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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

reuse transpose, bump version

github.com/BioJulia/BioStructures.jl - 453c233a445cd271f9e111c18e360708471fca02 authored over 2 years ago by Joe Greener <[email protected]>
Fix Kabsch Algorithm to Prevent Reflections (#37)

* fix kabsch algorithm

* suggestions

github.com/BioJulia/BioStructures.jl - 19e7106856acbb3e7a89f5222899b3b2747de01f authored over 2 years ago by nhz2 <[email protected]>
Update Kmer construction

github.com/BioJulia/Kmers.jl - f339c80151202acdf70c21051d8d334a868916ec authored almost 3 years ago by Ben J. Ward <[email protected]>
CompatHelper: bump compat for CSV to 0.10, (keep existing compat)

github.com/BioJulia/PopGenCore.jl - 66a1aa82b70741822540a5560734f68c51a83a4c authored almost 3 years ago by CompatHelper Julia <[email protected]>
Create CODE_OF_CONDUCT.md

github.com/BioJulia/PopGen.jl - d3c24c64d7171bc2f1a4b0b8949b3bfdb51665fc authored almost 3 years ago by Pavel V. Dimens <[email protected]>
Add `findall` method (#218)

Add `findall` method

BioSequences recently rewrote the entire set of `Base.find*` functions f...

github.com/BioJulia/BioSequences.jl - d3d8fc49c7483a1fc3c767e18d1ed3fb1a9a436b authored almost 3 years ago by Ciarán O'Mara <[email protected]>
Fixed delete!(gene) bug

github.com/BioJulia/GenomicAnnotations.jl - d615bea2fc66d9c5c5ab865c1119cda20529a363 authored almost 3 years ago by Karl Dyrhage <[email protected]>
Fixed delete!(gene) bug

github.com/BioJulia/GenomicAnnotations.jl - 19ad755d02ad702c266a626c28065fcc70215aee authored almost 3 years ago by Karl Dyrhage <[email protected]>
Fixed delete!(gene) bug

github.com/BioJulia/GenomicAnnotations.jl - ed59559d01660820d565ba498026b735b5361ae0 authored almost 3 years ago by Karl Dyrhage <[email protected]>
Updated DataFrames API

github.com/BioJulia/GenomicAnnotations.jl - 4dca4fb2573245cc7d64b7e76917cd30749e8351 authored almost 3 years ago by Karl Dyrhage <[email protected]>
Updated version number

github.com/BioJulia/GenomicAnnotations.jl - ec7c72700f43be77c1003f455fea7b99c83b40f4 authored almost 3 years ago by Karl Dyrhage <[email protected]>
Updated to BioSequences v3 API

github.com/BioJulia/GenomicAnnotations.jl - f1fb6fe64dd0278040c1503a4780c0f99a2ce67b authored almost 3 years ago by Karl Dyrhage <[email protected]>
Update Project.toml

github.com/BioJulia/BioSequences.jl - 8d0080affc53db7dc69c25c83dabc3a198a13add authored almost 3 years ago by Sabrina Jaye Ward <[email protected]>
Correct Julia compatibility entry (#214)

Co-authored-by: Ciarán O’Mara <[email protected]>

github.com/BioJulia/BioSequences.jl - 3c8f501b0ec4e971433816bd057c11ac33466cb8 authored almost 3 years ago by Ciarán O'Mara <[email protected]>
CompatHelper: bump compat for GLMakie to 0.5, (keep existing compat)

github.com/BioJulia/BioMakie.jl - 86b48571f3b56572843cda112bf1bb426c3a7119 authored almost 3 years ago by CompatHelper Julia <[email protected]>
CompatHelper: bump compat for CairoMakie to 0.7, (keep existing compat)

github.com/BioJulia/BioMakie.jl - 3edb9a399387d40898efd0a37dfd5a99dc6390b4 authored almost 3 years ago by CompatHelper Julia <[email protected]>
CompatHelper: bump compat for WGLMakie to 0.5, (keep existing compat)

github.com/BioJulia/BioMakie.jl - 675ba9250a66825e4c5f0f519852b9ee4294b4e9 authored almost 3 years ago by CompatHelper Julia <[email protected]>
Remove backers from README.md

github.com/BioJulia/Kmers.jl - 6d0dc293be65956fe483e2fc961e7f3e5b7586ad authored almost 3 years ago by Ben J. Ward <[email protected]>
Get tests passing

github.com/BioJulia/Kmers.jl - 621d32c5bc7796cb572ffe7c088c54f9e5a77b6f authored almost 3 years ago by Ben J. Ward <[email protected]>
CompatHelper: bump compat for Makie to 0.16, (keep existing compat)

github.com/BioJulia/BioMakie.jl - 598fbd8fd4786ed05093c7073fd758dec06468ab authored almost 3 years ago by CompatHelper Julia <[email protected]>
CompatHelper: bump compat for BioSequences to 3, (keep existing compat)

github.com/BioJulia/BioMakie.jl - 91a2aa137339db02f28ffab747ec941ad15205b4 authored almost 3 years ago by CompatHelper Julia <[email protected]>
Small internal refactors (#210)

* Bugfix: Fix unbound function call `count_zero_nibbles` to `count_0000_nibbles`
* Bugfix: Fix ...

github.com/BioJulia/BioSequences.jl - 9918be2cea9f293d0b1657d4bce21c788a22e6f5 authored almost 3 years ago by Jakob Nybo Nissen <[email protected]>
Update some project files

github.com/BioJulia/Kmers.jl - 31a9a48123d38220e0930b00ed3aaa3a4bb104ee authored almost 3 years ago by Ben J. Ward <[email protected]>
Fixup a file header

github.com/BioJulia/BioSequences.jl - d82c88791455b439df62005cd7d1b6099ebe3a50 authored almost 3 years ago by Ben J. Ward <[email protected]>
Merge remote-tracking branch 'origin/compathelper/new_version/2021-10-13-00-17-41-749-03151575129'

github.com/BioJulia/Kmers.jl - 4f8e8c97d6107e3f8fff089f921590b1a12d68e6 authored almost 3 years ago by Ben J. Ward <[email protected]>
Update TagBot config

github.com/BioJulia/BioSequences.jl - aa17ff8839a39a174b2a9a7b2601063c0dceca26 authored almost 3 years ago by Ben J. Ward <[email protected]>
Update TagBot

github.com/BioJulia/BioSequences.jl - 125c31ce632b0bf232ef69aef11dbe33f6cda5ef authored almost 3 years ago by Ben J. Ward <[email protected]>
Add Jakob to Project.toml

github.com/BioJulia/BioSequences.jl - 16ec1ca0a7b1992ad2a9af76dd7da6824ec59802 authored almost 3 years ago by Ben J. Ward <[email protected]>
Update changelog

github.com/BioJulia/BioSequences.jl - 53d2e93f61b8aea6c59950890fbca0ca5c04aca5 authored almost 3 years ago by Ben J. Ward <[email protected]>
Update interface manual section

github.com/BioJulia/BioSequences.jl - c447ee74063ddbc6ea086014ed08e9ef38a3cbb6 authored almost 3 years ago by Ben J. Ward <[email protected]>
Fix bugs in minimal Alphabet interface example (#208)

github.com/BioJulia/BioSequences.jl - 137408d4e586fcb003c2b8057d5a954b9a957452 authored almost 3 years ago by Jakob Nybo Nissen <[email protected]>
Fixup Doctring

github.com/BioJulia/BioSequences.jl - 4cdc27e889e904ebfab2ae24b52aaaf04d6abe26 authored almost 3 years ago by Ben J. Ward <[email protected]>
Fix issues from v3/master merge (#207)

* CHANGELOG: Point users to MinHash.jl / Kmers.jl for removed functionality in v3
* CHANGELOG: ...

github.com/BioJulia/BioSequences.jl - 67cf42041c3e66018082760ac4325cfea364bb79 authored almost 3 years ago by Jakob Nybo Nissen <[email protected]>
Merge branch 'v3'

github.com/BioJulia/BioSequences.jl - 6afc528928c547b8c1961e78015a3ed1a0629328 authored almost 3 years ago by Ben J. Ward <[email protected]>
Search API redo (#190)

Co-authored-by: Ciarán O'Mara <[email protected]>

github.com/BioJulia/BioSequences.jl - ee961162a918a1b1c07698406d59c98cfa0e6b4b authored almost 3 years ago by Sabrina Jaye Ward <[email protected]>
Update authors (#61)

github.com/BioJulia/FASTX.jl - 0093974d36022bf6606f49fb54f47bd4e2979091 authored almost 3 years ago by Jakob Nybo Nissen <[email protected]>
Add an eof block check (#27)

* Add tests for virtual offset

The virtual offsets produced when writing data should be the s...

github.com/BioJulia/BGZFStreams.jl - 5597502592b088ea519e52b66d31011d69a3e23e authored almost 3 years ago by Ciarán O'Mara <[email protected]>
Maintenance (#26)

* Update .gitignore

* Add Project.toml

* Update license

* Remove CHANGELOG.md

* Remo...

github.com/BioJulia/BGZFStreams.jl - 5535913baf4fbe38c8d83eae88e1f9830f02aa22 authored almost 3 years ago by Ciarán O'Mara <[email protected]>
new1

github.com/BioJulia/BioMakie.jl - 1116cf6414a19b59461d25fae58ff8fa59526e22 authored almost 3 years ago by kool7d <[email protected]>
doc2

github.com/BioJulia/BioMakie.jl - 928491b86547b072381ae979a297b0a774a0678d authored almost 3 years ago by kool7d <[email protected]>
doc1

github.com/BioJulia/BioMakie.jl - eff6c082312f519e0cfdc1a5eae47415a56a3040 authored almost 3 years ago by kool7d <[email protected]>
Merge pull request #381 from kool7d/compathelper/new_version/2021-10-07-00-55-45-301-03235134901

CompatHelper: add new compat entry for DocumenterTools at version 0.1, (keep existing compat)

github.com/BioJulia/BioMakie.jl - ccfadb8c24a6b15c8518d545aa34b6656a2564a3 authored almost 3 years ago by Dan Kool <[email protected]>
Merge pull request #383 from kool7d/compathelper/new_version/2021-10-20-00-57-10-388-00921675062

CompatHelper: bump compat for GraphMakie to 0.3, (keep existing compat)

github.com/BioJulia/BioMakie.jl - a5bb5db1aa15d55591a726fa559d45eb350dcf4e authored almost 3 years ago by Dan Kool <[email protected]>
Merge pull request #384 from kool7d/compathelper/new_version/2021-10-28-00-53-03-111-03173361175

CompatHelper: bump compat for Pluto to 0.17, (keep existing compat)

github.com/BioJulia/BioMakie.jl - bafe7465037139b35a4eef8563f3aed67143e86f authored almost 3 years ago by Dan Kool <[email protected]>
Merge pull request #385 from kool7d/compathelper/new_version/2021-11-06-00-51-45-126-03644461906

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

github.com/BioJulia/BioMakie.jl - cc4db9305c8befd3cbe1bce7fe60aec4e40b6940 authored almost 3 years ago by Dan Kool <[email protected]>
Merge pull request #387 from kool7d/compathelper/new_version/2021-11-12-00-55-12-251-04289634135

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

github.com/BioJulia/BioMakie.jl - 0c7d7567ddca92a67fc67faeaab5f00d2e5d66f4 authored almost 3 years ago by Dan Kool <[email protected]>
Merge pull request #388 from kool7d/compathelper/new_version/2021-11-12-00-55-18-048-03812017594

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

github.com/BioJulia/BioMakie.jl - 8b5030ac81f54c52d47a96d8212bd0e26d13cd88 authored almost 3 years ago by Dan Kool <[email protected]>
Merge pull request #393 from kool7d/compathelper/new_version/2021-12-15-00-55-24-103-03542462145

CompatHelper: bump compat for Meshes to 0.19, (keep existing compat)

github.com/BioJulia/BioMakie.jl - e888a375b19a53655fccebe55557046a7ad93c3b authored almost 3 years ago by Dan Kool <[email protected]>
Merge branch 'master' into compathelper/new_version/2021-12-15-00-55-24-103-03542462145

github.com/BioJulia/BioMakie.jl - 664fca75b7f81ae45f265c81ebc866eb324bbba4 authored almost 3 years ago by Dan Kool <[email protected]>
lilbit

github.com/BioJulia/BioMakie.jl - 81a486f6f671a559df493940747d94d5025af5a8 authored almost 3 years ago by kool7d <[email protected]>
require Julia v1.6

github.com/BioJulia/BioStructures.jl - 876de6bf928546bf9710c0b14965866eec64a383 authored almost 3 years ago by Joe Greener <[email protected]>
enable CI on Mac

github.com/BioJulia/BioStructures.jl - 31bb7f6376389bbf3621f0da5dee08750b605e01 authored almost 3 years ago by Joe Greener <[email protected]>
firstindex and lastindex

github.com/BioJulia/BioStructures.jl - 9ec5632180707b5a4c053ca8efe19f29318150f2 authored almost 3 years ago by Joe Greener <[email protected]>
Add LTS release to test matrix

github.com/BioJulia/XAM.jl - dc0992ff540ffff13c54d2647052ddabcebcad86 authored almost 3 years ago by Ciarán O’Mara <[email protected]>
Update README.md

github.com/BioJulia/BioMakie.jl - 66fc6511fbcff9585592349cb90a9e3ffb7ac553 authored almost 3 years ago by Dan Kool <[email protected]>
Update README.md

github.com/BioJulia/BioMakie.jl - b32c1bcb2ddbce0f5235da332b77151572685583 authored almost 3 years ago by Dan Kool <[email protected]>
Merge pull request #394 from kool7d/dev

Dev

github.com/BioJulia/BioMakie.jl - c631d9014e0171bcb3ef40aeb1cc4436523a4ab3 authored almost 3 years ago by Dan Kool <[email protected]>
mostlydocs

github.com/BioJulia/BioMakie.jl - 0416098c54185f34a5410dad9d3b0004e40a7c6a authored almost 3 years ago by kool7d <[email protected]>
Updated travis versions

github.com/BioJulia/GenomicAnnotations.jl - ec2209273f031760c777d6be079a7f232ab666ca authored almost 3 years ago by Karl Dyrhage <[email protected]>
Updated CodecZlib compat entry

github.com/BioJulia/GenomicAnnotations.jl - 569eb14961f800228452c86e4890b406a033192d authored almost 3 years ago by Karl Dyrhage <[email protected]>
Updated version number

github.com/BioJulia/GenomicAnnotations.jl - d3c6912ea5ecdda48d22b9b271ea04bd1a4b20a2 authored almost 3 years ago by Karl Dyrhage <[email protected]>
Added CodecZlib dependency

github.com/BioJulia/GenomicAnnotations.jl - bee3b95a1177d6aa2a30bc6a4c469649c43e2ab0 authored almost 3 years ago by Karl Dyrhage <[email protected]>
CompatHelper: bump compat for Meshes to 0.19, (keep existing compat)

github.com/BioJulia/BioMakie.jl - e20aa1e570c52fb69231fe5154a8e523e551c289 authored almost 3 years ago by CompatHelper Julia <[email protected]>
disable CI on Mac

github.com/BioJulia/BioStructures.jl - e78dcbf583f43c5c5019ab24fba49a9f4404ec16 authored almost 3 years ago by Joe Greener <[email protected]>
Merge pull request #58 from jakobnissen/master

Export all user-facing functions

github.com/BioJulia/FASTX.jl - f6e82ec1a717996102c19beb3d4cf12c3ec1ef85 authored almost 3 years ago by Jakob Nybo Nissen <[email protected]>
Update README.md

github.com/BioJulia/Indexes.jl - 0f82c88c27acf08fccc4afe2c09ef9f6667a4007 authored almost 3 years ago by Pavel V. Dimens <[email protected]>
Include documenter tests in unit tests

github.com/BioJulia/Indexes.jl - 8abe585299ca97d1a180824b2d8432cb268e8c75 authored almost 3 years ago by Ciarán O'Mara <[email protected]>
Add downstream tests

github.com/BioJulia/Indexes.jl - de1b00c35a2b77c5efb85a083dc49b78eb4c0573 authored almost 3 years ago by Ciarán O'Mara <[email protected]>
Migrate to slack

github.com/BioJulia/Indexes.jl - ad7a3bd13030284a13e5791edba689e80e2fb9b2 authored almost 3 years ago by Ciarán O'Mara <[email protected]>
Remove Gitter badge

github.com/BioJulia/Indexes.jl - bf1590d70322856b1b951f47bdf4becc5f016d05 authored almost 3 years ago by Ciarán O'Mara <[email protected]>
Update status badges

github.com/BioJulia/Indexes.jl - 25c7d118fec8a66513cbd47cbfed545db58bbc49 authored almost 3 years ago by Ciarán O'Mara <[email protected]>
Update UnitTests workflow

github.com/BioJulia/Indexes.jl - dff17833772f721d7f52ca7630b23fc1d14aff22 authored almost 3 years ago by Ciarán O'Mara <[email protected]>
Update TagBot workflow

github.com/BioJulia/Indexes.jl - a43b0474490978b597ba2d99c70abdbba49cbdea authored almost 3 years ago by Ciarán O'Mara <[email protected]>
Update CompatHelper workflow

github.com/BioJulia/Indexes.jl - 50e82c893327de6a53915d73fbfc0e43c12e9a3d authored almost 3 years ago by Ciarán O'Mara <[email protected]>
Loosen types

This commit contains breaking changes.

github.com/BioJulia/GenomicFeatures.jl - 06f73422ffe134422e503fb0bc37ee75ca529d63 authored almost 3 years ago by Ciarán O'Mara <[email protected]>
Merge branch 'master' into develop

github.com/BioJulia/GenomicFeatures.jl - 30437841b2905c7421fd18bcad7ba81578aebf71 authored almost 3 years ago by Ciarán O'Mara <[email protected]>
Merge pull request #47 from BioJulia/release/v2.0.5

Release/v2.0.5

github.com/BioJulia/GenomicFeatures.jl - 483a38eeed7d63fd1ae47c0a3d0d04a78ab45fe1 authored almost 3 years ago by Ciarán O'Mara <[email protected]>
Merge pull request #43 from jakobnissen/flagdocs

Improve documentation of flag function

github.com/BioJulia/XAM.jl - c7114bce16c331804b748cbbede224d4c35b906f authored almost 3 years ago by Ciarán O'Mara <[email protected]>
update news

github.com/BioJulia/BioStructures.jl - 37b72bcf5dd10ab72aa6c2dc7980ef9b12a5a9a8 authored almost 3 years ago by Joe Greener <[email protected]>
consistent error printing

github.com/BioJulia/BioStructures.jl - bc747e77f4133c658805ae9517f9e39ee9abb681 authored almost 3 years ago by Joe Greener <[email protected]>
mention chainid! in docs

github.com/BioJulia/BioStructures.jl - 3cfd6d9fb185c90c6de07881f1d37c081117847a authored almost 3 years ago by Joe Greener <[email protected]>
docs for writing contact and distance maps

github.com/BioJulia/BioStructures.jl - cfb60e685b9f86b1473baaa33abae2b734c5d67b authored almost 3 years ago by Joe Greener <[email protected]>
switch from LightGraphs to Graphs

github.com/BioJulia/BioStructures.jl - a538f9165b6e6a08e85f558c28ae2b65e5decf73 authored almost 3 years ago by Joe Greener <[email protected]>
update docs with alignment pos introduced by #44 (#61)

github.com/BioJulia/BioAlignments.jl - 36a5e75778ec80cb3b556ea9963184917839c1f9 authored almost 3 years ago by Alexey Stukalov <[email protected]>
Update badges to show the status of the default branch

github.com/BioJulia/GenomicFeatures.jl - 18f7d4dbab93d6cce343ae52a78bd260d562515c authored almost 3 years ago by Ciarán O'Mara <[email protected]>
Add badge for downstream tests

github.com/BioJulia/GenomicFeatures.jl - a612b6471085e6d6f9c0bf34d21fcd80347da0cd authored almost 3 years ago by Ciarán O'Mara <[email protected]>
Merge remote-tracking branch 'origin/compathelper/new_version/2021-11-16-00-54-21-571-00723714791' into dev

github.com/BioJulia/BioMakie.jl - 99455b1e41893996218d4619c61acb07e4c42b27 authored almost 3 years ago by Daniel Kool <[email protected]>
activ1

github.com/BioJulia/BioMakie.jl - 9a52dd84a9c499d3a65b8a37f32713aa6d62f030 authored almost 3 years ago by kool7d <[email protected]>
Merge pull request #392 from kool7d/master

ms1

github.com/BioJulia/BioMakie.jl - ae13bafa0fd5e67789a02c11121d6a9ba0f9b5e5 authored almost 3 years ago by Dan Kool <[email protected]>
Merge pull request #391 from kool7d/dev

Merge pull request #390 from kool7d/master

github.com/BioJulia/BioMakie.jl - cec3132cf3b738478037647881b82baff49101dd authored almost 3 years ago by Dan Kool <[email protected]>
mc2

github.com/BioJulia/BioMakie.jl - 489c0a58773bda9f47c4c082c9e8fcb1b92ad725 authored almost 3 years ago by kool7d <[email protected]>
Merge pull request #390 from kool7d/master

msdev1

github.com/BioJulia/BioMakie.jl - 776fa9972051bac325faeabed95bb69365be2e5d authored almost 3 years ago by Dan Kool <[email protected]>
dc1

github.com/BioJulia/BioMakie.jl - 8fcc0a3f82f06303d4692b11f4e06d1400b189b1 authored almost 3 years ago by kool7d <[email protected]>
Drop changelog in favour of GitHub features

github.com/BioJulia/GenomicFeatures.jl - 22e66217bb6c38a0badbc22e43b2f7316f27ed9b authored almost 3 years ago by Ciarán O'Mara <[email protected]>
Filtering example

github.com/BioJulia/GenomicFeatures.jl - 551028de1f95298a76793c8d3cdb99ea6076c18f authored almost 3 years ago by Ciarán O’Mara <[email protected]>
Increment version

github.com/BioJulia/GenomicFeatures.jl - 0932d2f723715c4507187bce1eaa3f8f2bccdcd3 authored almost 3 years ago by Ciarán O'Mara <[email protected]>
Tweak strand definition

github.com/BioJulia/GenomicFeatures.jl - 2d881022d8369aad6731e0d4e77829e8fa0cf2ae authored almost 3 years ago by Ciarán O’Mara <[email protected]>
Add CI (#14)

github.com/BioJulia/FMIndexes.jl - 908e0fe022d4b04f4d4f06f89c2ae58a0dcc4ced authored almost 3 years ago by Jakob Nybo Nissen <[email protected]>
Fix constructor for String (#12)

github.com/BioJulia/FMIndexes.jl - 5fe3d617222dcdcb463e5f6b89369159b2774a7f authored almost 3 years ago by Jakob Nybo Nissen <[email protected]>
CompatHelper: bump compat for Meshes to 0.18, (keep existing compat)

github.com/BioJulia/BioMakie.jl - 31a26e2e9e74f2ec32020aea9ba399757f434cb4 authored almost 3 years ago by CompatHelper Julia <[email protected]>