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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 test scripts

github.com/BioJulia/MicrobiomePlots.jl - 24ca3ec5ac112038352d965d646307aaf621a821 authored about 6 years ago by Kevin Bonham <[email protected]>
Merge pull request #3 from joels94/master

Support Julia 0.7 & 1.0 and Drop 0.6

github.com/BioJulia/MMTF.jl - 7e1166f07c17670e8df69a9fcfbd654045733939 authored about 6 years ago by Joel S <[email protected]>
Appveyor - Fix "Could not create SSL/TLS secure channel"

github.com/BioJulia/MMTF.jl - db7e4a5353f7885f6590ffdc9d3ca7604c14617c authored about 6 years ago by Joel S <[email protected]>
add top=level files

github.com/BioJulia/MicrobiomePlots.jl - 2e354c9e9c722c1688c8e0aa0f1c8627cb2bc1dd authored about 6 years ago by Kevin Bonham <[email protected]>
Supports Julia 0.7, 1.0 & Drops Julia 0.6

github.com/BioJulia/MMTF.jl - 632b958d2b5176f4301e8694f01bf335542c35d9 authored about 6 years ago by Joel S <[email protected]>
Add LICENSE

github.com/BioJulia/IntervalTrees.jl - a123c23ee7345f980f26948491df76669778091f authored about 6 years ago by Ben J. Ward <[email protected]>
Add HUMANS.md

github.com/BioJulia/IntervalTrees.jl - 4dd11f06ad6713cbe10f3b0d97d02864a7826d03 authored about 6 years ago by Ben J. Ward <[email protected]>
Add changelog and change lifecycle badge

github.com/BioJulia/IntervalTrees.jl - 667d0ab494dc93e96c0d4355b82af3fcd0ae8749 authored about 6 years ago by Ben J. Ward <[email protected]>
Add project files, and documentation generation

Use Documenter.jl in travis

Add sticker

Add logo.png for documentation

Make git ignore .DN_St...

github.com/BioJulia/IntervalTrees.jl - f7870ccac0690e0996cfa881d23152b1e887e748 authored about 6 years ago by Ben J. Ward <[email protected]>
Merge pull request #28 from tanmaykm/tan/julia10

Julia 1.0 compat

github.com/BioJulia/Codecs.jl - 5d692bd603a7bf882e040819a80362378e57f9ed authored about 6 years ago by Randy Zwitch <[email protected]>
Merge pull request #2 from joels94/master

Support for Julia v0.7

github.com/BioJulia/MMTF.jl - cad4eae6bb46f3bfb71da143f728763244601eef authored about 6 years ago by Joel S <[email protected]>
Fix deprecations (#43)

github.com/BioJulia/IntervalTrees.jl - 7b46279b4e3552681ff371530414ddd9f27df942 authored about 6 years ago by Kenta Sato <[email protected]>
Merge pull request #41 from bicycle1885/drop-0.6

github.com/BioJulia/IntervalTrees.jl - 9892c527336864ae43d77e02a5e6984cd42b6dcc authored about 6 years ago by Kenta Sato <[email protected]>
do not run Travis Ci on Julia 0.6

github.com/BioJulia/IntervalTrees.jl - c29c219649c709cdb632e6ee2ea1c67cdc8a6c58 authored about 6 years ago by Kenta Sato <[email protected]>
Merge remote-tracking branch 'remotes/origin/version-1.0' into drop-0.6

github.com/BioJulia/IntervalTrees.jl - 937d38df0f75b1aa2e298aadba8ba303dcd8998b authored about 6 years ago by Kenta Sato <[email protected]>
get code from Microbiome

github.com/BioJulia/MicrobiomePlots.jl - 32279043da962b5eb6f7cc38c60ce047f7dd0204 authored about 6 years ago by Kevin Bonham <[email protected]>
initial commit

github.com/BioJulia/MicrobiomePlots.jl - c89644c3c15311a52a54aa4baf22f0f87ecee4b2 authored about 6 years ago by Kevin Bonham <[email protected]>
Support for Julia v0.7

github.com/BioJulia/MMTF.jl - 135b028e223b0773b3970a3b4ab90bdbbf11b680 authored about 6 years ago by Joel S <[email protected]>
update benchmark script (#40)

github.com/BioJulia/Automa.jl - 254dd4b04901157d2f358f414681da1c8dc37c82 authored about 6 years ago by Kenta Sato <[email protected]>
Support Julia 0.7 and drop 0.6 (#39)

github.com/BioJulia/Automa.jl - 31653ceae770d58c2583f67e5f1ef92b56eb634f authored about 6 years ago by Kenta Sato <[email protected]>
update appveyor.yml

github.com/BioJulia/Codecs.jl - 72c55a78015788d71f0a0aa7794d66c314147377 authored about 6 years ago by tan <[email protected]>
Julia 1.0 compat

- Julia 0.7 and 1.0 compatible
- dropped support 0.5 and 0.6
- dropped Compat.jl

github.com/BioJulia/Codecs.jl - 5464f39833f45327e37dcb24a10540ad475cc7b0 authored about 6 years ago by tan <[email protected]>
Drop julia 0.6

github.com/BioJulia/IntervalTrees.jl - ed63ee7dacb022261c2127ef0c801b4680d5ab48 authored about 6 years ago by Ben J. Ward <[email protected]>
Update README.md

github.com/BioJulia/IntervalTrees.jl - f552262e63c32ae333c8eb7539154104fac4f9db authored about 6 years ago by Ben J. Ward <[email protected]>
Changes pertaining to supporting 0.7 (#37)

* fix README.md

* Fix a bug in firstintersection that can lead to missed intersections.

* ...

github.com/BioJulia/IntervalTrees.jl - 65b8d1e2932253cf8269f6249d20fb11284e7a53 authored about 6 years ago by Sambit Kumar Dash <[email protected]>
Merge pull request #16 from BioJulia/nsamples

Fix n_samples method for BCF records

github.com/BioJulia/GeneticVariation.jl - dee5f670270a151e43ef4174ebeceab91abaf93b authored about 6 years ago by Ben J. Ward <[email protected]>
Fix readme and add sticker

github.com/BioJulia/GeneticVariation.jl - 98d95aad2eb05081994dc9d814e092df2afb2589 authored about 6 years ago by Ben J. Ward <[email protected]>
Add CHANGELOG.md file

github.com/BioJulia/GeneticVariation.jl - cc0d29efa3e1e504720d6da5ca82ffbd2a54615a authored about 6 years ago by Ben J. Ward <[email protected]>
Added HUMANS.md project file

github.com/BioJulia/GeneticVariation.jl - a880c0ad2c649e78db393832582730cf1b83893c authored about 6 years ago by Ben J. Ward <[email protected]>
Updated README.md project file

github.com/BioJulia/GeneticVariation.jl - eaff72b5b1af7d25414c27887ff420e09680d1b4 authored about 6 years ago by Ben J. Ward <[email protected]>
Fix a minor error in the README.md

github.com/BioJulia/BioServices.jl - 75b396fd2b3420208840dbcc404f3544a7e2f69d authored about 6 years ago by Ben J. Ward <[email protected]>
Fix n_samples method for BCF records

github.com/BioJulia/GeneticVariation.jl - 29b60ac5626084f7119e36b72d64eb899e1443ad authored about 6 years ago by Ben J. Ward <[email protected]>
Merge pull request #1 from BioJulia/rollout-contributing

Contributing files rollout

github.com/BioJulia/MMTF.jl - 4dac379e2345916ac90dee4d9c775b9a634f6bea authored over 6 years ago by Joel S <[email protected]>
Restore inclusion of BioServices

github.com/BioJulia/Bio.jl - d48cf42e42e88ee9a0e283ccf80ecce02d03d8f4 authored over 6 years ago by Ben J. Ward <[email protected]>
Merge pull request #17 from BioJulia/humans-patch-1

Missing fernandogelin

github.com/BioJulia/BioServices.jl - 5c7852d3340c0e9a5cd80dd210630d3252215a34 authored over 6 years ago by Maria Isabel Restrepo <[email protected]>
Update CHANGELOG.md

github.com/BioJulia/BioServices.jl - bb792cc6d6610634a3877148f9a12712420af7a4 authored over 6 years ago by Maria Isabel Restrepo <[email protected]>
Missing fernandogelin

github.com/BioJulia/BioServices.jl - d1724966bd2df471fe3f390e0af21f623877f951 authored over 6 years ago by Maria Isabel Restrepo <[email protected]>
fix CHANGELOG.md [ci skip] (#16)

github.com/BioJulia/BioServices.jl - 29bf3d99b8c4f6205c1476d3ac06e6d846676edd authored over 6 years ago by Kenta Sato <[email protected]>
add some touch-ups to GGGnome (#15)

* add some touch-ups to GGGnome (#12)

* prepare for v0.2.0

github.com/BioJulia/BioServices.jl - df68418a2c554ef7248d2a5c79a24d542657117d authored over 6 years ago by Kenta Sato <[email protected]>
Backwards compatibility with 0.2 releases for zstream init functions (#63)

* Backwards compatibility with 0.2 releases for init_inflate_zstream and init_deflate_zstream.
...

github.com/BioJulia/Libz.jl - c22e7a1970ae060953329ad915ad61ab10cacae3 authored over 6 years ago by Gunnar Farnebäck <[email protected]>
add GGGenome (#12)

* add GGGenome

* change function names

* 'query' argument is changed to a required augment...

github.com/BioJulia/BioServices.jl - 9e8f000b5ec36500a94b8a0717f90a424e3d6387 authored over 6 years ago by Haruka Ozaki <[email protected]>
Merge pull request #13 from BioJulia/restore-ezxml

Project file updates

github.com/BioJulia/BioServices.jl - 1965128c7e803911565b959dd61c29ffcd9029e9 authored over 6 years ago by Maria Isabel Restrepo <[email protected]>
add delay between call to not exceen EUtils limit of 3/second

github.com/BioJulia/BioServices.jl - 02763eeb7d48d193deac49f4bbb7bcfaa64e7c60 authored over 6 years ago by Isabel Restrepo (pencil) <[email protected]>
Update project files

github.com/BioJulia/BioServices.jl - b34f090a97e21a982e3834bc94ffa9d79fcd5a93 authored over 6 years ago by Ben J. Ward <[email protected]>
Fix deprecations (#62)

github.com/BioJulia/Libz.jl - d0b2a2e0f984f71b6af4a365302131c99fcb4164 authored over 6 years ago by femtocleaner[bot] <femtocleaner[bot]@users.noreply.github.com>
Fix Julia 0.7 deprecations (#61)

This pull fixes Julia 0.7 deprecations, and drops julia v0.5

github.com/BioJulia/Libz.jl - 89698ec6995c76be1a7fe4a0d0dd367f2d5db935 authored over 6 years ago by Gunnar Farnebäck <[email protected]>
Fix escaping - and ^ inside character classes. (#36)

github.com/BioJulia/Automa.jl - 3c9891053dcd1125024f55a8f9a425fc24984ff5 authored over 6 years ago by Daniel C. Jones <[email protected]>
Merge pull request #27 from dcjones/master

Add ERCC92.gff3 example

github.com/BioJulia/BioFmtSpecimens - 24975677f191d6ca2f1739efcbfea4f1c56b67b5 authored over 6 years ago by Ben J. Ward <[email protected]>
Add ERCC92.gff3 example.

github.com/BioJulia/BioFmtSpecimens - a55767b4caae529688ad2d6c75ca933fed32827f authored over 6 years ago by Daniel C. Jones <[email protected]>
Initial commit

github.com/BioJulia/BSG.jl - 4f5bc05e7cdb972d6b955e1fb41782b2270ed4eb authored over 6 years ago by Ben J. Ward <[email protected]>
Merge pull request #22 from BioJulia/pmapfix

This PR fixed some errors when using the pmap method.
The error was caused by the NucleicAcid a...

github.com/BioJulia/BioSymbols.jl - 42c33533e2aa999fde5fe13d940ce1906886333f authored over 6 years ago by Ben J. Ward <[email protected]>
Update project files and add package sticker

github.com/BioJulia/BioSymbols.jl - 2585cd62a8ef88b7bd75902bd16636099c6f62a6 authored over 6 years ago by Ben J. Ward <[email protected]>
Initial commit

github.com/BioJulia/BioJulia-stickers - 54dc2696c94327adf4aa29223e124c677c8fc461 authored over 6 years ago by Ben J. Ward <[email protected]>
Update the changelog

github.com/BioJulia/BioSymbols.jl - 30434db22d4773f376b3d7a95e440412b9bb4c3f authored over 6 years ago by Ben J. Ward <[email protected]>
Add tests for read and write

github.com/BioJulia/BioSymbols.jl - 6f070f39573f546a018e69e3f05c30a0300d791c authored over 6 years ago by Ben J. Ward <[email protected]>
Add write and print methods

github.com/BioJulia/BioSymbols.jl - 0c77e938e7430487591308f7157046353f0854df authored over 6 years ago by Ben J. Ward <[email protected]>
Merge branch 'master' of github.com:BioJulia/BioSymbols.jl

github.com/BioJulia/BioSymbols.jl - 73b1034e04b82ea3fbce3c1121a2fc15fd73d719 authored over 6 years ago by Ben J. Ward <[email protected]>
Add CHANGELOG and update REQUIRE

github.com/BioJulia/BioSymbols.jl - 048ff9eb0e8d467032c00377d022f499cdf60c4b authored over 6 years ago by Ben J. Ward <[email protected]>
Merge pull request #11 from fernandogelin/master

Change functions to use XMLDict instead of EzXML

github.com/BioJulia/BioServices.jl - d74a3264794ee00a89f3fc75943868c32749736b authored over 6 years ago by Maria Isabel Restrepo <[email protected]>
updates REQUIRE

github.com/BioJulia/BioServices.jl - bbfa7f80735d757a188cc7816ccbd8a963a34c88 authored over 6 years ago by fgelin <[email protected]>
changes to XMLDict

github.com/BioJulia/BioServices.jl - e4a34278d446876a879b3ea4f7beb8b77c0a887a authored over 6 years ago by fgelin <[email protected]>
Disable BioServices temporarily

github.com/BioJulia/Bio.jl - 98084dd6341151a1129e27a620695eca7f4fe39a authored over 6 years ago by Ben J. Ward <[email protected]>
Remove Tools and Phylo temporarily

github.com/BioJulia/Bio.jl - 7f8eae97c4c1d373c2d22cb62592a682e4010932 authored over 6 years ago by Ben J. Ward <[email protected]>
Fix deprecations (#3)

github.com/BioJulia/WaveletMatrices.jl - 36d6df3a9ca71a41e66bd7b5b7a6d3848c6da747 authored over 6 years ago by femtocleaner[bot] <femtocleaner[bot]@users.noreply.github.com>
Fix deprecations (#6)

github.com/BioJulia/Phylogenies.jl - cdf801019b82c07fb4866ee1232bbbf24f0c462d authored over 6 years ago by femtocleaner[bot] <femtocleaner[bot]@users.noreply.github.com>
Fix deprecations (#15)

github.com/BioJulia/BioAlignments.jl - 35f1fb702e6348ecb036662adc1f4359e5c6c1c4 authored over 6 years ago by femtocleaner[bot] <femtocleaner[bot]@users.noreply.github.com>
Fix deprecations (#38)

github.com/BioJulia/BioSequences.jl - df2ed6f0d05e8637e03bcd57789f177f78b93347 authored over 6 years ago by femtocleaner[bot] <femtocleaner[bot]@users.noreply.github.com>
Fix deprecations (#15)

github.com/BioJulia/GeneticVariation.jl - 850ac09e08f99ffcb903efa7d164c537d34665f2 authored over 6 years ago by femtocleaner[bot] <femtocleaner[bot]@users.noreply.github.com>
Fix deprecations (#14)

github.com/BioJulia/BGZFStreams.jl - aa82d32c16031d9d85672003b7a347fc8442a7e8 authored over 6 years ago by femtocleaner[bot] <femtocleaner[bot]@users.noreply.github.com>
Support do block syntax with BGZFStreams (#8)

github.com/BioJulia/BGZFStreams.jl - 53f6c052be83f01ce79d0fc0f3c1f53caf1fe67c authored over 6 years ago by Christian Theil Have <[email protected]>
Add CHANGELOG.md and HUMANS.md files

github.com/BioJulia/BGZFStreams.jl - a41932a06cfe21091dbc7bce707f7f4bc909a7d2 authored over 6 years ago by Ben J. Ward <[email protected]>
Increace julia required version to 0.6

github.com/BioJulia/BGZFStreams.jl - f156b6e6912044c9c2bb826088799dcd66c59cf0 authored over 6 years ago by Ben J. Ward <[email protected]>
Check if position is supported by a stream before calling. (#12)

github.com/BioJulia/BGZFStreams.jl - c0e0f80286fd2d429b1a92a279685663dd037636 authored over 6 years ago by Daniel C. Jones <[email protected]>
Fix julia deprecations (#12)

This PR fixes many of the deprecations from julia v0.6, which
will become errors in v0.7 and be...

github.com/BioJulia/GenomicFeatures.jl - 4acbbd6d4950c0d822b435c47781e290f198ae32 authored over 6 years ago by femtocleaner[bot] <femtocleaner[bot]@users.noreply.github.com>
Removed Phylogenies until it is updated

github.com/BioJulia/Bio.jl - 3316faaa3e351a2b8cad1610595b96d5927f4e12 authored over 6 years ago by Ben J. Ward <[email protected]>
Remove BioSymbols requirement

github.com/BioJulia/Bio.jl - 4f078b156ee9e45a52b32336e353e19b89a96fe5 authored over 6 years ago by Ben J. Ward <[email protected]>
Use v0.3 of BioAlignments

github.com/BioJulia/Bio.jl - 15be5cd992ab19c6f35dae206ae55be11c826bd5 authored over 6 years ago by Ben J. Ward <[email protected]>
Update project README, LICENSE and add HUMANS.md

github.com/BioJulia/Bio.jl - b41ecb774d3040965920e0da67232153e2c744a1 authored over 6 years ago by Ben J. Ward <[email protected]>
Add package lifecycle and open-collective sections

github.com/BioJulia/Contributing - d16d7d1cfff56985907707b72621512f700e6546 authored over 6 years ago by Ben J. Ward <[email protected]>
Update CHANGELOG before release

github.com/BioJulia/BioAlignments.jl - 4afde86399e0ae9eea6b0d788ef44a2fedcd20ef authored over 6 years ago by Ben J. Ward <[email protected]>
Remove alias of BioCore

github.com/BioJulia/BioAlignments.jl - 52419aadf69f009b4070b7b9c6f85495b29d35ed authored over 6 years ago by Ben J. Ward <[email protected]>
Update license

github.com/BioJulia/BioAlignments.jl - 3def85be9a9c498e1155d8971be38c48a38fce05 authored over 6 years ago by Ben J. Ward <[email protected]>
Merge github.com:BioJulia/BioAlignments.jl

github.com/BioJulia/BioAlignments.jl - 24556e886b09ace764d2fabf6a72ecf092646a6d authored over 6 years ago by Ben J. Ward <[email protected]>
Bio revamp (#494)

* Update project files

* Make test suite run each required package's suite

* :art: Update ...

github.com/BioJulia/Bio.jl - e80a25985d0837cecffaee2987ffa441f772e59f authored over 6 years ago by Ben J. Ward <[email protected]>
Make README and HUMANS consistent with that of Bio

github.com/BioJulia/BioAlignments.jl - 63b0b883cb55915eaa730825489c93774dfa37e1 authored over 6 years ago by Ben J. Ward <[email protected]>
Support >65535 CIGAR op-codes in BAM files (#13)

These changes add support for >65535 CIGAR op-codes in
CIGAR strings in BAM records. SAM records...

github.com/BioJulia/BioAlignments.jl - 37abec46a1e4effc3c92d4aaf2ce46e48fcb49ec authored over 6 years ago by Ben J. Ward <[email protected]>
Support >65535 CIGAR op-codes in BAM files (#13)

These changes add support for >65535 CIGAR op-codes in
CIGAR strings in BAM records. SAM records...

github.com/BioJulia/BioAlignments.jl - 2dd8ae1b377a792f1a570546aa2cd8c0a269d072 authored over 6 years ago by Ben J. Ward <[email protected]>
Merge pull request #2 from BioJulia/updates

Project files

github.com/BioJulia/GenomeBrowsers.jl - 3dff14eca87d0556b29d4e8b0e65ab98fd463bc5 authored over 6 years ago by Ben J. Ward <[email protected]>
add .gitignore

github.com/BioJulia/GenomeBrowsers.jl - 78ca8f34e5e3284f390fdf9578a183ba792b030e authored over 6 years ago by Ben J. Ward <[email protected]>
add appveyor.yml

github.com/BioJulia/GenomeBrowsers.jl - 83e9ee5af096df7b0dafd1da0a50ffbd934ca154 authored over 6 years ago by Ben J. Ward <[email protected]>
add travis.yml

github.com/BioJulia/GenomeBrowsers.jl - f3c4c7c1fa57e8cded1712fd6a3c7b15d5f341f9 authored over 6 years ago by Ben J. Ward <[email protected]>
update README.md and REQUIRE

github.com/BioJulia/GenomeBrowsers.jl - d8ef6be4880e5e82a3c3b948d3b62a4b1c1f9abf authored over 6 years ago by Ben J. Ward <[email protected]>
Merge pull request #1 from BioJulia/rollout-contributing

Contributing files rollout

github.com/BioJulia/GenomeBrowsers.jl - fcd81ce14b3260bdcbd6a5e1757583258e7ac6d7 authored over 6 years ago by Ben J. Ward <[email protected]>
Add flag test for alignment to the positive strand (#14)

* add ispositivestrand flag test for a BAM record

* test for ispositivestrand

* revert a f...

github.com/BioJulia/BioAlignments.jl - 1489ebe01dd507c565e316c0d8585099c89477e2 authored over 6 years ago by Peter Haverty <[email protected]>
Added GeneDataView

github.com/BioJulia/GenomicAnnotations.jl - 8f6a0b9983c4f7228fab097cdf416e491e7ac81a authored over 6 years ago by Karl Dyrhage <[email protected]>
Merge pull request #26 from BioJulia/long-cigars

Long CIGAR BAM and SAM

github.com/BioJulia/BioFmtSpecimens - bac4e896b6ccd6faf31a079487fd795929d22fb4 authored over 6 years ago by Ben J. Ward <[email protected]>
add file with records containing >65535 cigar operations

github.com/BioJulia/BioFmtSpecimens - 55da239a18292a433e49d301d25468d4b4f3bdec authored over 6 years ago by Ben J. Ward <[email protected]>
add bam files containing records with >65535 cigar operations

github.com/BioJulia/BioFmtSpecimens - a64b7eabb83043d6edc49f6a356f609e1abbcc79 authored over 6 years ago by Ben J. Ward <[email protected]>
Removed large example GenBank file

github.com/BioJulia/GenomicAnnotations.jl - 2f8113ce2d5d614914699bbbb31a3eed2875d047 authored over 6 years ago by Karl Dyrhage <[email protected]>
Initial commit

github.com/BioJulia/GenomicAnnotations.jl - a76021582571c7afc6e5972587e8a050e12e31d0 authored over 6 years ago by Karl Dyrhage <[email protected]>