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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

update tests

github.com/BioJulia/PopGen.jl - ed87bbde770809fbd5296197a3c8ec05b7ed5d16 authored over 2 years ago by Pavel Dimens <[email protected]>
update deps and compat

github.com/BioJulia/PopGen.jl - 750c5be3e92247fdda0a263de2eccc2a8c091e86 authored over 2 years ago by Pavel Dimens <[email protected]>
add clust methods: kmedoids, fuzzycmeans, dbscan

github.com/BioJulia/PopGen.jl - 5b9d918fd34b4154e59dab168dbc56d855e554e9 authored over 2 years ago by Pavel Dimens <[email protected]>
add Kmedoids

github.com/BioJulia/PopGen.jl - cd726690281c068ddaaf0f2cc2a8cdd3e6dc6333 authored over 2 years ago by Pavel Dimens <[email protected]>
Merge pull request #98 from BioJulia/compathelper/new_version/2022-04-11-20-51-42-006-02555815443

CompatHelper: add new compat entry for Clustering at version 0.14, (keep existing compat)

github.com/BioJulia/PopGen.jl - 07e80fba9a199afed7073ade934005ad940933bd authored over 2 years ago by Pavel V. Dimens <[email protected]>
CompatHelper: add new compat entry for Clustering at version 0.14, (keep existing compat)

github.com/BioJulia/PopGen.jl - 840c0a4dca90d47b26e7ea9cf192d54fbb5b432a authored over 2 years ago by CompatHelper Julia <[email protected]>
Update Project.toml

github.com/BioJulia/PopGen.jl - 3bdaaf77ad771ee3f3b0409068827d31a2b037b7 authored over 2 years ago by Pavel V. Dimens <[email protected]>
update docstrings

github.com/BioJulia/PopGen.jl - f3e9926079efb926c136a8a0e17d4fcd347ce6a3 authored over 2 years ago by Pavel Dimens <[email protected]>
Merge pull request #97 from BioJulia/pca

add:
- Principal Component Analysis
- K-Means clustering
- allele matrices: count, frequency
...

github.com/BioJulia/PopGen.jl - e0c206c0b77313c8a45287d6e35fb9382b8c7a68 authored over 2 years ago by Pavel V. Dimens <[email protected]>
deprecate julia 1.5 support b/c of new count() methods

github.com/BioJulia/PopGen.jl - cde4ea9d4a76090743ac07fa96b17c72d36dc30c authored over 2 years ago by Pavel Dimens <[email protected]>
change testing logic for missing values

github.com/BioJulia/PopGen.jl - 2757a7b91d7b0a8ebfcd55a02f66a58f4d27e844 authored over 2 years ago by Pavel Dimens <[email protected]>
fix more tests

github.com/BioJulia/PopGen.jl - c08949ac619c7e294ea226cc76802769b8fb2d46 authored over 2 years ago by Pavel Dimens <[email protected]>
fix test typos

github.com/BioJulia/PopGen.jl - 385ca9c30cf6f382d325fc01cba75d3a47d21630 authored over 2 years ago by Pavel Dimens <[email protected]>
prepend PopGen. to _allelematrix tests

github.com/BioJulia/PopGen.jl - f3a7f9b76b650f06637d1244fd67ec2db0abb855 authored over 2 years ago by Pavel Dimens <[email protected]>
fix kmeans file name

github.com/BioJulia/PopGen.jl - afdeba3fd2feded94885f70a4f5b89e292a212ed authored over 2 years ago by Pavel Dimens <[email protected]>
add tests

github.com/BioJulia/PopGen.jl - df43f1e76c85095898f0addb4be59a0a2e8714aa authored over 2 years ago by Pavel Dimens <[email protected]>
add kmeans clustering and pca

github.com/BioJulia/PopGen.jl - 4dba374b37f3b9a7859ce751e7151fbf233720e0 authored over 2 years ago by Pavel Dimens <[email protected]>
Update CompatHelper yml

github.com/BioJulia/BED.jl - 2e082b1a9f8c6c543e5544a90a7f970110ca7e6b authored over 2 years ago by Ciarán O'Mara <[email protected]>
Increment Documenter compatibility

github.com/BioJulia/BED.jl - 4d386f1961aea4d709b4cc9c9824ed8a85383043 authored over 2 years ago by Ciarán O'Mara <[email protected]>
Tweak error messages

github.com/BioJulia/BED.jl - 130a6d94c76b4c088039db628229e313e702b231 authored over 2 years ago by Ciarán O'Mara <[email protected]>
Merge pull request #14 from CiaranOMara/develop

Skip blank lines and comment lines

github.com/BioJulia/BED.jl - 5dcf0f185b86fe53eb4f4cca3daab866b3d7610d authored over 2 years ago by Ciarán O'Mara <[email protected]>
Update README.md

github.com/BioJulia/PopGen.jl - d9ea4b5ac9917772c6134a7e70a472247421ddeb authored over 2 years ago by Pavel V. Dimens <[email protected]>
tidy up and optimize the matrix functions

github.com/BioJulia/PopGen.jl - 9154694c08f7b493d4c9ce56a3051a5188cafc30 authored over 2 years ago by Pavel Dimens <[email protected]>
Skip blank lines and comment lines

github.com/BioJulia/BED.jl - 201a1569a2ff342bd03654f074355609fc5b71e4 authored over 2 years ago by Ciarán O'Mara <[email protected]>
Update build links

github.com/BioJulia/BED.jl - cd1a7d73e2d8e8ee3816eec1fd9fb7274c1909d3 authored over 2 years ago by Ciarán O'Mara <[email protected]>
Remove references to Gitter

github.com/BioJulia/BED.jl - 2d9dc0b7ee5e79547c6f07f0353e7b6c359ede5d authored over 2 years ago by Ciarán O'Mara <[email protected]>
Remove obsolete coverage

github.com/BioJulia/BED.jl - 20b7484ce117f785361e0757659bd80b8ec2e35f authored over 2 years ago by Ciarán O'Mara <[email protected]>
Update README.md

github.com/BioJulia/PopGen.jl - 0f5e06d4572f9f7456a241d6949b4f74bbcebe4d authored over 2 years ago by Pavel V. Dimens <[email protected]>
Add test for canonical method

github.com/BioJulia/Kmers.jl - 1756818d46a895d98848165b073423492adba0f2 authored over 2 years ago by Ben J. Ward <[email protected]>
Optimise canonical function

github.com/BioJulia/Kmers.jl - ff15beb24cbbb747bfdf4d252decff3b47c761d7 authored over 2 years ago by Ben J. Ward <[email protected]>
Remove Gitter chat links

github.com/BioJulia/XAM.jl - 52d0ce21b0930fde1f97e781c3839670f8ee2cc7 authored over 2 years ago by Ciarán O’Mara <[email protected]>
Remove Gitter chat links

github.com/BioJulia/BioAlignments.jl - ebea200c803398ef918e7d7a897553457a4b999e authored over 2 years ago by Ciarán O’Mara <[email protected]>
newstruc

github.com/BioJulia/BioMakie.jl - 0bfa206a0e11177502a852b6fec4f360de9e91d9 authored over 2 years ago by kool7d <[email protected]>
updates

github.com/BioJulia/PopGen.jl - fa9b094088f5ce5bad0ead00a87aa842d0bf4a13 authored over 2 years ago by Pavel Dimens <[email protected]>
add docstring

github.com/BioJulia/PopGen.jl - 9c60ec45135123aa63d57130cbf39604cc2aab47 authored over 2 years ago by Pavel Dimens <[email protected]>
add better Kmeans integration

github.com/BioJulia/PopGen.jl - d204b00f77cdcc416dc9c17feaf1ce970579a9d2 authored over 2 years ago by Pavel Dimens <[email protected]>
update DAPC code

github.com/BioJulia/PopGen.jl - 4cf98f1ca46355d274bd6c1c1ba35b0981e80c9e authored over 2 years ago by Pavel Dimens <[email protected]>
add PCA and deps

github.com/BioJulia/PopGen.jl - 96d4d7969d8264058e709d614f7a708bdc227621 authored over 2 years ago by Pavel Dimens <[email protected]>
add _relabel

github.com/BioJulia/PopGen.jl - 0b993c3c04e1d49752cf81bb425f043161192457 authored over 2 years ago by Pavel Dimens <[email protected]>
add new PCA things

github.com/BioJulia/PopGen.jl - 14bc5f08fbc1b46f231840e759a9a37d84da4e1c authored over 2 years ago by Pavel Dimens <[email protected]>
bump version number

github.com/BioJulia/PopGen.jl - 26f76756ad81e7c83c2b27825097521963a9088f authored over 2 years ago by Pavel Dimens <[email protected]>
rm redundant export call

github.com/BioJulia/PopGen.jl - 454a5efe7fb4cb1072091793e235024869dded14 authored over 2 years ago by Pavel Dimens <[email protected]>
add collect statements to sample pairs

github.com/BioJulia/PopGen.jl - 5c26df924d69260ea71c10cd46f1b56bce48ac08 authored over 2 years ago by Pavel Dimens <[email protected]>
update kinship things

github.com/BioJulia/PopGen.jl - ec680fe4c68c6408e60b80348480739c043002a3 authored over 2 years ago by Pavel Dimens <[email protected]>
Merge pull request #404 from kool7d/dev

Dev

github.com/BioJulia/BioMakie.jl - 79f9b169603c2d58604f8fa2807ed072a55c1229 authored over 2 years ago by Dan Kool <[email protected]>
bigred1

github.com/BioJulia/BioMakie.jl - 49abe0dc841ced286378a579f1878803994a494b authored over 2 years ago by kool7d <[email protected]>
Merge pull request #403 from kool7d/master

mastertodev

github.com/BioJulia/BioMakie.jl - ca48e9c29b34f33f6b7e58223f9f8275f1d23bb8 authored over 2 years ago by Dan Kool <[email protected]>
Merge pull request #402 from kool7d/compathelper/new_version/2022-02-15-01-06-45-094-02966819025

CompatHelper: bump compat for Meshes to 0.21, (keep existing compat)

github.com/BioJulia/BioMakie.jl - c89b01344a74883ae7f88ffd7eabfe0d6d25a5fc authored over 2 years ago by Dan Kool <[email protected]>
Merge branch 'master' into compathelper/new_version/2022-02-15-01-06-45-094-02966819025

github.com/BioJulia/BioMakie.jl - 3dcdf73c5e030037af877941877dda4d902cf2b2 authored over 2 years ago by Dan Kool <[email protected]>
Merge pull request #400 from kool7d/compathelper/new_version/2022-02-06-01-04-09-883-00218713323

CompatHelper: bump compat for Pluto to 0.18, (keep existing compat)

github.com/BioJulia/BioMakie.jl - fb0d5fe44ec1ae8a86d7b23f522cddc3232c3b4e authored over 2 years ago by Dan Kool <[email protected]>
Merge pull request #399 from kool7d/compathelper/new_version/2022-01-09-01-01-45-837-00350300172

CompatHelper: bump compat for GLMakie to 0.5, (keep existing compat)

github.com/BioJulia/BioMakie.jl - ce53e34865bcab64cc5d0cf3b98d9da02e16cfaf authored over 2 years ago by Dan Kool <[email protected]>
Merge pull request #398 from kool7d/compathelper/new_version/2022-01-09-01-01-41-945-03871455148

CompatHelper: bump compat for CairoMakie to 0.7, (keep existing compat)

github.com/BioJulia/BioMakie.jl - f67631eefa0ba21f68474f61c6ba1f89d9c8f458 authored over 2 years ago by Dan Kool <[email protected]>
Merge pull request #397 from kool7d/compathelper/new_version/2022-01-09-01-01-36-352-02662424340

CompatHelper: bump compat for WGLMakie to 0.5, (keep existing compat)

github.com/BioJulia/BioMakie.jl - 8136f3451d3c86eda7d8368f0eb660b8b60cc7c9 authored over 2 years ago by Dan Kool <[email protected]>
Merge pull request #396 from kool7d/compathelper/new_version/2022-01-08-00-58-27-815-02997271527

CompatHelper: bump compat for Makie to 0.16, (keep existing compat)

github.com/BioJulia/BioMakie.jl - 2b521fb00e130b415a6e53318f68bc2fe04c3740 authored over 2 years ago by Dan Kool <[email protected]>
Merge pull request #395 from kool7d/compathelper/new_version/2022-01-08-00-58-20-125-03041306432

CompatHelper: bump compat for BioSequences to 3, (keep existing compat)

github.com/BioJulia/BioMakie.jl - 41afe5bef1c19e004be3b8dd3949e025ff77a610 authored over 2 years ago by Dan Kool <[email protected]>
remove kidera

github.com/BioJulia/BioMakie.jl - 8b3c346b586618a7c9ddf23bf41cd2d816444ede authored over 2 years ago by kool7d <[email protected]>
move export calls

github.com/BioJulia/PopGen.jl - 61b5595ed23ac4d3b3eedbb9b3f44ffd479d6fa5 authored over 2 years ago by Pavel Dimens <[email protected]>
Fix missing character in docs example (#74)

github.com/BioJulia/FASTX.jl - f03bccfbafd4a76ec08bc616877a77e0dc7fcd95 authored over 2 years ago by Jakob Nybo Nissen <[email protected]>
Clarify that streams take ownership of IO (#72)

Clarify that streams take ownership of IO

github.com/BioJulia/FASTX.jl - c3c802d4c3e18acffa520b16ef00ddf99ccb2840 authored over 2 years ago by Jakob Nybo Nissen <[email protected]>
fix more tests

github.com/BioJulia/PopGenCore.jl - 54fc5e19d636c03ef8facfa4b2206a11f198a39f authored over 2 years ago by Pavel Dimens <[email protected]>
update test

github.com/BioJulia/PopGenCore.jl - 636f004f5e1152514c1746bafa4b88241ed8349b authored over 2 years ago by Pavel Dimens <[email protected]>
fix deprecation/warning

github.com/BioJulia/PopGenCore.jl - 6d2e1191b10655b8736bee6aeeb98b4f24a2c3fc authored over 2 years ago by Pavel Dimens <[email protected]>
fix locations!

github.com/BioJulia/PopGenCore.jl - f76276904614b546e422129402acc85636ff8efd authored over 2 years ago by Pavel Dimens <[email protected]>
add precompilation

github.com/BioJulia/PopGenCore.jl - bc31254c1719db7b9fbadb8475e41351d72193df authored over 2 years ago by Pavel Dimens <[email protected]>
fix method

github.com/BioJulia/PopGenCore.jl - 5cc9715707dead113b9fd700010bc6628c3d2e03 authored over 2 years ago by Pavel Dimens <[email protected]>
add some precompile, add NamedTuple indexing

github.com/BioJulia/PopGenCore.jl - e7f77b6e46d979e2bd68c8d046d407f883157bfd authored over 2 years ago by Pavel Dimens <[email protected]>
Update TagBot.yml (#67)

github.com/BioJulia/FASTX.jl - 5e7efd6dc1e65a9783dd401ecef776b38c6732a4 authored over 2 years ago by Ciarán O'Mara <[email protected]>
Bump BioSequences/BioSymbols to v3/v5 (#66)

* Bump BioSequences/BioSymbols to v3/v5

* Bump Julia version

github.com/BioJulia/FASTX.jl - b1537390930d319e41ea37f1f14defe66bf66b6d authored over 2 years ago by Jakob Nybo Nissen <[email protected]>
Update PopGenCore.jl

github.com/BioJulia/PopGenCore.jl - af07ad90ed73b5f2be97cb914abead707c13db3e authored over 2 years ago by Pavel V. Dimens <[email protected]>
Update pkgtests.yaml

github.com/BioJulia/PopGenCore.jl - 136ca2496ae2f44a4cc4542f42f98e57f80a24b3 authored over 2 years ago by Pavel V. Dimens <[email protected]>
move all exports to package definition file

github.com/BioJulia/PopGenCore.jl - 2818f9e855576d44ca3c9817d8f2ca3cf47dca88 authored over 2 years ago by Pavel V. Dimens <[email protected]>
add location string-string vector method

github.com/BioJulia/PopGenCore.jl - c65b78e38f65f82363d53c0e95a294b755257072 authored over 2 years ago by Pavel V. Dimens <[email protected]>
Merge pull request #16 from BioJulia/compathelper/new_version/2022-01-20-01-15-36-540-02336516142

CompatHelper: bump compat for CSV to 0.10, (keep existing compat)

github.com/BioJulia/PopGenCore.jl - 71ebdada3df37354c18515268daa91874d803b11 authored over 2 years ago by Pavel V. Dimens <[email protected]>
Merge pull request #71 from CiaranOMara/tagbot

Add ssh key to TagBot workflow

github.com/BioJulia/BioAlignments.jl - 5f2c790ebf9afa2a7ff38e6e0c44970dff55984e authored over 2 years ago by Ciarán O'Mara <[email protected]>
Add ssh key to TagBot workflow

The ssh secret is needed to deploy documentation builds triggered by the tag event as the defaul...

github.com/BioJulia/BioAlignments.jl - 81aaf7ce3fd9d2c1624222d55f93f9639267136f 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 - 807204eba4ac511f4d42727076fd426b56f8359e authored over 2 years ago by Ciarán O'Mara <[email protected]>
CompatHelper: bump compat for Meshes to 0.21, (keep existing compat)

github.com/BioJulia/BioMakie.jl - 607e4dac67cdf8efcf26810255388582ce02271a authored over 2 years ago by CompatHelper Julia <[email protected]>
Update README.md

github.com/BioJulia/PopGen.jl - 62c171d9e87991c0908f00c4fe324e8cf2fa32aa authored over 2 years ago by Pavel V. Dimens <[email protected]>
Update README.md

github.com/BioJulia/PopGen.jl - 2eae68373aa934bfa895b97aabe811f02cbae95b authored over 2 years ago by Pavel V. Dimens <[email protected]>
Update README.md

github.com/BioJulia/BioMakie.jl - c2a1fd3edbcf21d813788b21bd0ef91bb705a457 authored over 2 years ago by Dan Kool <[email protected]>
Migrate from Gitter to Slack

github.com/BioJulia/TwoBit.jl - f7b649a38ff46d21ab217e8fc13bcec06570bb00 authored over 2 years ago by Ciarán O’Mara <[email protected]>
Upgrade to BioSequences v3

- Drops `BioSequences.ReferenceSequence` type.
- Changes compatibility.

github.com/BioJulia/TwoBit.jl - 752cf8a65d715c333a428bde4d0108469da3a5d1 authored over 2 years ago by Ciarán O’Mara <[email protected]>
Update CI

- Migrate to GitHub Actions.
- Include doctests in tests.
- Dynamic authors (docs/make.jl).

github.com/BioJulia/TwoBit.jl - 68511662618b162e051f391e0d558d87a9256f83 authored over 2 years ago by Ciarán O’Mara <[email protected]>
Tidy documentation

- Sentence per line.
- Method/Function indentations.
- Update email address.

github.com/BioJulia/TwoBit.jl - 612a91f8ea5f8fede538a3b6ef410f2a792a46f5 authored over 2 years ago by Ciarán O’Mara <[email protected]>
Increment version

github.com/BioJulia/TwoBit.jl - c2d450c22974c54022858c4f7b912854a1d01485 authored over 2 years ago by Ciarán O’Mara <[email protected]>
Add downstream tests

github.com/BioJulia/BioAlignments.jl - 541ea68248a2e0dccbbbaff4bb535907ebb49b0b authored over 2 years ago by Ciarán O’Mara <[email protected]>
Update Project.toml and CHANGELOG

- Increment version.
- Adjust compat section.
- Add extras and targets sections.
- Update email ...

github.com/BioJulia/BioTools.jl - 200a94cf00dca0ac83257cb94da52b7b80adf2aa authored over 2 years ago by Ciarán O’Mara <[email protected]>
Update .gitignore

github.com/BioJulia/BioTools.jl - 866a032da02e2ceca62e777cb8e5fa9d0f5c25fd authored over 2 years ago by Ciarán O’Mara <[email protected]>
Remove Manifest.toml

github.com/BioJulia/BioTools.jl - 48fdaa2cb7ad21dd69967780742aa12521999dbc authored over 2 years ago by Ciarán O’Mara <[email protected]>
Add downstream tests

github.com/BioJulia/BGZFStreams.jl - ecf347e1ecffc38d47b17c8c24da24a76f7f3ab7 authored over 2 years ago by Ciarán O’Mara <[email protected]>
Increment version

github.com/BioJulia/BGZFStreams.jl - 51af9df5ad5bf929c50cff3f45d4a18481fb276f authored over 2 years ago by Ciarán O’Mara <[email protected]>
Update email addresses

github.com/BioJulia/BGZFStreams.jl - 12659aa5621238415037f2578c3762abdaa8b36f authored over 2 years ago by Ciarán O’Mara <[email protected]>
Because of julia version change

github.com/BioJulia/BioAlignments.jl - 1195d3ec8b7059d49b0c9aeaf612eda2ffba0f5e authored over 2 years ago by Kevin Bonham <[email protected]>
Add Zenodo badge

github.com/BioJulia/BioAlignments.jl - c49bb0a3cd377ce1652ad6de0718881d05a942d8 authored over 2 years ago by Kevin Bonham <[email protected]>
Patch version

github.com/BioJulia/BioAlignments.jl - a97628422b30eac077957439c242a62dea20d8e4 authored over 2 years ago by Kevin Bonham <[email protected]>
Merge pull request #66 from BioJulia/zenodo-prep

Zenodo Prep

github.com/BioJulia/BioAlignments.jl - a823d73b390e36965da6cde29082c0aeda9c13a6 authored over 2 years ago by Ciarán O'Mara <[email protected]>
CompatHelper: bump compat for Pluto to 0.18, (keep existing compat)

github.com/BioJulia/BioMakie.jl - 850244770a3ed359e8dd3263b082adef906cf682 authored over 2 years ago by CompatHelper Julia <[email protected]>
update authors

github.com/BioJulia/BioAlignments.jl - 81ebf34886bf47ade3d51ba9eb786efcee7433ae authored over 2 years ago by Kevin Bonham <[email protected]>
Predicates docs

github.com/BioJulia/Kmers.jl - 39ea4bd57b9f5e368fefca854c26ab279a11c5ce authored over 2 years ago by Ben J. Ward <[email protected]>
Implement translate

github.com/BioJulia/SequenceVariation.jl - 92a2d40553f4d7e5c6e7e757543b81526f7b79b4 authored over 2 years ago by Jakob Nybo Nissen <[email protected]>