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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

:art: Fix up enahncement suggestion guidance formatting

github.com/BioJulia/Contributing - 452bf3eff6a7cc25761c3fac896b3a0344b8ab2c authored over 6 years ago by Ben J. Ward <[email protected]>
:art: Fix up bug report guidance formatting

github.com/BioJulia/Contributing - 0b7cdf954b7ffc6b550269f4f982b9196786ef5b authored over 6 years ago by Ben J. Ward <[email protected]>
:tada: Add first draft CONTRIBUTING file

github.com/BioJulia/Contributing - ce30a6731f795997052cddb707b7c08f68fcf6d6 authored over 6 years ago by Ben J. Ward <[email protected]>
:memo: Add an enhancement suggestion issue template

github.com/BioJulia/Contributing - a02449610c2de4cb70551e2e7cd5501589ae94cd authored over 6 years ago by Ben J. Ward <[email protected]>
:memo: Add a bug report issue template

github.com/BioJulia/Contributing - 35aa8f2490cc0e84f59dc7fd480d80936c8a3eb1 authored over 6 years ago by Ben J. Ward <[email protected]>
:fire: Removed old site and Documenter.jl stuff

github.com/BioJulia/Contributing - 98575fff977379bb75f760a47bb8159cb19be44a authored over 6 years ago by Ben J. Ward <[email protected]>
:memo: Add example changelog and new changelog file

github.com/BioJulia/Contributing - 92c43dca5aca8de4dfdcea75b47345813a5107fb authored over 6 years ago by Ben J. Ward <[email protected]>
:memo: Add changelog

github.com/BioJulia/Contributing - f8f5b380daa4813edef2600d677af370b5d458c1 authored over 6 years ago by Ben J. Ward <[email protected]>
Updated LICENSE

github.com/BioJulia/GenomicAnnotations.jl - 6f58bd7fc87c2e2d046c512e170eb342330f1b5f authored over 6 years ago by Karl Dyrhage <[email protected]>
Initial commit

github.com/BioJulia/GenomicAnnotations.jl - a952512313286164b0eb8a44c750621d76354eba authored over 6 years ago by kdyrhage <[email protected]>
Update README.md

github.com/BioJulia/MMTF.jl - c829b5a8bae89c6be9e9d0eb56bfa474e9847cbd authored over 6 years ago by Joel S <[email protected]>
Fix documentation building (#12)

github.com/BioJulia/BioCore.jl - 27ef0609b7221243999e7bb8e18e949785ea6c76 authored over 6 years ago by Ben J. Ward <[email protected]>
Readme fix

github.com/BioJulia/BioCore.jl - c3943fcc75295d8f1493f332247c79fdfc44812f authored over 6 years ago by Ben J. Ward <[email protected]>
More 0.7 compatiblity updates (#11)

* 0.7 updates

* using Cvoid in RecordHelper

* readme edits

github.com/BioJulia/BioCore.jl - 86b8160d853f4d7e7abb19673215f3edae1e9ce4 authored over 6 years ago by Ben J. Ward <[email protected]>
Update README.md

github.com/BioJulia/BioCore.jl - 46ccd5ee49db3db73cfe6838504eb910280dd424 authored over 6 years ago by Ben J. Ward <[email protected]>
Julia 0.7 compatibility and testing (#10)

* Removed depreceated syntax

* Updated README

* Updated docs generation files

* put bio...

github.com/BioJulia/BioCore.jl - d83bb8f14bec2ee0ffc5b85d69f5a34d4c8b2615 authored over 6 years ago by Ben J. Ward <[email protected]>
modify the figure

github.com/BioJulia/Automa.jl - 7a0791c562356a846cc44527fcc35f65a2a78dc0 authored over 6 years ago by Kenta Sato <[email protected]>
add a figure of Automa.jl in README.md

github.com/BioJulia/Automa.jl - 5b38bcdc2a45c99b93bccdc5001f68bc12bc4790 authored over 6 years ago by Kenta Sato <[email protected]>
add some description of Automa.jl to README.md

github.com/BioJulia/Automa.jl - c769ee79e19b4615d930f53b6287e3b17b55bcd7 authored over 6 years ago by Kenta Sato <[email protected]>
fix benchmark deprecations

github.com/BioJulia/Automa.jl - 8e6c94b4557c03d259a429c559e05dd4eca49dea authored over 6 years ago by Kenta Sato <[email protected]>
fix some deprecations (#33)

github.com/BioJulia/Automa.jl - 5e8192a1f7f324fcd3e8813442e5e28b934aaa96 authored over 6 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Update README.md

github.com/BioJulia/MMTF.jl - 868c1bdd1e062ff81d596650f92f82cb2a391d05 authored over 6 years ago by Joel S <[email protected]>
Update README.md

github.com/BioJulia/MMTF.jl - b21a1360a8449c77aae566049127733a70f50829 authored over 6 years ago by Joel S <[email protected]>
Initial commit

github.com/BioJulia/MMTF.jl - 2b5871e1f96e8582e911eb027101da1503599f54 authored over 6 years ago by Joel S <[email protected]>
Initial commit

github.com/BioJulia/MMTF.jl - 41b5f482252b6597b709b30543a96d147caefc29 authored over 6 years ago by Joel S <[email protected]>
Update news with release notes

github.com/BioJulia/BioStructures.jl - d44c07c88136ffd6da97ccc8398fbc838ed38f0f authored over 6 years ago by Joe Greener <[email protected]>
Add lower bound requirement for Compat

github.com/BioJulia/BioSymbols.jl - 1e7b4e9fccd5f55897c5f2b0d19c59f8b3a17aa4 authored over 6 years ago by Ben J. Ward <[email protected]>
Update readme and appveyor

github.com/BioJulia/BioSymbols.jl - 85db2208f54464aa01515d47e76e8505b75cbb3d authored over 6 years ago by Ben J. Ward <[email protected]>
Prep syntax for julia 0.7, drop julia 0.5 (#17)

* Updated parametric syntax

* Using Nullables and Test from Compat

* Use convert to Char r...

github.com/BioJulia/BioSymbols.jl - 1a7495fc4bf9375dac2aa3ea017dc7a1e0665429 authored over 6 years ago by Ben J. Ward <[email protected]>
fix deprecation of findfirst (#32)

github.com/BioJulia/Automa.jl - 19a9e20925e509c5b94ab513903d7fb1ee8972d5 authored over 6 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Support streaming reader (#29)

github.com/BioJulia/Automa.jl - bc7a83a0f81767e9eca99e2a911cd7fdfd56f1f6 authored over 6 years ago by Kenta Sato (佐藤 建太) <[email protected]>
fix deprecated string <=> bytes conversions (#31)

github.com/BioJulia/Automa.jl - 2f29cf54added3b5724e8edf319a782a0cfb605d authored over 6 years ago by Kenta Sato (佐藤 建太) <[email protected]>
remove deprecated functions of codegen (#30)

github.com/BioJulia/Automa.jl - 6dbf5804ef41a295f0683e24f9810dca322c4e9d authored over 6 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Updates prepping for julia 0.7 (#28)

github.com/BioJulia/Automa.jl - 01ff5f2faca6a4d12078b605291a13d85a2d0d17 authored over 6 years ago by Ben J. Ward <[email protected]>
Small changes before release (#5)

github.com/BioJulia/BioStructures.jl - c50a4536c55150775879c809cc29ccba6fb757f5 authored over 6 years ago by Joe Greener <[email protected]>
Enable julia 0.7 testing

github.com/BioJulia/BioTools.jl - 2fd0e3d7c8b5a121cd4262827ff014161f9c83dc authored over 6 years ago by Ben J. Ward <[email protected]>
Update README.md

github.com/BioJulia/BioTools.jl - f3362dedb21d512b965b4a9bb103cc40da393f6a authored over 6 years ago by Ben J. Ward <[email protected]>
Update to the latest EzXML syntax (#4)

* Added changelog

* Updated for API changes to EzXML

github.com/BioJulia/BioTools.jl - 738d59ad64b24e293acee0ed80b716720c7b7b60 authored over 6 years ago by Ben J. Ward <[email protected]>
Added BioCore.sequence with ability to specify type (#34)

github.com/BioJulia/BioSequences.jl - 35c6414ac7792c40d6886927900ce9cbbf7dbb1b authored over 6 years ago by Ben J. Ward <[email protected]>
add using BioSequences

github.com/BioJulia/GenomeGraphs.jl - 20f342d1c0992ea7238325c74351c862fcbcaaca authored over 6 years ago by Ben J. Ward <[email protected]>
appveyor url fix

github.com/BioJulia/GenomeGraphs.jl - 113ba9d432cf3b28a5be60d26fc9b8da95e9c578 authored over 6 years ago by Ben J. Ward <[email protected]>
readme edit

github.com/BioJulia/GenomeGraphs.jl - 9dc15384890f55eeb620b1de00e4d276b831e314 authored over 6 years ago by Ben J. Ward <[email protected]>
CI files edit

github.com/BioJulia/GenomeGraphs.jl - 7d3039019c6b52705e5a809122d32dd60291fbbb authored over 6 years ago by Ben J. Ward <[email protected]>
Add basic files

github.com/BioJulia/GenomeGraphs.jl - c33c301c116d1be512dd700bb4af2aa4ecfab59a authored over 6 years ago by Ben J. Ward <[email protected]>
Added changelog

github.com/BioJulia/BioTools.jl - e08222bca3bb9a564ed6bb6fcee28d5be09edda1 authored over 6 years ago by Ben J. Ward <[email protected]>
Add changelog

github.com/BioJulia/BioSequences.jl - ff52b992003117edd5b2f35b00fdbada16147174 authored over 6 years ago by Ben J. Ward <[email protected]>
Bugfix: Writing FASTA sequences when width <= 0 (#33)

* Bugfix: Writing FASTA sequences when with <= 0

A typo / bracket error prevented writing seq...

github.com/BioJulia/BioSequences.jl - 0c3a698c178cbf79f2fd2fa45bd4a46e8e051a99 authored over 6 years ago by Ben J. Ward <[email protected]>
mmCIF reader and writer (#4)

github.com/BioJulia/BioStructures.jl - 5ea964cca0667cd3bdc69a4ad581f207377eb7a0 authored over 6 years ago by Joe Greener <[email protected]>
Added changelog

github.com/BioJulia/BioCore.jl - 194236f246f30d6d19cab91292dc1d530e3c9e97 authored over 6 years ago by Ben J. Ward <[email protected]>
get_bio_fmt_specimens improvements (#9)

* get_bio_fmt_specimens checks out the latest tag by default.

* Add fresh option

* Update ...

github.com/BioJulia/BioCore.jl - 913b25fd6e1db3b2910e0c10721959cd0bd50979 authored over 6 years ago by Ben J. Ward <[email protected]>
Merge pull request #23 from jgreener64/mmcif

Some mmCIF files (protein structures)

github.com/BioJulia/BioFmtSpecimens - 297ad58ff32082de92ab8a83d97c3a805435a3c1 authored over 6 years ago by Ben J. Ward <[email protected]>
Some invalid mmCIF files

github.com/BioJulia/BioFmtSpecimens - f2d050b5acf6e1819eccbe99565a0f92de1eae97 authored over 6 years ago by Joe Greener <[email protected]>
index.yml file for mmCIF

github.com/BioJulia/BioFmtSpecimens - a458eb4b73b8876adef9af356be7ac9ea29f4ff4 authored over 6 years ago by Joe Greener <[email protected]>
Some mmCIF files (protein structures)

github.com/BioJulia/BioFmtSpecimens - e74e4d7be655cad448877d8404b62a515b27b714 authored over 6 years ago by Joe Greener <[email protected]>
Update README.md

github.com/BioJulia/BioTools.jl - 7f741e07395364daead7b0deec1233c6b8626a17 authored over 6 years ago by Ben J. Ward <[email protected]>
Fixup docs and make.jl

github.com/BioJulia/BioTools.jl - 470e449e889e2c20bf6cf8e3bbdbbdedb4983629 authored over 6 years ago by Ben J. Ward <[email protected]>
Fixed docs index symlink.

github.com/BioJulia/BioTools.jl - ab167013990cc94d5b9764f5d3b694a6b4b01645 authored over 6 years ago by Ben J. Ward <[email protected]>
Readme and docs (#2)

* Fix appveyor.yml

* Added documentation

github.com/BioJulia/BioTools.jl - fabcbb897b84f4e098ab668674d1d0417716da48 authored over 6 years ago by Ben J. Ward <[email protected]>
Source code and tests (#1)

* Added some files

* Added more source files

* Added tests for BLAST tool

* Added requi...

github.com/BioJulia/BioTools.jl - 651ab5cf6e3bc37b36e100dc4043acac7b93cf1f authored over 6 years ago by Ben J. Ward <[email protected]>
Add Kevin's mugshot to the member page ;P

github.com/BioJulia/biojulia.github.io - 7cc6f16432da96fdb175371baf1ed6d1f157c335 authored over 6 years ago by Ben J. Ward <[email protected]>
Fixed members page, and package listing page

github.com/BioJulia/biojulia.github.io - 67da9c0384796a9d6fee905b1544c27494e7716a authored over 6 years ago by Ben J. Ward <[email protected]>
test metadata api

github.com/BioJulia/biojulia.github.io - 7d4bc99886866a707fadfe393645a69842ab0cfa authored over 6 years ago by Ben J. Ward <[email protected]>
BioSequenceGraphs.jl generated files.

license: MIT
authors: Ben J. Ward
years: 2018
user: Ward9250

Julia Ver...

github.com/BioJulia/GenomeGraphs.jl - 782206b26322e5e966dd2203036534af9a1df061 authored over 6 years ago by Ben J. Ward <[email protected]>
initial empty commit

github.com/BioJulia/GenomeGraphs.jl - c82e22f345bd132e16d5d176fa4327f0cafbfd37 authored over 6 years ago by Ben J. Ward <[email protected]>
fix test failure on Julia 0.7 (#26)

github.com/BioJulia/Automa.jl - db0d66097ed02f6366d1dd111e5580c4de214182 authored almost 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Performance upgrade for NG86, introduce codon lookup tables (#4)

Perf upgrade for NG86, introduce codon lookup tables

github.com/BioJulia/NaturalSelection.jl - 180dc3b2b925d96c9b41ded7246618baa479da6f authored almost 7 years ago by Ben J. Ward <[email protected]>
Fix dead link (#8)

github.com/BioJulia/BioCore.jl - 9bf3acc2808f52ba2cf2224eff75a366cbea47dc authored almost 7 years ago by Kevin Bonham <[email protected]>
require Julia 0.6 (#25)

github.com/BioJulia/Automa.jl - 7c834712218b1a33e270011967672e8b553c9aca authored almost 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Removed more debug print lines

github.com/BioJulia/NaturalSelection.jl - 6dfedafbc505e33b82532c9ff6a270bb744458da authored almost 7 years ago by Ben J. Ward <[email protected]>
use bitmap to check membership (#24)

github.com/BioJulia/Automa.jl - ceb332b2f0d7c1a5d03ab002710abd4536f850b8 authored almost 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
add a benchmark

github.com/BioJulia/Automa.jl - f82e2ffb52560c00f93989d88c9b982e11728b74 authored almost 7 years ago by Kenta Sato <[email protected]>
add a benchmark

github.com/BioJulia/Automa.jl - 138f9e48d536e05db3e67f5f048c29ed74ae8a20 authored almost 7 years ago by Kenta Sato <[email protected]>
write SVG when benchmarking

github.com/BioJulia/Automa.jl - ff329ed4dfeeda788088a2dbd32cbcc974dc2f13 authored almost 7 years ago by Kenta Sato <[email protected]>
add benchmarks

github.com/BioJulia/Automa.jl - 627179814cf45e238173ea02f63b94837ca37bb1 authored almost 7 years ago by Kenta Sato <[email protected]>
Drop Julia 0.5 support (#23)

github.com/BioJulia/Automa.jl - d81f46ab0ac51ce47dcd49fbc444261ba6c6eb01 authored almost 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Removed printlns

github.com/BioJulia/NaturalSelection.jl - 12ace8b64b1fb5221d7c6b625df96fc1ea22f7b4 authored almost 7 years ago by Ben J. Ward <[email protected]>
MacDonald Kreitman test (#3)

* add mkt file

* Added CodonSet type

* CodonSet edits

* Move mkt.jl

* DS_DN_Enumerat...

github.com/BioJulia/NaturalSelection.jl - d44d5d2f0ad66000f1eebf0f42ba8e5832ca1ec8 authored almost 7 years ago by Ben J. Ward <[email protected]>
Message printed when sequence is empty. (#31)

github.com/BioJulia/BioSequences.jl - 8bffb31d747a04206479704919a754e3b097c8e3 authored almost 7 years ago by Ben J. Ward <[email protected]>
Add mantainers

github.com/BioJulia/BioServices.jl - 8cc43a8bfaaa940d3bf3432e3160bf08750a61ba authored almost 7 years ago by Maria Isabel Restrepo <[email protected]>
Update package installation for new release

github.com/BioJulia/BioServices.jl - 90d1a3c2386e305b2bd4ad991fbc9ea826649460 authored almost 7 years ago by Maria Isabel Restrepo <[email protected]>
Merge pull request #4 from bicycle1885/umls-style

add some stylistic touch-ups to UMLS

github.com/BioJulia/BioServices.jl - ca7c21a5c2814ef00ffc214f08c8fa3f9612032b authored almost 7 years ago by Maria Isabel Restrepo <[email protected]>
add some stylistic touch-ups to UMLS

github.com/BioJulia/BioServices.jl - 91c789fbc3d74008be8fcab0fef143b26a96a3e2 authored almost 7 years ago by Kenta Sato <[email protected]>
Merge pull request #3 from mirestrepo/umls

Add UMLS API

github.com/BioJulia/BioServices.jl - e9ddef6f1b6857bb18eebf8d511c3ffac7b17eab authored almost 7 years ago by Maria Isabel Restrepo <[email protected]>
Inline a couple Base.next methods.

github.com/BioJulia/IntervalTrees.jl - 4e609d30911a0658ae743d0e6753b168b9aee805 authored almost 7 years ago by Daniel C. Jones <[email protected]>
Fix a bug in firstintersection that can lead to missed intersections.

github.com/BioJulia/IntervalTrees.jl - 7c8a5bd6dc399feebe54c45b122b523a442b94f2 authored almost 7 years ago by Daniel C. Jones <[email protected]>
Fix a test

github.com/BioJulia/IntervalTrees.jl - 57943a0ed5597ae21b4230105948476065279bce authored almost 7 years ago by Daniel C. Jones <[email protected]>
Incorporate PR suggestions

github.com/BioJulia/BioServices.jl - 2503f8b9c0fc24dee3a6f9596be2e1569c65a42d authored almost 7 years ago by Maria Isabel Restrepo <[email protected]>
implement bit-parallel GC counter (#29)

github.com/BioJulia/BioSequences.jl - f42bf8c8fac2468a6927d18a12c714f40ec0f357 authored almost 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
More in-depth docs

github.com/BioJulia/BioServices.jl - 0c5b238dea06e7c47aeb751b06db2a3e44b88a88 authored almost 7 years ago by Maria Isabel Restrepo <[email protected]>
fix type definition keywords (#28)

github.com/BioJulia/BioSequences.jl - bec2ae2001c5fc943214d0ceafd2519d11dcd865 authored almost 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Update installation instructions for release ver

github.com/BioJulia/SubstitutionModels.jl - 9818fdbd6bf2db0311f4df5328e36414ed787756 authored almost 7 years ago by Justin Angevaare <[email protected]>
Merge pull request #6 from Ward9250/docs-update

Docs revamp

github.com/BioJulia/SubstitutionModels.jl - 0ff123395ccd9b297708430eab8050e2d2c1fb18 authored almost 7 years ago by Justin Angevaare <[email protected]>
Added index.md as a softlink

github.com/BioJulia/SubstitutionModels.jl - 8e69ef7f6c1ae8f3f71abd5ecb15288204c3cce2 authored almost 7 years ago by Ben J. Ward <[email protected]>
remove index.md

github.com/BioJulia/SubstitutionModels.jl - 9abb21f9e88ad127f584f31890c61900980d0871 authored almost 7 years ago by Ben J. Ward <[email protected]>
Remove mkdocs.yml

github.com/BioJulia/SubstitutionModels.jl - 062a59d721bfe7c8babf7400909b45312c72e655 authored almost 7 years ago by Ben J. Ward <[email protected]>
fixup

github.com/BioJulia/SubstitutionModels.jl - c756d2c03313be2364e299581f8558e72b02cda2 authored almost 7 years ago by Ben J. Ward <[email protected]>
mkdocs: change theme to material, and julia version

github.com/BioJulia/BioServices.jl - 832b65919082505286688d555a89806d572a1bac authored almost 7 years ago by Maria Isabel Restrepo <[email protected]>
disable umls test if environment variables are not available

- ENV are not available from forks

github.com/BioJulia/BioServices.jl - aa2aaaf08eca35db002b1d17b9ea970292915464 authored almost 7 years ago by Maria Isabel Restrepo <[email protected]>
Fix PR suggestions

github.com/BioJulia/SubstitutionModels.jl - 97fc1a12e68f0ebfbaedf6afe541baa479c026f7 authored almost 7 years ago by Ben J. Ward <[email protected]>
Add additional packages to REQUIRE

github.com/BioJulia/BioServices.jl - ee7ad9660c56a1b47ca9ebf5fcef4574d249864f authored almost 7 years ago by Maria Isabel Restrepo <[email protected]>