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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

Updated for DataFrames v0.19.0

github.com/BioJulia/GenomicAnnotations.jl - cff6aa395922b2bc6b0b4dfa939f4f8948a8a6a8 authored over 5 years ago by Karl Dyrhage <[email protected]>
Fix occasional bounds error when linking unitigs by their overlaps

github.com/BioJulia/GenomeGraphs.jl - a82b46002ff08a8efbdbbbd233f87da70c1c5d19 authored over 5 years ago by Ben J. Ward <[email protected]>
Fix push method for SequenceGraphPath

github.com/BioJulia/GenomeGraphs.jl - ed4af958f5e50b2d9a2a0accddb1ecf3563bf981 authored over 5 years ago by Ben J. Ward <[email protected]>
Add documentation

github.com/BioJulia/GenomeGraphs.jl - 09b9ce42b9d4cdc62d88233af3a5a17b4f97426e authored over 5 years ago by Ben J. Ward <[email protected]>
Add get_all_unitigs method

github.com/BioJulia/GenomeGraphs.jl - e23ba854c4b334246067a4db0a41347d2c515666 authored over 5 years ago by Ben J. Ward <[email protected]>
Add a SequenceGraphPath type

github.com/BioJulia/GenomeGraphs.jl - 207d2a47b0c09511ee327c4d3834b7a8aba251ae authored over 5 years ago by Ben J. Ward <[email protected]>
Gsoc/dbg (#8)

This PR adds a SequenceDistanceGraph type and implements efficient compressed
de Bruijn graph c...

github.com/BioJulia/GenomeGraphs.jl - 95ed3b62e0652b96b69d58c386384ac383304ec9 authored over 5 years ago by Arda Akdemir <[email protected]>
Remove deploydocs keywords no longer used

github.com/BioJulia/MicrobiomePlots.jl - 3bf8ed96eafcbfcc184cfc413761e7cb8da34dea authored over 5 years ago by Ben J. Ward <[email protected]>
Initial commit

github.com/BioJulia/ReadDatastores.jl - 12bbed91539dabab7426f2c5ec1ad841a4abdc60 authored over 5 years ago by Ben J. Ward <[email protected]>
Add source code and project files

github.com/BioJulia/TwoBit.jl - 7adad29d13d2a3d197975624ffce53bbd88560b0 authored over 5 years ago by Ben J. Ward <[email protected]>
Initial commit

github.com/BioJulia/TwoBit.jl - 5688b0a2055400e0d07ea3faca8b0b0efd7d8957 authored over 5 years ago by Ben J. Ward <[email protected]>
Merge pull request #16 from BioJulia/register/FASTX/v1.0.0

New package: FASTX v1.0.0

github.com/BioJulia/BioJuliaRegistry - fe46cfbc1e13f60fdb84094572c850a7031f412e authored over 5 years ago by Ben J. Ward <[email protected]>
New package: FASTX v1.0.0

UUID: c2308a5c-f048-11e8-3e8a-31650f418d12
Repo: https://github.com/BioJulia/FASTX.jl.git
Tree: ...

github.com/BioJulia/BioJuliaRegistry - bcc5d2ac312ebf9987320aff0e2a3bc31ba52c69 authored over 5 years ago by BioJuliaBot <[email protected]>
Get coverage working again

github.com/BioJulia/FASTX.jl - eb149bc546d43c247157b4acfb29d8cf1da9f865 authored over 5 years ago by Ben J. Ward <[email protected]>
Get documentation working again

github.com/BioJulia/FASTX.jl - ba9bd86b18f13e60f9939d6a5af0dc16488aba84 authored over 5 years ago by Ben J. Ward <[email protected]>
Accessor methods now return `nothing` rather than throw an exception.

github.com/BioJulia/FASTX.jl - f376618e82275a2622a7880d7254e60f927cadf9 authored over 5 years ago by Ben J. Ward <[email protected]>
Merge pull request #3 from kescobo/docs

Docs

github.com/BioJulia/MicrobiomePlots.jl - 43bd22bbb227e0fc97758e4bbb95635134e67f00 authored over 5 years ago by Kevin Bonham <[email protected]>
fix docs Project

github.com/BioJulia/MicrobiomePlots.jl - c2e40a6a9fb8ede48eaefe40040020514c14a0f0 authored over 5 years ago by Kevin Bonham <[email protected]>
update annotation bar and add docstring

github.com/BioJulia/MicrobiomePlots.jl - 7fcea0efbaaa034df3b5cf78bf153f3f655f160d authored over 5 years ago by Kevin Bonham <[email protected]>
New version: MicrobiomePlots v0.2.0

UUID: bed85cf4-5cc8-5ac4-9eb3-09fbf92b2ce2
Repo: https://github.com/kescobo/MicrobiomePlots.jl.g...

github.com/BioJulia/BioJuliaRegistry - d494ae754c3f0ef6cc1aced6235f487f945f72b8 authored over 5 years ago by BioJuliaBot <[email protected]>
Merge pull request #2 from kescobo/pkg3

Move from REQUIRE to Project.toml

github.com/BioJulia/MicrobiomePlots.jl - 5d52bccd76e40b8cdbe4a29a4045fd55262fab82 authored over 5 years ago by Kevin Bonham <[email protected]>
Fix documenter constraint

github.com/BioJulia/MicrobiomePlots.jl - 526489df50d5d32ed8651d3b9659da433fe0f799 authored over 5 years ago by Kevin Bonham <[email protected]>
fix comma in docs build

github.com/BioJulia/MicrobiomePlots.jl - 9c2448edfa01bc5d4d43718bb1b7d21a1d9d2c9f authored over 5 years ago by Kevin Bonham <[email protected]>
build docs on julia 1.1

github.com/BioJulia/MicrobiomePlots.jl - 2522d2d9be0027fdd688f73b30a4196fac4b8638 authored over 5 years ago by Kevin Bonham <[email protected]>
Remove support for julia 1.0

github.com/BioJulia/MicrobiomePlots.jl - 7fe1a4fcaf6776e01abeabb067ed59ca83326865 authored over 5 years ago by Kevin Bonham <[email protected]>
statSplots (didn't I do this already??)

github.com/BioJulia/MicrobiomePlots.jl - 1f793709fd318b2bdc89b764fc08eff868b919b8 authored over 5 years ago by Kevin Bonham <[email protected]>
update travis to get biojulia registry

github.com/BioJulia/MicrobiomePlots.jl - 318032e3e428e42e00096218c783a71ac6777288 authored over 5 years ago by Kevin Bonham <[email protected]>
update docs

github.com/BioJulia/MicrobiomePlots.jl - 108db42ad3a10c3222c4ecc60ecb329770561d63 authored over 5 years ago by Kevin Bonham, PhD <[email protected]>
update NEWS, version

github.com/BioJulia/MicrobiomePlots.jl - 1eb9848307cef7fba39a4e2eb816ecd82149d38e authored over 5 years ago by Kevin Bonham, PhD <[email protected]>
update Project, fix tests

github.com/BioJulia/MicrobiomePlots.jl - 1b2475143d88bab639e0f0022c1c4bbe52a4a3af authored over 5 years ago by Kevin Bonham, PhD <[email protected]>
Merge pull request #21 from BioJulia/docs_update

Docs update

github.com/BioJulia/SubstitutionModels.jl - 17ff99b6de9ada0085b65d474982d5dcd5ba602a authored over 5 years ago by Justin Angevaare <[email protected]>
Expand documentation reflecting updates to constructions methods; add a few more tests

github.com/BioJulia/SubstitutionModels.jl - ad5a28d4f2a58f88f56f8d8f30a3f98e0b63607c authored over 5 years ago by Justin Angevaare <[email protected]>
Add a few more tests for unsafe construction methods

github.com/BioJulia/SubstitutionModels.jl - f428d40844e27bf28fd7a559a38955ed6fbebb4a authored over 5 years ago by Justin Angevaare <[email protected]>
Prepare for v0.4.0

github.com/BioJulia/SubstitutionModels.jl - 526e5e94c1d0daaf0422b87d1678b3f2c48f8547 authored over 5 years ago by Justin Angevaare <[email protected]>
Merge pull request #18 from BioJulia/constructors

Expansion of constructors methods for Nucleic Acid Substitution Models

github.com/BioJulia/SubstitutionModels.jl - 9e33bac77c69f094af8cf73fc6e324ce92d5dd53 authored over 5 years ago by Justin Angevaare <[email protected]>
work on unit test coverage

work on unit test coverage

work on unit test coverage

github.com/BioJulia/SubstitutionModels.jl - bddaf04b5e83f9ea9ec85d23fadf78551af0b5c3 authored over 5 years ago by Justin Angevaare <[email protected]>
revamp testing, K80 error checking bugfix

github.com/BioJulia/SubstitutionModels.jl - d27c5658e744e5f52079e6499f3253b550f9717a authored over 5 years ago by Justin Angevaare <[email protected]>
update Project.toml

github.com/BioJulia/MicrobiomePlots.jl - 98b1b098063a8493a70804be490f516b4dc5278b authored over 5 years ago by Kevin Bonham <[email protected]>
Add convert methods, they may be useful...

github.com/BioJulia/SubstitutionModels.jl - 0b3f7cd214401b3bfbada9fd43401caaae5e349a authored over 5 years ago by Justin Angevaare <[email protected]>
reorganize outer constructors, add detection for abs vs rel forms when using parameter/freq vector based constructors

reorganize outer constructors, add detection for abs vs rel forms when using parameter/freq vect...

github.com/BioJulia/SubstitutionModels.jl - b072eee46663000cd031f9f402a56dfa3dbd922e authored over 5 years ago by Justin Angevaare <[email protected]>
Update .travis.yml

doc-build environment

Update make.jl

Add LinearAlgebra to deps

Remove non-working badge

github.com/BioJulia/SubstitutionModels.jl - 0f86165afe1603a3a3a5a5e2a096bedc431bdee2 authored over 5 years ago by Justin Angevaare <[email protected]>
test vector lengths, rather than ignore extra parameters with new outer constructors

github.com/BioJulia/SubstitutionModels.jl - 3f70e10d9c4360ebf2f6291fe5fca7e36bb2a3f8 authored over 5 years ago by Justin Angevaare <[email protected]>
Allow for construction using parameter vectors

github.com/BioJulia/SubstitutionModels.jl - de3d315638eb6a230dde4175701e91c2a1acc27b authored over 5 years ago by Justin Angevaare <[email protected]>
Update Project.toml

github.com/BioJulia/SubstitutionModels.jl - ed4348b67f24191d466327bdcc7f8605e8b0d686 authored over 5 years ago by Justin Angevaare <[email protected]>
Merge pull request #17 from BioJulia/project.toml

Transition to Project.toml

github.com/BioJulia/SubstitutionModels.jl - f2fa9edd8ffa8614f3d4f93c20120d05bdabe3ca authored over 5 years ago by Justin Angevaare <[email protected]>
add julia 1.1 testing

github.com/BioJulia/SubstitutionModels.jl - 7e44cd8cb8b90e5a88804944c930d9aad5ca2029 authored over 5 years ago by Justin Angevaare <[email protected]>
generate project.toml

github.com/BioJulia/SubstitutionModels.jl - 45c5d1a911a6b2a4f862adf35156658a5a91d5cc authored over 5 years ago by Justin Angevaare <[email protected]>
Merge pull request #16 from kgori/scale_q

Methods to scale all Q and P matrices such that a branch length of 1 = 1 expected substitution

github.com/BioJulia/SubstitutionModels.jl - b730fed9bbbf6a5762955e3648592e47fe8f0b5f authored over 5 years ago by Justin Angevaare <[email protected]>
Add scaling feature to P and Q matrix calculations

github.com/BioJulia/SubstitutionModels.jl - 32a1d6aa84268943b5a65e30e75d7295259dfe29 authored over 5 years ago by kgori <[email protected]>
actually add Project.toml

github.com/BioJulia/MicrobiomePlots.jl - 6012cb8a9e986d9e4fa9b71d61d1118d8755b276 authored over 5 years ago by Kevin Bonham <[email protected]>
Switch to Project.toml

github.com/BioJulia/MicrobiomePlots.jl - a5b203cb8fcd7e9b6ce3d094b1fd54e4c15fc4fc authored over 5 years ago by Kevin Bonham <[email protected]>
remove pcoa in favor of mds

github.com/BioJulia/MicrobiomePlots.jl - 3cbf6499918320b1d60b82c5c452f035f06281de authored over 5 years ago by Kevin Bonham <[email protected]>
Merge pull request #14 from BioJulia/register/BioSymbols/v4.0.1

Register BioSymbols: 4.0.1

github.com/BioJulia/BioJuliaRegistry - 262b563951f8362151c4387c4b4feebf1f006559 authored over 5 years ago by Ben J. Ward <[email protected]>
New version: BioSymbols v4.0.1

UUID: 3c28c6f8-a34d-59c4-9654-267d177fcfa9
Repo: https://github.com/BioJulia/BioSymbols.jl.git
T...

github.com/BioJulia/BioJuliaRegistry - e2405caeecca5256f5e65a654b35c9dfa08fbd00 authored over 5 years ago by BioJuliaBot <[email protected]>
Fixed missing iterate and length methods

github.com/BioJulia/BioSymbols.jl - ec7427d794c1952f29cb80f4dfe81eabb13d2520 authored over 5 years ago by Ben J. Ward <[email protected]>
Merge pull request #11 from BioJulia/register/BioSymbols/v4.0.0

Register BioSymbols: 4.0.0

github.com/BioJulia/BioJuliaRegistry - c082b6bb433a35654587ea92b719b302b6e03a00 authored over 5 years ago by Ben J. Ward <[email protected]>
Merge branch 'master' into register/BioSymbols/v4.0.0

github.com/BioJulia/BioJuliaRegistry - 438ba11db4bb0c561df4518aa0c829e78126864d authored over 5 years ago by Ben J. Ward <[email protected]>
Merge pull request #12 from BioJulia/register/Microbiome/v0.4.1

Register Microbiome: 0.4.1

github.com/BioJulia/BioJuliaRegistry - 2e184a6c7aa406e70db1b446de848c6435e29cab authored over 5 years ago by Ben J. Ward <[email protected]>
New version: Microbiome v0.4.1

UUID: 3bd8f0ae-a0f2-5238-a5af-e1b399a4940c
Repo: https://github.com/BioJulia/Microbiome.jl.git
T...

github.com/BioJulia/BioJuliaRegistry - 48be94ad6930a9038b724735b7d0d34f2186d328 authored over 5 years ago by BioJuliaBot <[email protected]>
First hugo build

github.com/BioJulia/biojulia.github.io - 6bbf8efb4962555692469ff7a9cb37133d153df2 authored over 5 years ago by Ben J. Ward <[email protected]>
New version: BioSymbols v4.0.0

UUID: 3c28c6f8-a34d-59c4-9654-267d177fcfa9
Repo: https://github.com/BioJulia/BioSymbols.jl.git
T...

github.com/BioJulia/BioJuliaRegistry - d2b27b677289e50b362f09226f32506a4bf410d1 authored over 5 years ago by BioJuliaBot <[email protected]>
Project update (#33)

This removes testing for julia v0.6 and removes the use of Nullables.

Prior to julia 1.0 (and 0...

github.com/BioJulia/BioSymbols.jl - ea6f595a4f14211b9cbba98ef01e4699b223a5cc authored over 5 years ago by Ben J. Ward <[email protected]>
Merge pull request #10 from BioJulia/register/BioGenerics/v0.1.0

Register BioGenerics: 0.1.0

github.com/BioJulia/BioJuliaRegistry - 326639b45365c91488b273f2bdb2c76342ad85c1 authored over 5 years ago by Ben J. Ward <[email protected]>
New version: BioGenerics v0.1.0

UUID: 47718e42-2ac5-11e9-14af-e5595289c2ea
Repo: https://github.com/BioJulia/BioGenerics.jl.git
...

github.com/BioJulia/BioJuliaRegistry - 5e1095cf78886be21503a271d2be7ef2f8f83a5b authored over 5 years ago by BioJuliaBot <[email protected]>
Update project files

- Update the readme.
- Remove the bors toml file and edit the travis and appveyor files
accord...

github.com/BioJulia/BioGenerics.jl - c828d5c6a67567f848248fa14e2f2e48fe3a3ddc authored over 5 years ago by Ben J. Ward <[email protected]>
Merge pull request #9 from BioJulia/register/Pseudoseq/v0.1.0

Register Pseudoseq: 0.1.0

github.com/BioJulia/BioJuliaRegistry - 2adbc2177770f2551c4f4d011a16d2049540e8c3 authored over 5 years ago by Ben J. Ward <[email protected]>
New version: Pseudoseq v0.1.0

UUID: 5fa9f68e-f4b0-11e8-18b8-fb82dd3c6483
Repo: https://github.com/bioinfologics/Pseudoseq.jl.g...

github.com/BioJulia/BioJuliaRegistry - db4267ace7548f16077b2a7a96f815879a048ba9 authored over 5 years ago by BioJuliaBot <[email protected]>
Remove pseudoseq

github.com/BioJulia/BioJuliaRegistry - c5a7ea8c029354cf7a053f675529fe7822977584 authored over 5 years ago by Ben J. Ward <[email protected]>
Merge pull request #8 from BioJulia/register/FormatSpecimens/v1.0.0

Register FormatSpecimens: 1.0.0

github.com/BioJulia/BioJuliaRegistry - 7d764975ecd09dcfe310595e80e3ec9a2f33af41 authored over 5 years ago by Ben J. Ward <[email protected]>
New version: FormatSpecimens v1.0.0

UUID: 3372ea36-2a1a-11e9-3eb7-996970b6ffbd
Repo: https://github.com/BioJulia/FormatSpecimens.jl....

github.com/BioJulia/BioJuliaRegistry - 36e855ace37b13bbc9e29e01cd572059240bf3c3 authored over 5 years ago by BioJuliaBot <[email protected]>
Merge pull request #6 from BioJulia/register/Pseudoseq/v0.1.0

Register Pseudoseq: 0.1.0

github.com/BioJulia/BioJuliaRegistry - 86eb38cdb7bbdd44a4859b6e571448574fbd167a authored over 5 years ago by Ben J. Ward <[email protected]>
New version: Pseudoseq v0.1.0

UUID: 5fa9f68e-f4b0-11e8-18b8-fb82dd3c6483
Repo: https://github.com/bioinfologics/Pseudoseq.jl.g...

github.com/BioJulia/BioJuliaRegistry - 3685acccf83efeb674e520b9011d01711cf1325f authored over 5 years ago by BioJuliaBot <[email protected]>
Reset the registry

github.com/BioJulia/BioJuliaRegistry - c3214956918468a7d22b29b637ca2c324c670f9a authored over 5 years ago by Ben J. Ward <[email protected]>
Merge pull request #3 from BioJulia/register/Pseudoseq/v0.1.0

Register Pseudoseq: 0.1.0

github.com/BioJulia/BioJuliaRegistry - 72aff957c9faee59a2ad0938d39e0ee6f76a3a64 authored over 5 years ago by Ben J. Ward <[email protected]>
New version: Pseudoseq v0.1.0

UUID: 5fa9f68e-f4b0-11e8-18b8-fb82dd3c6483
Repo: https://github.com/bioinfologics/Pseudoseq.jl.g...

github.com/BioJulia/BioJuliaRegistry - 85a8af1e2f888e2784fdc02c01096b85dfa2fd67 authored over 5 years ago by BioJuliaBot <[email protected]>
Merge pull request #2 from BioJulia/register/Pseudoseq/v0.1.0

Register Pseudoseq: 0.1.0

github.com/BioJulia/BioJuliaRegistry - 50a0da66096b46cb9ca25dfc323a49fb4bf2ca2b authored over 5 years ago by Ben J. Ward <[email protected]>
New version: Pseudoseq v0.1.0

UUID: 5fa9f68e-f4b0-11e8-18b8-fb82dd3c6483
Repo: https://github.com/bioinfologics/Pseudoseq.jl.g...

github.com/BioJulia/BioJuliaRegistry - 3f6040ba337d869e08a728cae1e6fa159407f3a8 authored over 5 years ago by BioJuliaBot <[email protected]>
Fix reading BAM files from processes. (#29)

github.com/BioJulia/BioAlignments.jl - cb5427ac704f5845a05c5bfeef583a5b2866caf0 authored over 5 years ago by Daniel C. Jones <[email protected]>
bump version to 0.8.0

github.com/BioJulia/Automa.jl - b6997f7415992a82e8538ca6ba8f5f3b5fc9a297 authored over 5 years ago by Kenta Sato <[email protected]>
add Project.toml (#45)

github.com/BioJulia/Automa.jl - dc79f25058e8462584f9963c150707e0ad0f54e2 authored over 5 years ago by Kenta Sato <[email protected]>
add .envrc

github.com/BioJulia/Automa.jl - 37575716ad04c7f3160033c945b259b8b4a43610 authored over 5 years ago by Kenta Sato <[email protected]>
fix backslash escaping (#42)

github.com/BioJulia/Automa.jl - 19c20b6fb3bf84f7d0db4102b4404c9e5ca35a65 authored over 5 years ago by Kenta Sato <[email protected]>
Fix deprecations (#44)

github.com/BioJulia/Automa.jl - b8e3ee2cd9f31a54dc6faed0cc1e1f04a247dd2f authored over 5 years ago by femtocleaner[bot] <femtocleaner[bot]@users.noreply.github.com>
Drop Julia 0.7 and update CI settings (#43)

github.com/BioJulia/Automa.jl - 189aab80ed48e5de3715c32de52351afd045fa62 authored over 5 years ago by Kenta Sato <[email protected]>
fix tests file

github.com/BioJulia/Bio.jl - 62e3441f00dcc52b102d9ae5e2a0a0e4981296af authored over 5 years ago by Ben J. Ward <[email protected]>
Add logo sticker

github.com/BioJulia/Bio.jl - 0f5ad8743d7e4d39f8e641f2e7e21278cc257777 authored over 5 years ago by Ben J. Ward <[email protected]>
Update readme

github.com/BioJulia/Bio.jl - 99838ef0542cc2abbf6804d574240ebff446c8db authored over 5 years ago by Ben J. Ward <[email protected]>
Update readme

github.com/BioJulia/FASTX.jl - e50d3228b755e23e2d3c1ab95ca5c71b63aa6594 authored over 5 years ago by Ben J. Ward <[email protected]>
Use TranscodingStreams

github.com/BioJulia/FASTX.jl - ab25467a35dcde230d30bb5eab5d00b7e8e95d8d authored over 5 years ago by Ben J. Ward <[email protected]>
Update for Julia 1.0 (#5)

- Substitute FactCheck for base Test

- Fix deprecated vector allocation

- Fix deprecated v...

github.com/BioJulia/WaveletMatrices.jl - 11085b395c3a698cee350ec063023033ae51ebe9 authored over 5 years ago by Tim Sterne-Weiler <[email protected]>
Merge pull request #15 from kgori/tn93_pmatrices

Bugfixes relating to P matrices of TN93 and related models

github.com/BioJulia/SubstitutionModels.jl - 7e831397c94f93d02206ce97f181adaba44d1557 authored over 5 years ago by Justin Angevaare <[email protected]>
Fix typo in P() for TN93 and related models

github.com/BioJulia/SubstitutionModels.jl - f12a60e70cfc9cfe6b4cbe626f245bf9eeccca62 authored over 5 years ago by kgori <[email protected]>
Merge pull request #14 from kgori/fix_eigen

Bugfixes: eig to eigen and JC69 P matrices.

github.com/BioJulia/SubstitutionModels.jl - 83a979a0205dc42004748967a39c4fcf50923618 authored over 5 years ago by Justin Angevaare <[email protected]>