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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

Add tests for array form of P_generic

github.com/BioJulia/SubstitutionModels.jl - 5e551e89973a2f215e702bf4cf166a0ab2a761d2 authored over 5 years ago by kgori <[email protected]>
Fix typo in Jukes Cantor probabilities

github.com/BioJulia/SubstitutionModels.jl - 8bdf2f0e4c515933cf7ea190087a899e58546942 authored over 5 years ago by kgori <[email protected]>
Updated to v1 eigen syntax

github.com/BioJulia/SubstitutionModels.jl - c59ab872a1e88723d8191ad8a13bff106fa9e3e2 authored over 5 years ago by kgori <[email protected]>
Update Compat.toml

github.com/BioJulia/BioJuliaRegistry - 2d94fe9943795632be1af518808aff8f6ca87731 authored over 5 years ago by Ben J. Ward <[email protected]>
Update Package.toml

github.com/BioJulia/BioJuliaRegistry - dce601e33592e202fec94910ae7eda53a0eb55a5 authored over 5 years ago by Ben J. Ward <[email protected]>
Fix docs

github.com/BioJulia/WAHVectors.jl - 847e5bf67830ebb65378944affae226b052d6adf authored over 5 years ago by Ben J. Ward <[email protected]>
Fix docs make script

github.com/BioJulia/WAHVectors.jl - 4c9108ff99291df8794db05dc9e6a78c571013f0 authored over 5 years ago by Ben J. Ward <[email protected]>
Fix docs make script

github.com/BioJulia/WAHVectors.jl - 67296af6ea94f3b5029a595258b234dc37761fb0 authored over 5 years ago by Ben J. Ward <[email protected]>
Add UInt32 constructor

github.com/BioJulia/WAHVectors.jl - 24db68ac7f09f0f7fb69d4f6586ebe7d733c7191 authored over 5 years ago by Ben J. Ward <[email protected]>
Fix WAHElements constructor

github.com/BioJulia/WAHVectors.jl - 3bbe0a400a841397bb895fee99058dd9817c5686 authored over 5 years ago by Ben J. Ward <[email protected]>
Fix elements constructor

github.com/BioJulia/WAHVectors.jl - 1fd4dc17df86fbe2e9dbb58a705bc8a3148769a1 authored over 5 years ago by Ben J. Ward <[email protected]>
Correct tests

github.com/BioJulia/WAHVectors.jl - b25d86b8d69ad45d913eb55860fe6f39da03c054 authored over 5 years ago by Ben J. Ward <[email protected]>
Update printing of elements

github.com/BioJulia/WAHVectors.jl - da0f5ec9bb05ec6d57edff459da383c7628d9669 authored over 5 years ago by Ben J. Ward <[email protected]>
Add WAHElement constructor

github.com/BioJulia/WAHVectors.jl - dee9d45ffe131c7da8718ff41ecaafa230a4df45 authored over 5 years ago by Ben J. Ward <[email protected]>
Comment out untested

github.com/BioJulia/WAHVectors.jl - 89d86b97485ed5e9c6cf16b06d8f7b573b0aa107 authored over 5 years ago by Ben J. Ward <[email protected]>
Update syntax

github.com/BioJulia/WAHVectors.jl - 10f73c8d30215dc67d879dfba2f7361276db3b6d authored over 5 years ago by Ben J. Ward <[email protected]>
Add tests to project

github.com/BioJulia/WAHVectors.jl - a4d502ec3ae682891b391357e94890eb1bef849a authored over 5 years ago by Ben J. Ward <[email protected]>
Edit tests

github.com/BioJulia/WAHVectors.jl - 3f44f202e008cfb802720c923a935531993f7939 authored over 5 years ago by Ben J. Ward <[email protected]>
Update documentation generation

github.com/BioJulia/WAHVectors.jl - caeaca3271b41d862955a6e131f34c1f3afc64f1 authored over 5 years ago by Ben J. Ward <[email protected]>
Updated version number

github.com/BioJulia/GenomicAnnotations.jl - b925f9df7da257aba92b6ad552cc3ac8b423a247 authored over 5 years ago by Karl Dyrhage <[email protected]>
Updated UUID

github.com/BioJulia/GenomicAnnotations.jl - f4b753b73b0471a8da286cbd6340455babe65eca authored over 5 years ago by Karl Dyrhage <[email protected]>
Updated README to include new features

github.com/BioJulia/GenomicAnnotations.jl - 45eb533f91ed54db0153338be1c5251a65eff535 authored over 5 years ago by Karl Dyrhage <[email protected]>
Added special cases to @genes

github.com/BioJulia/GenomicAnnotations.jl - 0a51534ca0d5f85f8cdcd0305d447fc39e1db8f7 authored over 5 years ago by Karl Dyrhage <[email protected]>
revert whitespace

github.com/BioJulia/BioStructures.jl - b7760508f3a17002b7d57918605cebbd17c21b5b authored over 5 years ago by Joe Greener <[email protected]>
Allow truncated MODEL line in PDB files (#12)

github.com/BioJulia/BioStructures.jl - 9cee0faaf20dca1f8a2d6da02a65b26a2657b896 authored over 5 years ago by tanhevg <[email protected]>
Merge pull request #28 from tanhevg/bugfix/BioStructures#11

Remove the error that is no longer an error; replace with a real file from SCOPe

github.com/BioJulia/BioFmtSpecimens - 1babfbc48ae33f98f12d8d5e6c932e63dc8c8dd3 authored over 5 years ago by Ben J. Ward <[email protected]>
Add a specimen from ASTRAL SCOP95

github.com/BioJulia/BioFmtSpecimens - 9055c69f577d6b73299457e6a713331a2088f5e8 authored over 5 years ago by Evgeny Tankhilevich <[email protected]>
wip gfa1 parser machine

github.com/BioJulia/GenomeGraphs.jl - f0e03c02cb0f3294303ebbde186a5e32e81680f4 authored over 5 years ago by Ben J. Ward <[email protected]>
Update Compat.toml

github.com/BioJulia/BioJuliaRegistry - 9f6afe6f10eb0e117a8c1485bc04c5f32bc31ce7 authored over 5 years ago by Ben J. Ward <[email protected]>
Change ssh repo links to https links

github.com/BioJulia/BioJuliaRegistry - 9ce87ffbd3c3c6f0249c3931233e9dba5d0054da authored over 5 years ago by Ben J. Ward <[email protected]>
Adjust julia number

github.com/BioJulia/BioJuliaRegistry - 3389e73bf758e9ac884315a42fd5c1196387d2ea authored over 5 years ago by Ben J. Ward <[email protected]>
Add BioGenerics

github.com/BioJulia/BioJuliaRegistry - ce7ba34b6773bd3a6bcd8aac2ec39511cb13f087 authored over 5 years ago by Ben J. Ward <[email protected]>
Merge #2

2: Update docs r=BenJWard a=BenJWard

## Types of changes

This PR implements the following ch...

github.com/BioJulia/BioGenerics.jl - d0489078113841dba24d43f51651e95d7a8fc527 authored over 5 years ago by biojulia-bors[bot] <biojulia-bors[bot]@users.noreply.github.com>
Update docs

github.com/BioJulia/BioGenerics.jl - 45a5e22e4f97d7aee343439bcbbb5637535c9d22 authored over 5 years ago by Ben J. Ward <[email protected]>
Update docs dev link in readme

github.com/BioJulia/BioGenerics.jl - 839e9f8a828a6fc46e17df92cea99eae3dc0c1da authored over 5 years ago by Ben J. Ward <[email protected]>
Fix docs make.jl

github.com/BioJulia/BioGenerics.jl - 7b7ac16080b412e9d1bbf27457238c48d2fc051e authored over 5 years ago by Ben J. Ward <[email protected]>
Fix travis

github.com/BioJulia/BioGenerics.jl - 573de2c669985ff707072bff350df35e9858c185 authored over 5 years ago by Ben J. Ward <[email protected]>
Fix documentation generation

github.com/BioJulia/BioGenerics.jl - 0907174a77365e83ca8939ecddf3e1277e13c907 authored over 5 years ago by Ben J. Ward <[email protected]>
Fix typo in travis file

github.com/BioJulia/BioGenerics.jl - 7a2ff9b734679a157cee0c3b68d1b595e0cef9c6 authored over 5 years ago by Ben J. Ward <[email protected]>
Add changelog file

github.com/BioJulia/BioGenerics.jl - f1ab656294d287255f0f9703fb6a3adc75cbccda authored over 5 years ago by Ben J. Ward <[email protected]>
Remove REQUIRE file

github.com/BioJulia/BioGenerics.jl - e684a68e8bacebdac24d635afc44b4741b6eabf1 authored over 5 years ago by Ben J. Ward <[email protected]>
Update readme

github.com/BioJulia/BioGenerics.jl - 88b66f23173a6feb4abde90b4cae9e18886be4d1 authored over 5 years ago by Ben J. Ward <[email protected]>
Update CI files

github.com/BioJulia/BioGenerics.jl - 18aa6d87317ae188bdd3b41169a04d438819541a authored over 5 years ago by Ben J. Ward <[email protected]>
Test master

github.com/BioJulia/BioGenerics.jl - 49238a09a6c896636e0769090f52b32232e01a24 authored over 5 years ago by Ben J. Ward <[email protected]>
Add sticker

github.com/BioJulia/BioGenerics.jl - ab00377fbb63aa12fffc5ba03b1d50411014c4de authored over 5 years ago by Ben J. Ward <[email protected]>
Update the readme

github.com/BioJulia/BioGenerics.jl - 004e435b1b5215fd10eb3ec0733e4f8172c580e4 authored over 5 years ago by Ben J. Ward <[email protected]>
Add issue and pr templates

github.com/BioJulia/BioGenerics.jl - 615fe71d80025ca51321495d88102f02e55e7a5a authored over 5 years ago by Ben J. Ward <[email protected]>
Add release-drafter config

github.com/BioJulia/BioGenerics.jl - fd022a424a77e9f9c68ac59a31631f7c7c7cb213 authored over 5 years ago by Ben J. Ward <[email protected]>
Merge #1

1: Add IO, Exceptions, and Automa modules r=BenJWard a=BenJWard

bors try

Co-authored-by: Ben J...

github.com/BioJulia/BioGenerics.jl - 8af2834cc8cfd5e9724f0f2c4ea5e8da7b5f8daa authored over 5 years ago by biojulia-bors[bot] <biojulia-bors[bot]@users.noreply.github.com>
Update Project.toml

github.com/BioJulia/BioGenerics.jl - bc41bea6b6c9b128d4dec422713aac561151380a authored over 5 years ago by Ben J. Ward <[email protected]>
Add generic method declarations

github.com/BioJulia/BioGenerics.jl - 36b2ba669a0d5166dcb56a5a4ef443746b1cc73d authored over 5 years ago by Ben J. Ward <[email protected]>
Add Automa module

github.com/BioJulia/BioGenerics.jl - f49fed8b8f9495007b0b3169bd0f0fdf29afff95 authored over 5 years ago by Ben J. Ward <[email protected]>
Add Exceptions module

github.com/BioJulia/BioGenerics.jl - b3e0d62ce00e171cc66bd93d9e90a33f22aaacf0 authored over 5 years ago by Ben J. Ward <[email protected]>
Update Package.toml

github.com/BioJulia/BioJuliaRegistry - 25dd5e27ae1be765ec9f983c8b184c3dbc6765dd authored over 5 years ago by Ben J. Ward <[email protected]>
Add IO module

github.com/BioJulia/BioGenerics.jl - 9f543767e2c76a86beb8b05e9797383b00af1f61 authored over 5 years ago by Ben J. Ward <[email protected]>
Add testing module

github.com/BioJulia/BioGenerics.jl - 12a01f5201463af888fca0cf9878ef5de83f840e authored over 5 years ago by Ben J. Ward <[email protected]>
Setup bors and edit CI files

github.com/BioJulia/BioGenerics.jl - dce44f6af630cbe5575a154309dcab51689bcc2b authored over 5 years ago by Ben J. Ward <[email protected]>
Files generated by PkgTemplates

github.com/BioJulia/BioGenerics.jl - 9dc6d6b77e5e77efa8d09950228881b87557c308 authored over 5 years ago by Ben J. Ward <[email protected]>
Initial commit

github.com/BioJulia/BioGenerics.jl - 70b8204b408b7798b34b1a91992c0811844fc887 authored over 5 years ago by Ben J. Ward <[email protected]>
Use tree sha not commit id

github.com/BioJulia/BioJuliaRegistry - f6c603a8480e7fc729274c673b13014ac4b2d520 authored over 5 years ago by Ben J. Ward <[email protected]>
alter path

github.com/BioJulia/BioJuliaRegistry - ba4458b90cb878a66a2718772bba25c394b84a5b authored over 5 years ago by Ben J. Ward <[email protected]>
alter repo

github.com/BioJulia/BioJuliaRegistry - eca451d1e2a60f398352fa020e69710d0338cfdf authored over 5 years ago by Ben J. Ward <[email protected]>
Rename

github.com/BioJulia/BioJuliaRegistry - ff9913ca73440636ba2d48fb13038b35ccdf10ff authored over 5 years ago by Ben J. Ward <[email protected]>
Add FormatSpecimens

github.com/BioJulia/BioJuliaRegistry - 0b5c4a8f57ab7dfa11bd3b4b29b294b4f2ae92a0 authored over 5 years ago by Ben J. Ward <[email protected]>
Add changelog

github.com/BioJulia/FormatSpecimens.jl - 0963a77db79271e219d50e31f31b7e87acf279c7 authored over 5 years ago by Ben J. Ward <[email protected]>
Add path_of_format method

github.com/BioJulia/FormatSpecimens.jl - 10f19db3bb58a63156a9e422338f60c3857c2de0 authored over 5 years ago by Ben J. Ward <[email protected]>
Correct get_all_specimens

github.com/BioJulia/FormatSpecimens.jl - d192567b3299c139a19af4cbc0b6736edd9e5cc6 authored over 5 years ago by Ben J. Ward <[email protected]>
Add Pkg as a dependency

github.com/BioJulia/FormatSpecimens.jl - 0919f6eb707f27ba940dedecb06e7d31877703fc authored over 5 years ago by Ben J. Ward <[email protected]>
Add project file

github.com/BioJulia/FormatSpecimens.jl - 0a5ef4ade07dcc91469262dc94443f139f5e9af7 authored over 5 years ago by Ben J. Ward <[email protected]>
Apply fix

github.com/BioJulia/FormatSpecimens.jl - 1f16be6b0917b4b92bd36470b5f63a1710dc87cd authored over 5 years ago by Ben J. Ward <[email protected]>
Finish module

github.com/BioJulia/FormatSpecimens.jl - 53bfc0a1beae2b525900c7bcdf2e9804aedea55d authored over 5 years ago by Ben J. Ward <[email protected]>
Add basic module

github.com/BioJulia/FormatSpecimens.jl - 1e580a0b2e344b856b990d72e66217e649568806 authored over 5 years ago by Ben J. Ward <[email protected]>
Add mmCIF, GFF3, and BBI specimens

github.com/BioJulia/FormatSpecimens.jl - cda103d7fbedd8f069c156dba64628f7337c7270 authored over 5 years ago by Ben J. Ward <[email protected]>
Add SAM specimens

github.com/BioJulia/FormatSpecimens.jl - 4aa1660dfd78897b5572edcdd79364af9a0ceb50 authored over 5 years ago by Ben J. Ward <[email protected]>
Add BLASTDB specimens

github.com/BioJulia/FormatSpecimens.jl - 96313afe55b965a40bab17342dbf7d4704a5a2ca authored over 5 years ago by Ben J. Ward <[email protected]>
Add BAM specimens

github.com/BioJulia/FormatSpecimens.jl - df5c28f68b3e6031ec220ca33203ad0610e89770 authored over 5 years ago by Ben J. Ward <[email protected]>
Add LSM, VCF, BCF, and BED

github.com/BioJulia/FormatSpecimens.jl - 3791b2fea09c7708755eeaced815d3103fcc846c authored over 5 years ago by Ben J. Ward <[email protected]>
Add ABI and FASTQ specimens

github.com/BioJulia/FormatSpecimens.jl - 57805ce83e133c38eb575bfb95be8d909cc3d43e authored over 5 years ago by Ben J. Ward <[email protected]>
Add 2bit specimens

github.com/BioJulia/FormatSpecimens.jl - 2eb04a44bdaa86a351ffcfedacc716f7aab06c90 authored over 5 years ago by Ben J. Ward <[email protected]>
Add PDB and FASTA specimens

github.com/BioJulia/FormatSpecimens.jl - 7626379e31b346820e9915680c0df99b0b7010fa authored over 5 years ago by Ben J. Ward <[email protected]>
Update CONTRIBUTING.md

github.com/BioJulia/Contributing - 089cbd88a864371da5290ac8b45ce2ec7c66a9fb authored over 5 years ago by Ben J. Ward <[email protected]>
Merge branch 'master' into develop

github.com/BioJulia/BBI.jl - a65f3222acd04a5a5af14735631e78feef59f8f0 authored almost 6 years ago by Ciarán O'Mara <[email protected]>
Merge branch 'release/v0.1.0'

github.com/BioJulia/BBI.jl - edb4b862b0f608765ff9c12d62371d01f8f174fa authored almost 6 years ago by Ciarán O'Mara <[email protected]>
Remove _init.jl

github.com/BioJulia/BBI.jl - a66e2ea6d0041c15d56217c7dbd8932f4e50d1db authored almost 6 years ago by Ciarán O'Mara <[email protected]>
Documentation

github.com/BioJulia/BBI.jl - 0731e60009ea84f2902dd87ccad32f02c29ef48f authored almost 6 years ago by Ciarán O'Mara <[email protected]>
Initial REQUIRE

github.com/BioJulia/BBI.jl - 9d1c3c5a6ee32c16b139ab45afc7f7c838bbc847 authored almost 6 years ago by Ciarán O'Mara <[email protected]>
Continuous integration

github.com/BioJulia/BBI.jl - a30b04995014c780456a3e24df596952157cf86a authored almost 6 years ago by Ciarán O'Mara <[email protected]>
examples of Bio3DView.jl in docs

github.com/BioJulia/BioStructures.jl - 69df3b35dd8c8052490632811bf86a3f88439783 authored almost 6 years ago by Joe Greener <[email protected]>
readme link updates

github.com/BioJulia/BioStructures.jl - eb8650f1e2f88bc826546157ca34a0e167b29d63 authored almost 6 years ago by Joe Greener <[email protected]>
Fix sequence search docs (#51)

* Fix search doc page

* Fix deprecated docs format specification

github.com/BioJulia/BioSequences.jl - e54ee6b7652e64647bb326fe321be206649aaf4a authored almost 6 years ago by Isaac Virshup <[email protected]>
:bug: Fix haskey(x::BAM.Record, y::String) (#24)

Fixes issue #20 by adding a `stop` argument to `getauxvalue` and `findauxtag`

github.com/BioJulia/BioAlignments.jl - 1057799e93ea535d54802b3844e1169c66801260 authored almost 6 years ago by Jakob Nybo Nissen <[email protected]>
Added GZip.jl as dependency

github.com/BioJulia/GenomicAnnotations.jl - a07c822b54f7b1804387fe7c5f74e226ae7bf8a7 authored almost 6 years ago by Karl Dyrhage <[email protected]>
Added GZip.jl as dependency

github.com/BioJulia/GenomicAnnotations.jl - f71afae16337df2cac7d18a5eb8e339ffa7ca951 authored almost 6 years ago by Karl Dyrhage <[email protected]>
Added GZip.jl as dependency

github.com/BioJulia/GenomicAnnotations.jl - 3ef380ae0aefceb2e3fbb6091924e456961c0f38 authored almost 6 years ago by Karl Dyrhage <[email protected]>
Update readme

github.com/BioJulia/Bio.jl - 804d33b36b7c9f881fbaa9dfcc1284f0a9100db5 authored almost 6 years ago by Ben J. Ward <[email protected]>
Add 'forceany' keyword to pushproprety

github.com/BioJulia/GenomicAnnotations.jl - 4a4bd48a04db2c3adcecd90d688922ba56c2ee42 authored almost 6 years ago by Karl Dyrhage <[email protected]>
Allow '^' in positions

github.com/BioJulia/GenomicAnnotations.jl - d71a1b795e03b8643c00ff55fd4942b9b9da6387 authored almost 6 years ago by Karl Dyrhage <[email protected]>
Add precompilation

github.com/BioJulia/GenomicAnnotations.jl - baa57943e14d87b0b1e188d18fa728a92760f2db authored almost 6 years ago by Karl Dyrhage <[email protected]>
Update CHANGELOG.md

github.com/BioJulia/BioServices.jl - 54a2e3e19cf323538cff1bdfa61783a6f80979ea authored almost 6 years ago by Maria Isabel Restrepo <[email protected]>
Fix travis

github.com/BioJulia/Bio.jl - d9de54e9b3e53239f2ace1a3e976a39c88b861a1 authored almost 6 years ago by Ben J. Ward <[email protected]>