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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

Initial commit

github.com/BioJulia/BioMakie.jl - d4114d217c57c54151e8a8ae4577bbf49cd0823e authored about 3 years ago by kool7d <[email protected]>
Merge pull request #80 from BioJulia/compathelper/new_version/2021-07-27-00-36-20-502-1664198753

CompatHelper: add new compat entry for "NaturalSort" at version "1"

github.com/BioJulia/PopGen.jl - 9ada6aafd8b547a157c460c4ae4f93c8a87ac93f authored about 3 years ago by Pavel V. Dimens <[email protected]>
CompatHelper: add new compat entry for "NaturalSort" at version "1"

github.com/BioJulia/PopGen.jl - 8bd820cddaf4caabb652cf90a22bc7690c0d3a8a authored about 3 years ago by github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Merge pull request #177 from jakobnissen/undefexp

Remove undefined exports

github.com/BioJulia/BioSequences.jl - 43030faedc015c1a35df73ba904334a771efc30a authored over 3 years ago by Jakob Nybo Nissen <[email protected]>
Remove undefined exports

github.com/BioJulia/BioSequences.jl - c661f215104be1e9107fb46a457d07ea2cba6e01 authored over 3 years ago by Jakob Nybo Nissen <[email protected]>
Merge pull request #166 from jakobnissen/findfirst

Add findfirst method for BioSymbol

github.com/BioJulia/BioSequences.jl - f1fdcdc48eaded0fc682d686341f0d6c02af8898 authored over 3 years ago by Jakob Nybo Nissen <[email protected]>
Amend docs for approxsearch returning nothing

github.com/BioJulia/BioSequences.jl - 3200f9cd7df1dfe752ef194a40d5062d65f11bdf authored over 3 years ago by Jakob Nybo Nissen <[email protected]>
Approximate search now returns nothing when no match is found

github.com/BioJulia/BioSequences.jl - 5ae42e4cd3ddb9122577f2322d2070d7fa72f2b9 authored over 3 years ago by Jakob Nybo Nissen <[email protected]>
Merge pull request #53 from jakobnissen/master

Allow compact printing of alignments

github.com/BioJulia/BioAlignments.jl - 5a3354eed4039d9e845adb82da6e144416451132 authored over 3 years ago by Jakob Nybo Nissen <[email protected]>
Add info to printing and add tests

github.com/BioJulia/BioAlignments.jl - 2c6f47f9a87091872e484d5394fd6ce86c241fdd authored over 3 years ago by Jakob Nybo Nissen <[email protected]>
Add test files or https://github.com/BioJulia/XAM.jl/issues/31 (#5)

* SRR7993829_1.100K.forward.bam

Add test files for https://github.com/BioJulia/XAM.jl/issues/...

github.com/BioJulia/FormatSpecimens.jl - 20770c9a2ddf1dae4cccfb8a8f62de204f550f72 authored over 3 years ago by Ciarán O'Mara <[email protected]>
fix typo

github.com/BioJulia/PopGen.jl - 70be376104637894738b8026bd04c2c09421918c authored over 3 years ago by Pavel Dimens <[email protected]>
fixes #77

github.com/BioJulia/PopGen.jl - 6ffdde743b958d9c4a428c354c5f96fd05a9013f authored over 3 years ago by Pavel Dimens <[email protected]>
fixes #76

github.com/BioJulia/PopGen.jl - ca5b654637327f3e4f18b3dbe44b6ddb4fb2c305 authored over 3 years ago by Pavel Dimens <[email protected]>
consolidate PopData marker printing

github.com/BioJulia/PopGen.jl - 8d3b60b8377c761b3af435d31aaecc5483e3d2ef authored over 3 years ago by Pavel Dimens <[email protected]>
fixes #75

github.com/BioJulia/PopGen.jl - 8faa648ada8ab1348d9ab85b2c145939f42c4e39 authored over 3 years ago by Pavel Dimens <[email protected]>
add NaturalSort

github.com/BioJulia/PopGen.jl - 41131325a2a955ea822167386f0918b8c3cbcade authored over 3 years ago by Pavel Dimens <[email protected]>
add NaturalSort, increase lower bounds of deps

github.com/BioJulia/PopGen.jl - df904cffaa440c2d370ea2cf7f5a58486b7b04b0 authored over 3 years ago by Pavel Dimens <[email protected]>
fixes [bug] export keep and keep! #78

github.com/BioJulia/PopGen.jl - 8ec38c08d3d299f20769be572a872dc4acc719af authored over 3 years ago by Pavel Dimens <[email protected]>
Merge pull request #9 from jakobnissen/iodo

Move to version 0.1.1

github.com/BioJulia/BioGenerics.jl - a75abaf459250e2b5e22b4d9adf25fd36d2acab6 authored over 3 years ago by Jakob Nybo Nissen <[email protected]>
Move to version 0.1.1

github.com/BioJulia/BioGenerics.jl - a95a008f7084f2610727536a3d9fd7cc9cbbb9e3 authored over 3 years ago by Jakob Nybo Nissen <[email protected]>
Merge pull request #5 from jakobnissen/iodo

Add do syntax to AbstractFormattedIO built from other IO objects

github.com/BioJulia/BioGenerics.jl - 4624fa9c76f39935868e4ab12e877c32e93f1fa1 authored over 3 years ago by Jakob Nybo Nissen <[email protected]>
Fix IO ambiguity

github.com/BioJulia/BioGenerics.jl - 5872c343f8c82ef4432fa186399acc34f4223a6c authored over 3 years ago by Jakob Nybo Nissen <[email protected]>
Merge pull request #73 from BioJulia/compathelper/new_version/2021-05-16-01-12-24-128-1843610568

CompatHelper: bump compat for "MultipleTesting" to "0.5"

github.com/BioJulia/PopGen.jl - 9d72d253738b0bf75599390111ed6a908ca73534 authored over 3 years ago by Pavel V. Dimens <[email protected]>
Allow compact printing of alignments

github.com/BioJulia/BioAlignments.jl - d71c3999f2d2c47ebd02abfe4b2a6decbab724f0 authored over 3 years ago by Jakob Nybo Nissen <[email protected]>
Translate between FASTQ & FASTA files (#53)

github.com/BioJulia/FASTX.jl - c7079979e8a6a83ac2a3860baea929498835cdf9 authored over 3 years ago by Ben J. Ward <[email protected]>
Fix error in docstring

github.com/BioJulia/BioSequences.jl - a8e5b48002b44c3c9afb79dbac98a9fa32949573 authored over 3 years ago by Jakob Nybo Nissen <[email protected]>
Merge pull request #169 from jakobnissen/v3

Export RE.Regex and RE.RegexMatch as BioRegex and BioRegexMatch

github.com/BioJulia/BioSequences.jl - c3b0cca49c3106f7fe636935ae9693117589c011 authored over 3 years ago by Jakob Nybo Nissen <[email protected]>
Export RE.Regex and RE.RegexMatch as BioRegex and BioRegexMatch

github.com/BioJulia/BioSequences.jl - 88de9c73bc80847cfaaaab0541e97918f32d139f authored over 3 years ago by Jakob Nybo Nissen <[email protected]>
Merge pull request #52 from jakobnissen/master

Allow trailing whitespace in sequences

github.com/BioJulia/FASTX.jl - 0d81f163d41eadb8e907a3471d1ab532402ddcff authored over 3 years ago by Jakob Nybo Nissen <[email protected]>
Allow trailing whitespace in sequences

github.com/BioJulia/FASTX.jl - af6b19ae667644055b919cd53d2a53b60f4119b7 authored over 3 years ago by Jakob Nybo Nissen <[email protected]>
Update Project.toml

github.com/BioJulia/FASTX.jl - c4f9fb81704908bb68a330c4c93a49f477e8eea9 authored over 3 years ago by Jakob Nybo Nissen <[email protected]>
Add changelog for 1.2.0

github.com/BioJulia/FASTX.jl - d69c33b976bc14a04c7184b5ddac472f354c97f9 authored over 3 years ago by Jakob Nybo Nissen <[email protected]>
Return early

github.com/BioJulia/XAM.jl - 9d2a70531a32ee11770aca2f4397b2a00e8a9c9b authored over 3 years ago by Ciarán O’Mara <[email protected]>
Comments

github.com/BioJulia/XAM.jl - 18dae0d45dc9432930fb7f880837d844c0b7ea9e authored over 3 years ago by Ciarán O’Mara <[email protected]>
Tidy state machines and improve error messages

Makes better use of the existing flow in [Automa.jl](https://github.com/BioJulia/Automa.jl/blob/...

github.com/BioJulia/XAM.jl - 8f26bbf4a728761de812dbfd296a286c988d7bbc authored over 3 years ago by Ciarán O’Mara <[email protected]>
Update Continuous Integration workflows

- Includes doctest in tests.

github.com/BioJulia/XAM.jl - c56eb0851a0876156656a002a119a311d596fe4e authored over 3 years ago by Ciarán O’Mara <[email protected]>
Readability

github.com/BioJulia/XAM.jl - fa10f3bfcfa0e0dec43d2059a57dcdd7d7939ea3 authored over 3 years ago by Ciarán O’Mara <[email protected]>
Merge branch 'master' into develop

github.com/BioJulia/GFF3.jl - 505519d08d017b0170c14b1a3d06e9645145b75c authored over 3 years ago by Ciarán O’Mara <[email protected]>
Merge branch 'hotfix/strand'

github.com/BioJulia/GFF3.jl - c0ba45a8ffc4bfdea2b6d89455a132f61f24e1e3 authored over 3 years ago by Ciarán O’Mara <[email protected]>
Remove`ismissing` check from strand accessor

Fixes #5.

github.com/BioJulia/GFF3.jl - adf203681b55f7a24df3ffb82ac1ea79a4ba5bec authored over 3 years ago by Ciarán O’Mara <[email protected]>
Increment version

github.com/BioJulia/GFF3.jl - 619cc79f6782eb4b35472e2c3be3fb98ebb21eea authored over 3 years ago by Ciarán O’Mara <[email protected]>
Merge branch 'master' into develop

github.com/BioJulia/GFF3.jl - f9066d8fe61d8073944fa97d64755b3690f84453 authored over 3 years ago by Ciarán O’Mara <[email protected]>
Merge branch 'release/v0.2.0'

github.com/BioJulia/GFF3.jl - 3278e1b73a8071d18d43c64fe52d1ee520275746 authored over 3 years ago by Ciarán O'Mara <[email protected]>
Increment version

github.com/BioJulia/GFF3.jl - f1281dbb35a376f4ff84a456fcd572edf265abaf authored over 3 years ago by Ciarán O’Mara <[email protected]>
Fix parser ambiguity

github.com/BioJulia/GFF3.jl - d2614d538bdc3ecbb5f602b54e15370e49074593 authored over 3 years ago by Jakob Nybo Nissen <[email protected]>
Merge branch 'feature/transcodingstreams' into develop

github.com/BioJulia/GFF3.jl - 3e56dedb5b5ba247c3e3e06d3ccc32e36391c245 authored over 3 years ago by Ciarán O’Mara <[email protected]>
In-place iteration

github.com/BioJulia/GFF3.jl - d3a1327a74ca83b0396c4cc69534dff15199c935 authored over 3 years ago by Ciarán O’Mara <[email protected]>
Index!

github.com/BioJulia/GFF3.jl - 1c86cb30e7a7a634e12f705fe7a788caaddbc024 authored over 3 years ago by Ciarán O’Mara <[email protected]>
Read!

github.com/BioJulia/GFF3.jl - 64a160f9f23ae5f53a5682dd82126fd0dda5786a authored over 3 years ago by Ciarán O’Mara <[email protected]>
Pipe into `eval`

github.com/BioJulia/GFF3.jl - f0218a0f543f2877cf05fd2667993493eb49803a authored over 3 years ago by Ciarán O'Mara <[email protected]>
Align emissions

github.com/BioJulia/GFF3.jl - 217f54c2b8cf90074820a63b9a6148cfa409baad authored over 3 years ago by Ciarán O’Mara <[email protected]>
Migrate from BufferedStreams to TranscodingStreams

github.com/BioJulia/GFF3.jl - 33114fed41b87293226e4f34f7eeed7d44cdb0c1 authored over 3 years ago by Ciarán O’Mara <[email protected]>
Use BioGenerics.Automa.State{S}

Finished to filled

github.com/BioJulia/GFF3.jl - 67710685c8b950ad56fdb17cf85a944ffc064293 authored over 3 years ago by Ciarán O’Mara <[email protected]>
Replace `resize_and_copy!` with `appendfrom!`

github.com/BioJulia/GFF3.jl - eddd420de43976a7ee243f15bb0198928805a2c3 authored over 3 years ago by Ciarán O'Mara <[email protected]>
Distinguish and use BioCore accessors in tests

github.com/BioJulia/GFF3.jl - da0c51e9f7869fc532ae62083020e329a564fcde authored over 3 years ago by Ciarán O'Mara <[email protected]>
Eltype

github.com/BioJulia/GFF3.jl - 47e12370246aa39832e8778315a311c02a730165 authored over 3 years ago by Ciarán O'Mara <[email protected]>
Use BioGenerics’ Automa.Stream.generate_reader

github.com/BioJulia/GFF3.jl - 672c08d4e160c1efa59d601b96a590a1718d400b authored over 3 years ago by Ciarán O'Mara <[email protected]>
Migrate from BioCore to BioGenerics

Basic find and replace.

github.com/BioJulia/GFF3.jl - d905810436b1416d32db61d6ab123052df76468d authored over 3 years ago by Ciarán O'Mara <[email protected]>
Merge branch 'master' into develop

github.com/BioJulia/GFF3.jl - 5da58eefe837be2bea4f11b3824e53007fdd4dad authored over 3 years ago by Ciarán O’Mara <[email protected]>
Merge branch 'release/v0.1.1'

github.com/BioJulia/GFF3.jl - b0da4b74a0fc8f5abe9ec4d153f3ee4dfbef7cbb authored over 3 years ago by Ciarán O'Mara <[email protected]>
Increment version

github.com/BioJulia/GFF3.jl - 768a0094136b8dfd2f531c4c339f9e365e45abf9 authored over 3 years ago by Ciarán O’Mara <[email protected]>
Using before import

github.com/BioJulia/GFF3.jl - 54100a66c59dacc3cbfcadba50d3fcacb6e4b1d3 authored over 3 years ago by Ciarán O'Mara <[email protected]>
Remove hardwraps

github.com/BioJulia/GFF3.jl - a20e5b596c87c0372e025368d4d49d56e1a51ed6 authored over 3 years ago by Ciarán O'Mara <[email protected]>
Update CI and documentation for the general registry

github.com/BioJulia/GFF3.jl - f4eee4764d0551bbdbbbc44f61268b062a86b273 authored over 3 years ago by Ciarán O'Mara <[email protected]>
Reverst Project.toml change

github.com/BioJulia/BioSequences.jl - e7cec9d23791a88ff8ab07ed72cdc36668246284 authored over 3 years ago by Jakob Nybo Nissen <[email protected]>
Add findfirst method for BioSymbol

github.com/BioJulia/BioSequences.jl - 8ae45af4151d339084426facebd0fb106ea49306 authored over 3 years ago by Jakob Nybo Nissen <[email protected]>
Change sequence type aliases (#163)

github.com/BioJulia/BioSequences.jl - aeb6435775eb6a46509d7a5e5a3a844d32f76887 authored over 3 years ago by Ben J. Ward <[email protected]>
Doctest setup

github.com/BioJulia/BED.jl - f63c3ace613f4b3bfdf3b77ea057211ec27373ce authored over 3 years ago by Ciarán O’Mara <[email protected]>
Correct badges

github.com/BioJulia/BED.jl - 2160827b839c119701c3e3c1cc56c8c64660ba46 authored over 3 years ago by Ciarán O’Mara <[email protected]>
Merge branch 'master' into develop

github.com/BioJulia/BED.jl - 2a988e2b2de895258e4df368b95d829e97b1487d authored over 3 years ago by Ciarán O’Mara <[email protected]>
Merge pull request #164 from jakobnissen/fasteq

Add fast equality for BioSequence

github.com/BioJulia/BioSequences.jl - 0c17505208763b721fb8b72456a2b952b5274a73 authored over 3 years ago by Jakob Nybo Nissen <[email protected]>
Add fast equality for BioSequence

github.com/BioJulia/BioSequences.jl - 43459ef8fb14c0884024c0fc0ca352fff0526d3d authored over 3 years ago by Jakob Nybo Nissen <[email protected]>
Merge pull request #11 from BioJulia/compat

Bump compatibility

github.com/BioJulia/BED.jl - beb02543b9bb12b1777899ba56f2461ed4393705 authored over 3 years ago by Ciarán O'Mara <[email protected]>
Merge pull request #49 from jakobnissen/newlineend

Allow trailing newlines for FASTQ files

github.com/BioJulia/FASTX.jl - 215360d88ca3c32fa6b6304eaf85c4a15d385c85 authored over 3 years ago by Jakob Nybo Nissen <[email protected]>
CompatHelper: bump compat for "ColorTypes" to "0.11"

github.com/BioJulia/BED.jl - 0fe0abfae9e30d129333493ed6c53019a3854958 authored over 3 years ago by github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
CompatHelper: bump compat for "ColorTypes" to "0.10"

github.com/BioJulia/BED.jl - 51a7ae90789d73bdaf2b875ac377bc4b9bcdc183 authored over 3 years ago by github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
CompatHelper: bump compat for "FixedPointNumbers" to "0.8"

github.com/BioJulia/BED.jl - 907c909d5a4a8bcfe5486bdf0577d0aec68f5bf2 authored over 3 years ago by github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Increment version

github.com/BioJulia/BED.jl - ef8b6c9d3405b726c3e4f1b995e494905b635952 authored over 3 years ago by Ciarán O’Mara <[email protected]>
Merge branch 'master' into develop

github.com/BioJulia/BED.jl - 1209dcf39c92b6247f4bafe3bd6f615fcc32d1b3 authored over 3 years ago by Ciarán O'Mara <[email protected]>
Merge branch 'release/v0.2.0'

github.com/BioJulia/BED.jl - 945845044e5bb10da761bd02ba7cc291c3f28c97 authored over 3 years ago by Ciarán O'Mara <[email protected]>
Add compat entry for TranscodingStreams

github.com/BioJulia/BED.jl - b6af780a8bc20cc334fb4fe01bdfa6dd1a316b1f authored over 3 years ago by Ciarán O'Mara <[email protected]>
Include doctests in tests.

github.com/BioJulia/BED.jl - 3028ff4c04e740baeccf76bee5ed298457c48acd authored over 3 years ago by Ciarán O'Mara <[email protected]>
Increment version

github.com/BioJulia/BED.jl - 7094f816147bcc78105ef18d4f5f2173a83ab6dd authored over 3 years ago by Ciarán O'Mara <[email protected]>
Merge branch 'feature/TranscodingStreams' into develop

github.com/BioJulia/BED.jl - 1cf7b259d5058c45c7473d096127da251ccfe91a authored over 3 years ago by Ciarán O'Mara <[email protected]>
Migrate from BufferedStreams to TranscodingStreams

github.com/BioJulia/BED.jl - b70b7603f55ec8837bf6e64c093c3e68ec252f83 authored over 3 years ago by Ciarán O’Mara <[email protected]>
Migrate from BioCore to BioGenerics

Rename `initialize!` method as `empty!`

github.com/BioJulia/BED.jl - 535e581530ac0298368ee5433f777d060509b517 authored over 3 years ago by Ciarán O'Mara <[email protected]>
Merge branch 'master' into develop

github.com/BioJulia/BED.jl - 400c1cd2cea57483330d2526900d0bfffe927663 authored over 3 years ago by Ciarán O’Mara <[email protected]>
Merge branch 'release/v0.1.1'

github.com/BioJulia/BED.jl - 3e694e4512ffaa6c02f3fa891f2adf2e215894a5 authored over 3 years ago by Ciarán O’Mara <[email protected]>
Increment version

github.com/BioJulia/BED.jl - d5c4752b721a6777f0497378cc45e4e7f1648a8d authored over 3 years ago by Ciarán O’Mara <[email protected]>
Flatten ifelse

github.com/BioJulia/BED.jl - b45bda43374ca003d84cd13d92aff0a7f1d6b5d0 authored over 3 years ago by Ciarán O'Mara <[email protected]>
Loosen Julia requirement

github.com/BioJulia/BED.jl - 43bc3f1cd41e2d3eeeae77cda637c357bcdc2911 authored over 3 years ago by Ciarán O’Mara <[email protected]>
Update CI and documentation for the general registry

github.com/BioJulia/BED.jl - d32557f457d0275fd71991170531401574dda0cd authored over 3 years ago by Ciarán O’Mara <[email protected]>
Update user manual (#160)

github.com/BioJulia/BioSequences.jl - 87f806c70a9fa861b7dc3a17f95dcc90654d2019 authored over 3 years ago by Ben J. Ward <[email protected]>
Update interface to version 3. (#161)

* Refactor internals: Part 1

* Refactor internals 2: Add Alphabet tests

* Refactor interna...

github.com/BioJulia/BioSequences.jl - 9d40795e7ed188e2257d0f455b908b523aedf2ab authored over 3 years ago by Jakob Nybo Nissen <[email protected]>
CompatHelper: bump compat for "BioSymbols" to "5" (#31)

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

github.com/BioJulia/BioStructures.jl - 609dc738845ccea059feed88b035127a6b2f7197 authored over 3 years ago by github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Update TagBot.yml

github.com/BioJulia/BioSymbols.jl - 3d796d12a6504a3a9d4495a42c87f239fd848250 authored over 3 years ago by Ben J. Ward <[email protected]>
Update TagBot.yml

github.com/BioJulia/BioSymbols.jl - 970189a986f4ddd544496eedbd531085c56857b7 authored over 3 years ago by Ben J. Ward <[email protected]>
Update Project.toml

Bump version number a major increment

github.com/BioJulia/BioSymbols.jl - 8e6966acfabf0c0b1fe51016b67e820cfb598b31 authored over 3 years ago by Ben J. Ward <[email protected]>
no alias in plot recipe

github.com/BioJulia/BioStructures.jl - 9983f9066d8dcdba8ab5c00cc6664b95cb366706 authored over 3 years ago by Joe Greener <[email protected]>