa21607a91280e12536d31 authored over 2 years ago by Pavel Dimens <[email protected]>
Update README.md

github.com/BioJulia/BioMakie.jl - 157e53d7aab17b58fb8a7824bf19a02d4eac25f9 authored over 2 years ago by Dan Kool <[email protected]>
Update README.md

github.com/BioJulia/BioMakie.jl - 9303339ceb029ec74c9e87c2ed3dfa9f2fa0f2fe authored over 2 years ago by Dan Kool <[email protected]>
Merge pull request #453 from kool7d/dev

Update README.md

github.com/BioJulia/BioMakie.jl - 732b442976de7c13da4a2f4aad9f2797fdfaa87f authored over 2 years ago by Dan Kool <[email protected]>
Update README.md

github.com/BioJulia/BioMakie.jl - fe87ba431287346821ca730f2a1fe41def6651ee authored over 2 years ago by Dan Kool <[email protected]>
Merge pull request #452 from kool7d/dev

docclean1

github.com/BioJulia/BioMakie.jl - c6151fe8c7b929faab5fa021baeb31de23836b07 authored over 2 years ago by Dan Kool <[email protected]>
docclean1

github.com/BioJulia/BioMakie.jl - 63ce4003204292bd588260bc60134c4216a8d229 authored over 2 years ago by kool7d <[email protected]>
CompatHelper: add new compat entry for FASTX at version 1, (keep existing compat)

github.com/BioJulia/BioMakie.jl - 4a81a2aad66fd870b3bda317892edf35ac39bdf3 authored over 2 years ago by CompatHelper Julia <[email protected]>
Merge pull request #450 from kool7d/dev

Dev

github.com/BioJulia/BioMakie.jl - c97a2e389a35af33d00965e2159632e85a3c23bd authored over 2 years ago by Dan Kool <[email protected]>
docsagain3

github.com/BioJulia/BioMakie.jl - 29699994603fb91d8784c6db87c8fa3aa66eb732 authored over 2 years ago by kool7d <[email protected]>
docsagain2

github.com/BioJulia/BioMakie.jl - 305bf3fbc9345359978559b7ef6c618e18fdcbfd authored over 2 years ago by kool7d <[email protected]>
docsagain

github.com/BioJulia/BioMakie.jl - 0fc3009f5c22a8ae5dcee1a37a4f011b7c01215a authored over 2 years ago by kool7d <[email protected]>
docfile

github.com/BioJulia/BioMakie.jl - a7de7f7c42afb32dfe08c55ff2fde326bad81d13 authored over 2 years ago by kool7d <[email protected]>
proj1

github.com/BioJulia/BioMakie.jl - 4903e8a3b10a55a035d24c4104ab23053e45ac7f authored over 2 years ago by kool7d <[email protected]>
Update Documenter.yml

github.com/BioJulia/BioMakie.jl - da33cff48b7c32ff37af4953bfa6b7ea1425a66c authored over 2 years ago by Dan Kool <[email protected]>
docs2

github.com/BioJulia/BioMakie.jl - 189689d39cb0ec95dfdf8544909ca0150cdc7893 authored over 2 years ago by kool7d <[email protected]>
docs

github.com/BioJulia/BioMakie.jl - 2686cee29e7419d5d76dfbb3d139f8fb9513f111 authored over 2 years ago by kool7d <[email protected]>
so mch optimization

github.com/BioJulia/PopGen.jl - f75ff8407564a9c4e3719a1ae404a8928c477c9c authored over 2 years ago by Pavel Dimens <[email protected]>
Fix inconsistent Variation positions (#4)

* Change Variant constructor to use alignment positions

Signed-off-by: Thomas A. Christensen ...

github.com/BioJulia/SequenceVariation.jl - ade9b7e41d2f28bc36850ed4c1e72d7e913e8937 authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Fix show function for Variations with Insertion edits (#3)

Signed-off-by: Thomas A. Christensen II <[email protected]>

github.com/BioJulia/SequenceVariation.jl - d0f0f65d7f77d4103dffed0188202f8b458211d8 authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Add EveryCanonicalKmer

github.com/BioJulia/Kmers.jl - bf0a61fd0376584a14afdc60b4870e62b3fa4826 authored over 2 years ago by Ben J. Ward <[email protected]>
bit of optimization

github.com/BioJulia/PopGen.jl - 57c9516c1b735a7135b0be5b20c4d15f5a985c82 authored over 2 years ago by Pavel Dimens <[email protected]>
Add workflow for downstream tests (#86)

github.com/BioJulia/Automa.jl - 6e75725e9923a69717b64f82bf79fee618e74355 authored over 2 years ago by Ciarán O'Mara <[email protected]>
Small cleanup of Automa codegen (#92)

* Fix typo geybyte to getbyte
* Use optimized final state check for Tokenizer
* Make Tokenizer...

github.com/BioJulia/Automa.jl - c7799997905d2add840dd7acfd9fbd5ba12e94a4 authored over 2 years ago by Jakob Nybo Nissen <[email protected]>
Small tweaks to Tokenizer internals (#90)

* Remove unused argument generate_table_code
* Do not needlessly specialize on args in Tokenize...

github.com/BioJulia/Automa.jl - 7b54b665abd428e87114fb5fd311fda2b35a7b05 authored over 2 years ago by Jakob Nybo Nissen <[email protected]>
Merge pull request #89 from jakobnissen/tokenize

# Closes #88

github.com/BioJulia/Automa.jl - 6abbdb4c82f39187c8883551063a3bbec75db145 authored over 2 years ago by Jakob Nybo Nissen <[email protected]>
Have Tokenizer check if in accept state when EOF

In the code generated by generate_table_code for Tokenizer, if the loop exits
due to reaching EO...

github.com/BioJulia/Automa.jl - 38dc46ba616a6b7c476da77b1c30ef46d0eafaea authored over 2 years ago by Jakob Nybo Nissen <[email protected]>
Add SpacedKmers

github.com/BioJulia/Kmers.jl - 1d0575fb057efc8cbbf6e8f283d677834e016ca3 authored over 2 years ago by Ben J. Ward <[email protected]>
Add EveryKmer

github.com/BioJulia/Kmers.jl - bddf7fa2abbf39683c07dfeb3a5de8f99ac5f611 authored over 2 years ago by Ben J. Ward <[email protected]>
docs3

github.com/BioJulia/BioMakie.jl - 8963c57555f14e059580a5d2f867a67ea23ca9d6 authored over 2 years ago by kool7d <[email protected]>
docs2

github.com/BioJulia/BioMakie.jl - 34617c86cda140da4c9c2d52fc64d5a60d3188f0 authored over 2 years ago by kool7d <[email protected]>
add initial methods

github.com/BioJulia/PopGen.jl - b71e0e804eb138fc60c92140cbf61238eb19153c authored over 2 years ago by Pavel Dimens <[email protected]>
Merge pull request #101 from BioJulia/compathelper/new_version/2022-04-23-01-48-22-850-00729158651

CompatHelper: add new compat entry for NamedArrays at version 0.9, (keep existing compat)

github.com/BioJulia/PopGen.jl - 165ae58698b553e075ecc61715bb51e07bfa19b8 authored over 2 years ago by Pavel V. Dimens <[email protected]>
CompatHelper: add new compat entry for NamedArrays at version 0.9, (keep existing compat)

github.com/BioJulia/PopGen.jl - 819bbcb54392b47ed8cf01fa462959299b932dec authored over 2 years ago by CompatHelper Julia <[email protected]>
restore this after fix

github.com/BioJulia/PopGenCore.jl - 32a3493467e61f1e4848cebd51203e9c3de7e358 authored over 2 years ago by Pavel Dimens <[email protected]>
fix introduced typo

github.com/BioJulia/PopGenCore.jl - cdc8e55a2d8f53e820facb1f167cd9aefefa1b64 authored over 2 years ago by Pavel Dimens <[email protected]>
simplify logic

github.com/BioJulia/PopGen.jl - 5f6c57d3bc02d21efa9198f8134440e75d14ce28 authored over 2 years ago by Pavel Dimens <[email protected]>
better solution for sorting

github.com/BioJulia/PopGenCore.jl - d341647ec751bf3f8e1ca400ab7ba86fe8a6ff3b authored over 2 years ago by Pavel Dimens <[email protected]>
minor cleanup

github.com/BioJulia/PopGen.jl - 3b70726538a0f67d09d64b7f6489ce3bef93e9ae authored over 2 years ago by Pavel Dimens <[email protected]>
fix dropmissing inconsistency

github.com/BioJulia/PopGenCore.jl - 8683735e8a9ce4137573a5ea9224690bf64d6b6a authored over 2 years ago by Pavel Dimens <[email protected]>
fix NamedArray using call

github.com/BioJulia/PopGen.jl - eff301dfdb0f525a8fb923379924fca6129b7187 authored over 2 years ago by Pavel Dimens <[email protected]>
update pwise tests

github.com/BioJulia/PopGen.jl - 8249b006c11e902c3ed181d7fe9937c496113f25 authored over 2 years ago by Pavel Dimens <[email protected]>
rewrite pairwise identical to use matrix logic

and return a NamedMatrix instead of dataframe

github.com/BioJulia/PopGen.jl - cd45d00adc2ec640ccfc20a9815ea5f52f8dea8a authored over 2 years ago by Pavel Dimens <[email protected]>
shorten the docstring

github.com/BioJulia/PopGenCore.jl - 4a56a9f7b5734dbbabf21b4dfca011b294fd01e8 authored over 2 years ago by Pavel Dimens <[email protected]>
fix Vector{Bool} annotations

github.com/BioJulia/PopGenCore.jl - 24f1a21d2f8a677a8b1abc4cd7de4b0078a8b5fc authored over 2 years ago by Pavel Dimens <[email protected]>
missing underscore

github.com/BioJulia/PopGen.jl - 08d35f7bd8537ac1d20f3f2172140f0da6e3c9cc authored over 2 years ago by Pavel Dimens <[email protected]>
update progressbar to fix CI

github.com/BioJulia/PopGen.jl - 9f914bb8e25dc03b486650a181fef5c500ac48a7 authored over 2 years ago by Pavel Dimens <[email protected]>
Merge pull request #444 from kool7d/dev

Dev

github.com/BioJulia/BioMakie.jl - 9d5687c4071ba6a3da9b6ff2f82931aca993c9d8 authored over 2 years ago by Dan Kool <[email protected]>
Update README.md

github.com/BioJulia/BioMakie.jl - a904f8ab249714ce28de66ac9e60ed4eb455ca56 authored over 2 years ago by Dan Kool <[email protected]>
assets2

github.com/BioJulia/BioMakie.jl - 4876fcc3bba2dba78c38ed53dc6f6d8c9fdb2c69 authored over 2 years ago by kool7d <[email protected]>
assets1

github.com/BioJulia/BioMakie.jl - 2e051a73016aad35a4b747fc0addfc4ddcb3e483 authored over 2 years ago by kool7d <[email protected]>
update conditionals test

github.com/BioJulia/PopGenCore.jl - 7cb6854474916550b4361b33d990962f409fb466 authored over 2 years ago by Pavel Dimens <[email protected]>
fix bad annotations

github.com/BioJulia/PopGenCore.jl - 60616eca61d428e249140f320ff8497d9955f8ff authored over 2 years ago by Pavel Dimens <[email protected]>
fix annotations

github.com/BioJulia/PopGenCore.jl - b2749d4f7be5d6ee82292c0a767b7bb2efb29422 authored over 2 years ago by Pavel Dimens <[email protected]>
extra annotations

github.com/BioJulia/PopGenCore.jl - 93a8a8489e430cf04e6ec1d55ce9f4cefe4abb3e authored over 2 years ago by Pavel Dimens <[email protected]>
slight optimizations

github.com/BioJulia/PopGenCore.jl - 552c8c83e770abef122c358b718e65a6b182d6c4 authored over 2 years ago by Pavel Dimens <[email protected]>
update conditionals

github.com/BioJulia/PopGenCore.jl - 94bd0629d5d07fd72df37d2cf11a50a1e36d8712 authored over 2 years ago by Pavel Dimens <[email protected]>
update conditionals logic. Some optimizations

github.com/BioJulia/PopGenCore.jl - 65db84988cb1dcc63a8bc9933e6fbe951da09ab4 authored over 2 years ago by Pavel Dimens <[email protected]>
Merge pull request #433 from kool7d/dev

Dev

github.com/BioJulia/BioMakie.jl - 5e445deff464b70d71039c5998b03b9b115187f2 authored over 2 years ago by Dan Kool <[email protected]>
flesh1

github.com/BioJulia/BioMakie.jl - e14c93712f641228fd3ce7fcb119bb3725b41b0a authored over 2 years ago by kool7d <[email protected]>
cleanup

github.com/BioJulia/PopGen.jl - 862f9f96d060ada6e15114182c677d5fdc9372da authored over 2 years ago by Pavel Dimens <[email protected]>
Update README.md

github.com/BioJulia/PopGen.jl - 6513c80be8bd1a7ccb85c551a910b59368810f74 authored over 2 years ago by Pavel V. Dimens <[email protected]>
Merge pull request #100 from BioJulia/pca

add cluster() wrapper

github.com/BioJulia/PopGen.jl - f40807e808521c3844b8c022a627d5eaddcb32a2 authored over 2 years ago by Pavel V. Dimens <[email protected]>
add cluster() wrapper

github.com/BioJulia/PopGen.jl - 5c782e29d61f4cced5e2020594673d90e3fc5288 authored over 2 years ago by Pavel Dimens <[email protected]>
Merge pull request #99 from BioJulia/pca

add more clustering methods

github.com/BioJulia/PopGen.jl - 29935a6190b8730139fbca783d0b7f7f385fe012 authored over 2 years ago by Pavel V. Dimens <[email protected]>
update testing project.tml

github.com/BioJulia/PopGen.jl - 25918066ea6987163ea9ec9aa99f5fa6dc384c10 authored over 2 years ago by Pavel Dimens <[email protected]>
Merge branch 'pca' of https://github.com/BioJulia/PopGen.jl into pca

github.com/BioJulia/PopGen.jl - 2d64ffa34d715ff9fe7575ae1373a80126d89de1 authored over 2 years ago by Pavel Dimens <[email protected]>
update docstrings

github.com/BioJulia/PopGen.jl - 1252a01340a677999a60b14d88a0830e0a0e26e0 authored over 2 years ago by Pavel Dimens <[email protected]>
Merge branch 'dev' into pca

github.com/BioJulia/PopGen.jl - 98d2ac63059b8e02f48cd5bb5aa723e6e0a16f77 authored over 2 years ago by Pavel V. Dimens <[email protected]>