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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 UTS_TGT from tests to gitignore

github.com/BioJulia/BioServices.jl - 4002f1744dc64587293c6d844579a7f63a09c370 authored almost 7 years ago by Maria Isabel Restrepo <[email protected]>
Minor typos

github.com/BioJulia/BioServices.jl - 129b7da99f4fd66fbf7145fc05b18a0c367bb2b8 authored almost 7 years ago by Maria Isabel Restrepo <[email protected]>
remove and gitignore docs/build dir

github.com/BioJulia/BioServices.jl - ca766f0850491a9b7254f3d3f41825ee4d9e4267 authored almost 7 years ago by Maria Isabel Restrepo <[email protected]>
Add UMLS API, and related tests and docs

github.com/BioJulia/BioServices.jl - 46812885c8afc6b6e29c0a7faca706de7a5b222a authored almost 7 years ago by Maria Isabel Restrepo <[email protected]>
fix README.md

github.com/BioJulia/IntervalTrees.jl - 3c21c732cab042462e8ba01e22c2f0334e21d220 authored almost 7 years ago by Kenta Sato <[email protected]>
Docs revamp

github.com/BioJulia/SubstitutionModels.jl - 71dcca938cf2df8dfbc08bbe6b9c9c4249bc0053 authored almost 7 years ago by Ben J. Ward <[email protected]>
Julia syntax updates (#3)

github.com/BioJulia/BioStructures.jl - 675254dbb5b638f84bbd4ec5a805a436c0ec7b39 authored almost 7 years ago by Joe Greener <[email protected]>
Merge pull request #5 from Ward9250/pre-release-review

Some minor review edits.

github.com/BioJulia/SubstitutionModels.jl - 602596cc3c45bfc3da8cc9b05afd3639076d69f4 authored almost 7 years ago by Justin Angevaare <[email protected]>
Update nucleic_acid.jl

github.com/BioJulia/SubstitutionModels.jl - f1698277aef4a1e6c0d406f218e444c6238c2e3b authored almost 7 years ago by Ben J. Ward <[email protected]>
Update core.jl

github.com/BioJulia/SubstitutionModels.jl - 9b72318762efd5eca732e28f57f19611f2a8f044 authored almost 7 years ago by Ben J. Ward <[email protected]>
Some minor review edits.

github.com/BioJulia/SubstitutionModels.jl - ae0d8c36b620aab91eb10976d5d1483a90b14d7b authored almost 7 years ago by Ben J. Ward <[email protected]>
fix README.md (#6)

github.com/BioJulia/FMIndexes.jl - 4dc7556d45ef8f07d619decb9a1c4c70b91bb3ce authored about 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Edited readme

github.com/BioJulia/IntervalTrees.jl - 82bcd10b79cf83cc1550077a686df176728fbba8 authored about 7 years ago by Ben J. Ward <[email protected]>
do not import methods from base (#5)

This is mainly for readability. Directly extending methods looks a little bit verbose but checki...

github.com/BioJulia/FMIndexes.jl - 8a3a245b0227f5a66b81a5a6f3f6b5c8d26828cd authored about 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
replace FactCheck with Base.Test (#4)

github.com/BioJulia/FMIndexes.jl - 8b31584a553f48701dec96f9ce631f5e9da533a1 authored about 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Edited news file.

github.com/BioJulia/NaturalSelection.jl - 8eb9c4573b8e322f55e558de786dd4fb6665caa2 authored about 7 years ago by Ben J. Ward <[email protected]>
method ambiguity fix (#2)

github.com/BioJulia/NaturalSelection.jl - 358e97bfe51015acda9c5ec40d39b8a742be95a0 authored about 7 years ago by Ben J. Ward <[email protected]>
fix docstrings so LaTeX will render with makedocs

github.com/BioJulia/SubstitutionModels.jl - 97b8c7b1617fbca8e55c223a7485ebf291aa7811 authored about 7 years ago by Justin Angevaare <[email protected]>
Merge pull request #2 from mirestrepo/basic_updates

Updates to README and drop Julia 0.5

github.com/BioJulia/BioServices.jl - ad7d4eb8c539a5192e90216039bd85c5004fea2a authored about 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Staticfloat updated ci url (#3)

* Update CI URLs to point to new caching infrastructure

* update versions

github.com/BioJulia/FMIndexes.jl - ed0292074a81990e89881b49125dfe471e66424a authored about 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Julia v0.6 Compatibility (#2)

* ACSIIString to String

* update runtests.jl: swap str.data access for Vector{UInt8}(str)

...

github.com/BioJulia/FMIndexes.jl - 8e72dae0c793d75e42e93b390cd82a0951b3c1f0 authored about 7 years ago by Tim Sterne-Weiler <[email protected]>
Correct Require

github.com/BioJulia/NaturalSelection.jl - 2b833179891869138ca2abfb4be50c9e3d102fcf authored about 7 years ago by Ben J. Ward <[email protected]>
Add Tajima's D documentation

github.com/BioJulia/NaturalSelection.jl - b0ad38b09385c9fd42fb74424a69944e3f69f95f authored about 7 years ago by Ben J. Ward <[email protected]>
avg_mut use in tajimad

github.com/BioJulia/NaturalSelection.jl - 630969d12d1d676d9c96e057a170965171828874 authored about 7 years ago by Ben J. Ward <[email protected]>
Added pairwise_dNdS_NG86

github.com/BioJulia/NaturalSelection.jl - 53b99053f87b18e42aeccf698acd055d496665f5 authored about 7 years ago by Ben J. Ward <[email protected]>
Update the news.md file

github.com/BioJulia/GeneticVariation.jl - b7899bc231bb3ee47b3ee439fe41966486f90885 authored about 7 years ago by Ben J. Ward <[email protected]>
Add avg_mut (#13)

* Add avg_mut

* added docstring

* fix test

github.com/BioJulia/GeneticVariation.jl - 65169ef8ceacaaf4d931d5cc63844a3b073de065 authored about 7 years ago by Ben J. Ward <[email protected]>
Add Tajima's D draft

github.com/BioJulia/NaturalSelection.jl - 6f21500726b3310819972c3debde886994b30418 authored about 7 years ago by Ben J. Ward <[email protected]>
Make downloadpdb return the filename again (#2)

github.com/BioJulia/BioStructures.jl - 526a8590489693d723e1b069ae7a3d7b29f5e4a8 authored about 7 years ago by The ultimate Renan <[email protected]>
Merge pull request #1 from timbitz/master

Julia v0.6 Compatibility

github.com/BioJulia/WaveletMatrices.jl - f0500e5a71707a090f57c8027b3c0d3d304eae7e authored about 7 years ago by Ben J. Ward <[email protected]>
update appveyor for julia 0.6

github.com/BioJulia/BioServices.jl - ed5b08d8d70812f6f53e1a7f650b5edd14184e4b authored about 7 years ago by Maria Isabel Restrepo <[email protected]>
remove julia build badge, since pkg is not yet registered

github.com/BioJulia/BioServices.jl - 7cde12470c684dffc234fdec6cbb0fba40f704eb authored about 7 years ago by Maria Isabel Restrepo <[email protected]>
update README and travis for 0.6

github.com/BioJulia/BioServices.jl - 586c5efeb1dbbbd3be40c1ea37fa658440f7082b authored about 7 years ago by Maria Isabel Restrepo <[email protected]>
Drop julia 0.5

- Drop support for Julia 0.5
- Fix deprecated warnings

github.com/BioJulia/BioServices.jl - 43c83afdad9cb8e8f2ce0b5ba63cd30bf51aad71 authored about 7 years ago by Maria Isabel Restrepo <[email protected]>
update travis to 0.6, remove nightly

github.com/BioJulia/WaveletMatrices.jl - 437c127a009354838d6e1b75db335191b0b25eb4 authored about 7 years ago by Tim Sterne-Weiler <[email protected]>
fixed deprecated call interface with v0.6 constructor syntax

github.com/BioJulia/WaveletMatrices.jl - f6e0501f6735850cc65acbb17d1edd8a0565b615 authored about 7 years ago by Tim Sterne-Weiler <[email protected]>
attempt to fix TypeError: apply_type: in Vararg count

github.com/BioJulia/WaveletMatrices.jl - 618fdb67a580782d081c0e271cd82596167497f3 authored about 7 years ago by Tim Sterne-Weiler <[email protected]>
deprecated Base.call syntax

github.com/BioJulia/WaveletMatrices.jl - 0a97a134bba8c7e5fbf3e96bdadc1278636a4098 authored about 7 years ago by Tim Sterne-Weiler <[email protected]>
invalid subtyping

github.com/BioJulia/WaveletMatrices.jl - b063aa991d8d39177fd4c754ced09c30ce2738eb authored about 7 years ago by Tim Sterne-Weiler <[email protected]>
inner constructor where syntax

github.com/BioJulia/WaveletMatrices.jl - 68fefcfd29029ec2e48aea9c619380b51c99e802 authored about 7 years ago by Tim Sterne-Weiler <[email protected]>
added where syntax

github.com/BioJulia/WaveletMatrices.jl - 22661158ad58bf6c9412a14acbfade1c61dc930d authored about 7 years ago by Tim Sterne-Weiler <[email protected]>
fix immutable to struct

github.com/BioJulia/WaveletMatrices.jl - 663dba64f844f926acbcff347d901d6d51ed8fa9 authored about 7 years ago by Tim Sterne-Weiler <[email protected]>
julia v0.6 in REQUIRE

github.com/BioJulia/WaveletMatrices.jl - 1efe9cb1c5aa2fc261af9b40d3390c239ddb6cb2 authored about 7 years ago by Tim Sterne-Weiler <[email protected]>
types to struct

github.com/BioJulia/WaveletMatrices.jl - 3b0b45a9e363d9fbd6a9c8ba9e6f72b01eefb6e4 authored about 7 years ago by Tim Sterne-Weiler <[email protected]>
Minor documentation fix

github.com/BioJulia/GeneticVariation.jl - 4ad828442cc3c6e8f1fe3ab3b69ce5877e882fb2 authored about 7 years ago by Ben J. Ward <[email protected]>
Compute the number of segregating sites in a set of DNA sequences.

github.com/BioJulia/GeneticVariation.jl - 1477f922ad33e85531e0e6328bedba1462a7cac7 authored about 7 years ago by Ben J. Ward <[email protected]>
more docs on tokenizer

github.com/BioJulia/Automa.jl - af39fab19d88aa4a9b7665e986d28d302fc0f505 authored about 7 years ago by Kenta Sato <[email protected]>
Remove IO helper files (#488)

github.com/BioJulia/Bio.jl - e6e03b5fb32a5bde830618eb32854db9ee18f96e authored about 7 years ago by Ben J. Ward <[email protected]>
Merge pull request #27 from yuyichao/0.7

Fix 0.7 depwarns and errors

github.com/BioJulia/Codecs.jl - e6dd7966fd1bc4a9bbffbd725f37da3a9a131a79 authored about 7 years ago by Randy Zwitch <[email protected]>
Fix 0.7 depwarns and errors

* Drop 0.4 support due to Compat requirement
* Improve test coverage
* Fix zlib encode/decode wh...

github.com/BioJulia/Codecs.jl - 0cbefee108b471491732259fccb5162d1fed6530 authored about 7 years ago by Yichao Yu <[email protected]>
Update README.md

github.com/BioJulia/Bio.jl - 15749db493804ac49ae639d6a55719f015ec7d8f authored about 7 years ago by Ben J. Ward <[email protected]>
Update documentation generation (#26)

github.com/BioJulia/BioSequences.jl - 57c2810ccd36f6d0beb411603759f96851832404 authored about 7 years ago by Ben J. Ward <[email protected]>
Added a fork button for packages

github.com/BioJulia/biojulia.github.io - 7f67a218c25af489c42374bcc62675c1025cf77a authored about 7 years ago by Ben J. Ward <[email protected]>
Add more in depth guide to contributing with PRs

github.com/BioJulia/Contributing - b1891eb54e1128baba5d33bb20966a4ab60dfcf3 authored about 7 years ago by Ben J. Ward <[email protected]>
Add extra linebreak

github.com/BioJulia/biojulia.github.io - 5b08b9d76936bab90d8f30eae5020d766b117fed authored about 7 years ago by Ben J. Ward <[email protected]>
Updated and corrected typos in incident response, code of conduct, and community org

github.com/BioJulia/Contributing - 62bbe1202f4e88621a8b5a494caae90ada3b87bb authored about 7 years ago by Ben J. Ward <[email protected]>
Decompose Bio.Structure (#485)

* Remove code and tests

* Reexport BioStructures package

* Remove src/Structure.jl

github.com/BioJulia/Bio.jl - b278c00619be1995e33ecf454ce83737d8feb430 authored about 7 years ago by Joe Greener <[email protected]>
Drop Mkdocs

github.com/BioJulia/Contributing - 68a83c9f2fd2c1ec42b3233cb7f7e9e01cdef5f7 authored about 7 years ago by Ben J. Ward <[email protected]>
Update the CI (#487)

* Edited CI files

* Changed a testing function

github.com/BioJulia/Bio.jl - ec237ab0dd9e5c7da474f385b46610f057a30f30 authored about 7 years ago by Ben J. Ward <[email protected]>
Docs system update

github.com/BioJulia/GeneticVariation.jl - 2c2d9fa2ac9c840641d5e489373e54f9e1157672 authored about 7 years ago by Ben J. Ward <[email protected]>
Drop mkdocs

github.com/BioJulia/NaturalSelection.jl - d1dea4a00f1e8a4dfa9f9c7225b475098c30986e authored about 7 years ago by Ben J. Ward <[email protected]>
Added folder for documentation assets

github.com/BioJulia/assets - 2b6d2079323e0d33efe4d9a6df5fc7e9fd1b1d03 authored about 7 years ago by Ben J. Ward <[email protected]>
Decompose Var (#473)

* Remove the Var module, and replaced with reexport of GeneticVariation

* remove var module
...

github.com/BioJulia/Bio.jl - 0e9690487937f060b9d8b264faffe0f170f83ca7 authored about 7 years ago by Ben J. Ward <[email protected]>
Remove Iterators.jl dependency (not used) (#474)

github.com/BioJulia/Bio.jl - 8f117a9391862a562c0fb67bdb6efd9207b95e69 authored about 7 years ago by Eric Davies <[email protected]>
Add allele frequency and nucleotide diversity methods (#11)

* add nuc div file

* Added a method that computes allele frequencies for a set of sequences
...

github.com/BioJulia/GeneticVariation.jl - 5b9b0ac8df5a742a4bb4b3a258e8f3b65796296d authored about 7 years ago by Ben J. Ward <[email protected]>
dNdS - NG86 (#1)

* Added extra repo files

* Added source files

* Added unit test

* Add travis

* Added...

github.com/BioJulia/NaturalSelection.jl - 791ffc152f767b8be94401d10332606fa9fa01e8 authored about 7 years ago by Ben J. Ward <[email protected]>
Second Commit

github.com/BioJulia/NaturalSelection.jl - cb04a2d68be451f02b6e49e93db1279ee51fd9a7 authored about 7 years ago by Ben J. Ward <[email protected]>
Initial commit

github.com/BioJulia/NaturalSelection.jl - fb77b64c6247ca6a24db12588991722dd7ea56ca authored about 7 years ago by Ben J. Ward <[email protected]>
Add news post for BioStructures release (#4)

* Add joe_greener to authors

* BioStructures release post

github.com/BioJulia/biojulia.github.io - 6477d42738a061675b770ea0f6767e7c43734f0c authored about 7 years ago by Joe Greener <[email protected]>
Update docs index.md

github.com/BioJulia/BioStructures.jl - 3c302833b4a66c59c32a92acafcdb97b5eb606aa authored about 7 years ago by Joe Greener <[email protected]>
Fix license link

github.com/BioJulia/BioStructures.jl - 11a562edaa1dcec4817adc4dc14eeac31465983c authored about 7 years ago by Joe Greener <[email protected]>
Add NEWS.md

github.com/BioJulia/BioStructures.jl - 1db9c3edf89c71975a07d85cf83f42e72807f1e8 authored about 7 years ago by Joe Greener <[email protected]>
Fix readme badges

github.com/BioJulia/BioStructures.jl - 75b0ac2b13163ac8d3738f4eb4af73c956b6478a authored about 7 years ago by Joe Greener <[email protected]>
Update README.md prior to release (#1)

github.com/BioJulia/BioStructures.jl - 55949619bd4c029ea3dbf5a4c0c64c9569096e0c authored about 7 years ago by Ben J. Ward <[email protected]>
Limit the small postlist to the 4 most recent posts

github.com/BioJulia/biojulia.github.io - f293059f96825851a1c3a3f140dbf793f0e8991c authored about 7 years ago by Ben J. Ward <[email protected]>
Fix build by changing PDB download test (#486)

github.com/BioJulia/Bio.jl - f3afbf63d461ec64a74b8d37ec0f4fee38002343 authored about 7 years ago by Joe Greener <[email protected]>
Check file exists before opening

github.com/BioJulia/BioStructures.jl - c9c5cd9536d8978fc5d5cd5fbea3199656116c91 authored about 7 years ago by Joe Greener <[email protected]>
Remove PDB update test that may fail

github.com/BioJulia/BioStructures.jl - b3f609ef6d42331662896393c175edf718030770 authored about 7 years ago by Joe Greener <[email protected]>
Direct copy of 484 from Bio.jl by h3nnn4n

github.com/BioJulia/BioStructures.jl - 1a5d3e4d4072215c6ee2b78e90ca8a803c1ade22 authored about 7 years ago by Joe Greener <[email protected]>
Indexed versions of {omega,phi,psi}angle (#484)

github.com/BioJulia/Bio.jl - 8142f2b7785ace6a0620135883efbe5ba6117be6 authored about 7 years ago by The ultimate Renan <[email protected]>
Edited navbar links

github.com/BioJulia/biojulia.github.io - 451b4ff32bd5d4c783e5209fb598eed15a4ce136 authored about 7 years ago by Ben J. Ward <[email protected]>
Update posts to correct errors, also make BioStructures.jl appear in menu

github.com/BioJulia/biojulia.github.io - df63db5b03596d4db4b466db35b5734a7990ba86 authored about 7 years ago by Ben J. Ward <[email protected]>
Merge remote-tracking branch 'origin/master'

github.com/BioJulia/biojulia.github.io - 9189b38d54a263ab35ebcfda8c915d3e19b3a1b4 authored about 7 years ago by Ben J. Ward <[email protected]>
Add recent news posts.

github.com/BioJulia/biojulia.github.io - 03385e039c497153095ecdbcc60e2d9e1da9ea48 authored about 7 years ago by Ben J. Ward <[email protected]>
Add BioStructures (#3)

github.com/BioJulia/biojulia.github.io - 89b187357997642b2c9b8866113fe00dbe92755b authored about 7 years ago by Joe Greener <[email protected]>
Docs correction

github.com/BioJulia/BioStructures.jl - 9f30f236884b59c5ba9b921196fe675ddd01b4ce authored about 7 years ago by Joe Greener <[email protected]>
Fix contribution link

github.com/BioJulia/BioStructures.jl - 1d0e794677debb6bd08e624ceaaaaf84a7ae88a7 authored about 7 years ago by Joe Greener <[email protected]>
Docs formatting

github.com/BioJulia/BioStructures.jl - 235c53aafbb8f9f832dc0a42e6731fb43b3c5a87 authored about 7 years ago by Joe Greener <[email protected]>
Update docs badge link

github.com/BioJulia/BioStructures.jl - 0d778539f2c63ea6ff8f5fdf4d3ada96da1d8205 authored about 7 years ago by Joe Greener <[email protected]>
Update gitignore

github.com/BioJulia/BioStructures.jl - 24b68881c19c912df2c8eb388aec02d15d8dca6e authored about 7 years ago by Joe Greener <[email protected]>
Trigger build

github.com/BioJulia/BioStructures.jl - 25829657f876056e967dad9098e426bfc8e9a6ef authored about 7 years ago by Joe Greener <[email protected]>
Documenter build files

github.com/BioJulia/BioStructures.jl - fb85b56ab61f734b2c7c8e7c8ac8e0f5fb622411 authored about 7 years ago by Joe Greener <[email protected]>
Docs rename Bio.Structure to BioStructures

github.com/BioJulia/BioStructures.jl - efcc5f5966445d44c4996e50cabc0b592b92b0d4 authored about 7 years ago by Joe Greener <[email protected]>
Direct copy of docs from Bio.jl master

github.com/BioJulia/BioStructures.jl - 0f22da18e470cd602c7ce00f246e5fb3074450e2 authored about 7 years ago by Joe Greener <[email protected]>
Docs badge

github.com/BioJulia/BioStructures.jl - 6723bf70e93956af8bfa19ef010dabd2e23d9922 authored about 7 years ago by Joe Greener <[email protected]>
Add Appveyor badge

github.com/BioJulia/BioStructures.jl - 4c193ba8eb88fab10027f7cf4a1b2a9eec07ed36 authored about 7 years ago by Joe Greener <[email protected]>
Appveyor remove win32

github.com/BioJulia/BioStructures.jl - 383b358a97b8d63dcdba116d4931f86281e92ab5 authored about 7 years ago by Joe Greener <[email protected]>
License link fix

github.com/BioJulia/BioStructures.jl - 8051c78dd30785a371e5feed1a0f28cdccf270bd authored about 7 years ago by Joe Greener <[email protected]>
Readme description and instructions

github.com/BioJulia/BioStructures.jl - cc62387b14e1fd1c7e001cd8b846e4b9d09be07c authored about 7 years ago by Joe Greener <[email protected]>
Travis and Appveyor setup

github.com/BioJulia/BioStructures.jl - e97a0f0a650d9a4a4fd4852c6dad8c623c8d075c authored about 7 years ago by Joe Greener <[email protected]>