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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

little additions

github.com/BioJulia/PopGen.jl_archive - 3050fcc8de3f49fa4c5034a8b42545c96a688991 authored over 4 years ago by Pavel Dimens <[email protected]>
little additions

github.com/BioJulia/PopGen.jl - 3050fcc8de3f49fa4c5034a8b42545c96a688991 authored over 4 years ago by Pavel Dimens <[email protected]>
Flatten ifelse

github.com/BioJulia/BigWig.jl - b9253fff28e072bdeb850925c874159cfa535e27 authored over 4 years ago by Ciarán O'Mara <[email protected]>
Flatten ifelse

github.com/BioJulia/BigBed.jl - cf78e21c3c55ed9bb77eb9b3fa4b9c2eb6949774 authored over 4 years ago by Ciarán O'Mara <[email protected]>
Update README.md

github.com/BioJulia/GenomeGraphs.jl - 0c3d5b627788281c471edec1265474f0907bb738 authored over 4 years ago by Ben J. Ward <[email protected]>
Update README.md

github.com/BioJulia/GenomeGraphs.jl - 116d8a734b2705991141c3fa48c90f4724abea3b authored over 4 years ago by Ben J. Ward <[email protected]>
CompatHelper: bump compat for "ReadDatastores" to "0.3" (#27)

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

github.com/BioJulia/GenomeGraphs.jl - 03ab7f6cbf1dde127bd5f9858f5a4a5f606e7f14 authored over 4 years ago by github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
New package: BigWig v0.1.0 (#71)

UUID: 9d649c22-cb6b-11e8-1fa9-f3896fced444
Repo: https://github.com/BioJulia/BigWig.jl.git
Tre...

github.com/BioJulia/BioJuliaRegistry - 931db9abceeedb3e021ffb7d18d6da6ae3cafc3a authored over 4 years ago by Helix <[email protected]>
New package: BigBed v0.1.0 (#70)

UUID: 97aa930e-cb6b-11e8-0809-05c95cd953e2
Repo: https://github.com/BioJulia/BigBed.jl.git
Tre...

github.com/BioJulia/BioJuliaRegistry - a46a8b3ef3049f42f9536b0336373b5962eb0892 authored over 4 years ago by Helix <[email protected]>
New package: TwoBit v0.1.0 (#72)

UUID: 75842c30-9b2d-11e9-3f58-f17fe2b89951
Repo: https://github.com/BioJulia/TwoBit.jl.git
Tre...

github.com/BioJulia/BioJuliaRegistry - 8ef988233707ec228bb0dac6835054f7cb88f62d authored over 4 years ago by Helix <[email protected]>
Add compat entry for julia

github.com/BioJulia/TwoBit.jl - 8ff24ac634711f448c8a14f1ee903c62bf1fea76 authored over 4 years ago by Ben J. Ward <[email protected]>
Fix typo

github.com/BioJulia/TwoBit.jl - a207f46337f4b9dd22129661510611f6b85bd9a2 authored over 4 years ago by Ben J. Ward <[email protected]>
Add missing docstring

github.com/BioJulia/TwoBit.jl - 1855775edd6dc9df907a7914fd6afdbe46f9b07e authored over 4 years ago by Ben J. Ward <[email protected]>
Merge branch 'master' of github.com:BioJulia/TwoBit.jl

github.com/BioJulia/TwoBit.jl - 4bb2016dd9ba66d123b9902d9fcbde5ed5a759d8 authored over 4 years ago by Ben J. Ward <[email protected]>
Fixup doc links

github.com/BioJulia/TwoBit.jl - 82d5362a12cbc7da4991ad5bebc00a9ecbdaee4d authored over 4 years ago by Ben J. Ward <[email protected]>
Merge pull request #2 from BioJulia/compathelper/new_version/2020-05-16-16-06-52-292-586694392

CompatHelper: add new compat entry for "BioGenerics" at version "0.1"

github.com/BioJulia/TwoBit.jl - 1becc5ddfcf73e7109bc56879f56c3786ae56814 authored over 4 years ago by Ben J. Ward <[email protected]>
Add Documenter setup

github.com/BioJulia/TwoBit.jl - bfdf6af76241b3035fad2bf91cd1df6398392ada authored over 4 years ago by Ben J. Ward <[email protected]>
CompatHelper: add new compat entry for "BioGenerics" at version "0.1"

github.com/BioJulia/TwoBit.jl - e4aa688c94d0864d91f399a22a4a87f1bd719f9d authored over 4 years ago by github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Add docs and CompatHelper actions

github.com/BioJulia/TwoBit.jl - 9f0296918622908f9e3b89912d2aa471288be64c authored over 4 years ago by Ben J. Ward <[email protected]>
Install TagBot action

github.com/BioJulia/TwoBit.jl - 2129b48d7f44f5d800b85885d0601fdca927f766 authored over 4 years ago by Ben J. Ward <[email protected]>
Fix up tests

github.com/BioJulia/TwoBit.jl - be141bf8a15891c011b8de7027f3bbe8a3734eb3 authored over 4 years ago by Ben J. Ward <[email protected]>
Merge branch 'release/v0.1.0'

github.com/BioJulia/BigBed.jl - 983fdb369005c6b6a2fd8e553ad724a6ef14efcb authored over 4 years ago by Ciarán O'Mara <[email protected]>
Merge branch 'master' into develop

github.com/BioJulia/BigBed.jl - 81a67894d3b401317e4e2eaa77632abdc4512e50 authored over 4 years ago by Ciarán O'Mara <[email protected]>
Merge branch 'master' into develop

github.com/BioJulia/BigWig.jl - 0797ff016695ce5b1f87472c0b199207116d4534 authored over 4 years ago by Ciarán O'Mara <[email protected]>
Merge branch 'release/v0.1.0'

github.com/BioJulia/BigWig.jl - 1773c4554e43a4632880d8198b51a07359c1e34c authored over 4 years ago by Ciarán O'Mara <[email protected]>
Minimal code adjustments for working separation

- Ignore BioFmtSpecimens.
- Upgrade to use GenomicFeatures v2.
- Add BBI.

github.com/BioJulia/BigWig.jl - 73f2d00bb00cef4c9ce7b89114a85bd44d069f1e authored over 4 years ago by Ciarán O'Mara <[email protected]>
Add funding

github.com/BioJulia/BigWig.jl - 519c452ffd13dc717df2b5ce2fa7761f08d90d5e authored over 4 years ago by Ciarán O'Mara <[email protected]>
Documentation roundup

github.com/BioJulia/BigWig.jl - 380226507b0e0a1aa6ea14095b1f4e1fbb0fb62b authored over 4 years ago by Ciarán O'Mara <[email protected]>
Add TagBot workflow

github.com/BioJulia/BigWig.jl - b753a3b420e022b53e2f8baa02f1f5655db67edd authored over 4 years ago by Ciarán O'Mara <[email protected]>
Use FormatSpecimens

github.com/BioJulia/BigWig.jl - effc80dbf5f5600df3ad03269a6dca1b5ab14e4a authored over 4 years ago by Ciarán O'Mara <[email protected]>
Naive code roundup

github.com/BioJulia/BigWig.jl - 7aa494e8a2400ffb7d583b3854aac382c09ca776 authored over 4 years ago by Ciarán O'Mara <[email protected]>
Update project status

github.com/BioJulia/BigWig.jl - e03e2ce497539b14ebcd200219e71aed61bf8e7b authored over 4 years ago by Ciarán O'Mara <[email protected]>
Add documentation workflow

github.com/BioJulia/BigWig.jl - a964df55c952085ca1e6c3046355594fabbb994d authored over 4 years ago by Ciarán O'Mara <[email protected]>
Documentation

- API autodocs.
- Logo.
- Badges.

github.com/BioJulia/BigWig.jl - cb74884bf64d0f6a7dcfa537c58d2f86230b1bf8 authored over 4 years ago by Ciarán O'Mara <[email protected]>
Add CompatHelper workflow

github.com/BioJulia/BigWig.jl - 7cd04331299a70da32145879d293cd019235a108 authored over 4 years ago by Ciarán O'Mara <[email protected]>
Continuous Integration

github.com/BioJulia/BigWig.jl - a0f255ecd4dbd72d76949e06fd029b0e78807464 authored over 4 years ago by Ciarán O'Mara <[email protected]>
Add CompatHelper workflow

github.com/BioJulia/BigBed.jl - 89825631b2a4667b2d0040e3d5a7b70f92df04bd authored over 4 years ago by Ciarán O'Mara <[email protected]>
Minimal code adjustments for working separation

- Ignore BioFmtSpecimens.
- Upgrade to use GenomicFeatures v2.
- Add BBI.
- Add BED.

github.com/BioJulia/BigBed.jl - 89ded595728fb3603cb59ec4f440c6f688770fd4 authored over 4 years ago by Ciarán O'Mara <[email protected]>
Naive code roundup

github.com/BioJulia/BigBed.jl - 0b7ed8eb3f1eb0d1af372bafd1e5e68e2808f7b2 authored over 4 years ago by Ciarán O'Mara <[email protected]>
Update project status

github.com/BioJulia/BigBed.jl - 89f59d6bc09f205892e3c751b41f80ea3e7fbe8d authored over 4 years ago by Ciarán O'Mara <[email protected]>
Use FormatSpecimens

github.com/BioJulia/BigBed.jl - 34bd389dcee4bc0cd622b3be89621cb8391e778b authored over 4 years ago by Ciarán O'Mara <[email protected]>
Documentation roundup

github.com/BioJulia/BigBed.jl - 31bb6d136b43b89d36ff6469f8e172b37bfe41b3 authored over 4 years ago by Ciarán O'Mara <[email protected]>
Documentation

- API autodocs.
- Logo.
- Badges.

github.com/BioJulia/BigBed.jl - 6e42956969726cc056f687bdcbe7c145aad8797f authored over 4 years ago by Ciarán O'Mara <[email protected]>
Add funding

github.com/BioJulia/BigBed.jl - 60dc18762fe6455a7960171d305fd074cac6677a authored over 4 years ago by Ciarán O'Mara <[email protected]>
Add documentation workflow

github.com/BioJulia/BigBed.jl - 195136e744457758f8ab428a6ad2d3a4e8aceef0 authored over 4 years ago by Ciarán O'Mara <[email protected]>
Add TagBot workflow

github.com/BioJulia/BigBed.jl - 2f85b87a1e6b0d7eb99db065b81d264b57f71976 authored over 4 years ago by Ciarán O'Mara <[email protected]>
Continuous Integration

github.com/BioJulia/BigBed.jl - 5d7a60571aaa8607ce8dd2fe6c3a7c2bc67ac589 authored over 4 years ago by Ciarán O'Mara <[email protected]>
Implement support for Makie surface like plots for for 2D spectra

github.com/BioJulia/KmerAnalysis.jl - a301c4d08fab943263bc345d5f6667532ee4630e authored over 4 years ago by Ben J. Ward <[email protected]>
Removed unnecessary line

github.com/BioJulia/GenomicAnnotations.jl - 666a651c292ac10abda05f77cc103b463bc42268 authored over 4 years ago by Karl Dyrhage <[email protected]>
Added examples

github.com/BioJulia/GenomicAnnotations.jl - 447353308d3154bd205ca5d66710e73c2880a6f3 authored over 4 years ago by Karl Dyrhage <[email protected]>
Regenerate website

github.com/BioJulia/biojulia.github.io - dfcfbf9684869641264dd6ff3d628cb849737d0b authored over 4 years ago by Ben J. Ward <[email protected]>
CompatHelper: add new compat entry for "AbstractPlotting" at version "0.10" (#3)

* Add point based plotting type recipe for 1D kmer spectra

* CompatHelper: add new compat ent...

github.com/BioJulia/KmerAnalysis.jl - 111df52de01fb529d0d32e1408e5997e72c646f4 authored over 4 years ago by github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Add point based plotting type recipe for 1D kmer spectra

github.com/BioJulia/KmerAnalysis.jl - 198905625b305d0638cbad7405b7982d8c00eba6 authored over 4 years ago by Ben J. Ward <[email protected]>
Change package name

github.com/BioJulia/KmerAnalysis.jl - 7bc0646edc3d1ced7591467a4b581d9b85bb95f5 authored over 4 years ago by Ben J. Ward <[email protected]>
housekeeping

github.com/BioJulia/PopGen.jl_archive - 6d2a509ea8afd8b38f112d2bfc6ad9882ed008e8 authored over 4 years ago by Pavel Dimens <[email protected]>
housekeeping

github.com/BioJulia/PopGen.jl - 6d2a509ea8afd8b38f112d2bfc6ad9882ed008e8 authored over 4 years ago by Pavel Dimens <[email protected]>
More Documentation

github.com/BioJulia/KmerAnalysis.jl - 5399844b8643a848473712915d14fdc4129fab4f authored over 4 years ago by Ben J. Ward <[email protected]>
tag release

github.com/BioJulia/BioStructures.jl - deee9eefd7e20323acef763e4a51bfab6ce84504 authored over 4 years ago by Joe Greener <[email protected]>
CompatHelper: bump compat for "DataFrames" to "0.21" (#19)

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

github.com/BioJulia/BioStructures.jl - 6472208b5909f8ea53dd1b442f91e959ae14f087 authored over 4 years ago by github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
New version: BiobakeryUtils v0.3.3 (#69)

UUID: fa5322f5-bd84-5069-834a-abf3230fb8f8
Repo: https://github.com/BioJulia/BiobakeryUtils.jl.g...

github.com/BioJulia/BioJuliaRegistry - d57560c6e99c097e4858da206d53fbbce37263a6 authored over 4 years ago by Helix <[email protected]>
Merge pull request #68 from BioJulia/registrator/microbiome/3bd8f0ae/v0.6.4

New version: Microbiome v0.6.4

github.com/BioJulia/BioJuliaRegistry - 25917737c00f36bbeed43d3d3e4f8b524fa05638 authored over 4 years ago by Kevin Bonham <[email protected]>
New version: Microbiome v0.6.4

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

github.com/BioJulia/BioJuliaRegistry - 73d79113c20afa71c78280a1f8ba2f2d521656da authored over 4 years ago by BioJuliaBot <[email protected]>
Move logo

github.com/BioJulia/IntervalTrees.jl - f3ddfca43d1288fb60fa78a76717e273483b203f authored over 4 years ago by Ciarán O'Mara <[email protected]>
Remove badge style

github.com/BioJulia/IntervalTrees.jl - baef1713666560078eb043e7097d503fe0334290 authored over 4 years ago by Ciarán O'Mara <[email protected]>
Use first and last accessors for downstream flexibility (#53)

* Update .gitignore

* Remove .DS_Stores

* Add Project.toml

UUID matches https://github....

github.com/BioJulia/IntervalTrees.jl - e37edab61568d08141a3e9c25ec55caac21e5aa5 authored over 4 years ago by Ciarán O'Mara <[email protected]>
general changes

github.com/BioJulia/PopGen.jl_archive - e91d1a2bfdc5433c2699a390f619ba2a382245d0 authored over 4 years ago by Pavel <[email protected]>
general changes

github.com/BioJulia/PopGen.jl - e91d1a2bfdc5433c2699a390f619ba2a382245d0 authored over 4 years ago by Pavel <[email protected]>
Add jknissen blog post

github.com/BioJulia/biojulia.github.io - 0a0752828f7fc002f2c1307bc3dd7cf28f14fea6 authored over 4 years ago by Ben J. Ward <[email protected]>
Add initial draft of dist_mem (#2)

github.com/BioJulia/KmerAnalysis.jl - 27fb7da0370b352dfafc081f8f3dedac2f64bded authored over 4 years ago by Ben J. Ward <[email protected]>
Implement ReadDatastore specific exceptions for file validation (#14)

github.com/BioJulia/ReadDatastores.jl - 4342a6937bfeb7a35a792ff38ae92309c9f1fec1 authored over 4 years ago by Ben J. Ward <[email protected]>
New version: XAM v0.2.3 (#67)

UUID: d759349c-bcba-11e9-07c2-5b90f8f05f7c
Repo: https://github.com/BioJulia/XAM.jl.git
Tree: 4e...

github.com/BioJulia/BioJuliaRegistry - fe3378c1681ec0ae3c32f1ead13e820abb328cc9 authored over 4 years ago by Helix <[email protected]>
Merge branch 'hotfix/iteration'

github.com/BioJulia/XAM.jl - 060349bd2be1320d360d5892802513696324736a authored over 4 years ago by Ciarán O'Mara <[email protected]>
Merge branch 'master' into develop

github.com/BioJulia/XAM.jl - 32a2b129e1d473860668b5820bee18ae02a7f333 authored over 4 years ago by Ciarán O'Mara <[email protected]>
Empty records during iteration

github.com/BioJulia/XAM.jl - f00547177f8aac5168a5c8178012b1f51bd571e4 authored over 4 years ago by Ciarán O'Mara <[email protected]>
Update documentation

github.com/BioJulia/XAM.jl - b440bc3c4d3b77d2f062d422387a7337557f3a76 authored over 4 years ago by Ciarán O'Mara <[email protected]>
Record equivalency functions

github.com/BioJulia/XAM.jl - 300158dbef8b23e122f258bf22a08a331efd6892 authored over 4 years ago by Ciarán O'Mara <[email protected]>
Tests for in-place-reading pattern

github.com/BioJulia/XAM.jl - 5fa8c5bd2eb31d56b2bec67a8634e596ff43ec38 authored over 4 years ago by Ciarán O'Mara <[email protected]>
Increment version

github.com/BioJulia/XAM.jl - bb13a38cf70b3eab70eccde534098466b5a5b2ec authored over 4 years ago by Ciarán O'Mara <[email protected]>
Fixup MinimizerTable

github.com/BioJulia/KmerAnalysis.jl - 378b5c23878cbef7d8e4117a04ad3520a58596cd authored over 4 years ago by Ben J. Ward <[email protected]>
Merge pull request #1 from BioJulia/compathelper/new_version/2020-04-16-17-05-18-196-1011816935

CompatHelper: bump compat for "ReadDatastores" to "0.3"

github.com/BioJulia/KmerAnalysis.jl - ae9608f64019f24029dc740d7fe6a2cd0f19f00c authored over 4 years ago by Ben J. Ward <[email protected]>
CompatHelper: bump compat for "ReadDatastores" to "0.3"

github.com/BioJulia/KmerAnalysis.jl - b7e9613d6c0a984bb86d1c08ea7faea7c2b6ebb7 authored over 4 years ago by github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
New version: ReadDatastores v0.3.0 (#66)

UUID: 70a005b8-9d8a-11e9-0d98-c909fa2e52d2
Repo: https://github.com/BioJulia/ReadDatastores.jl.g...

github.com/BioJulia/BioJuliaRegistry - 85c59ed67b20b4c2ebda38569ec1cf6b80da9f08 authored over 4 years ago by Helix <[email protected]>
Update version number

github.com/BioJulia/ReadDatastores.jl - 7452ac5fd2c4ead72b4307c0f8896b7879a258d8 authored over 4 years ago by Ben J. Ward <[email protected]>
Add more openreads options

github.com/BioJulia/ReadDatastores.jl - d13ad9277a9c4c52a53ee074a9e48482a7cd78a2 authored over 4 years ago by Ben J. Ward <[email protected]>
Merge pull request #65 from BioJulia/registrator/biobakeryutils/fa5322f5/v0.3.2

New version: BiobakeryUtils v0.3.2

github.com/BioJulia/BioJuliaRegistry - dc7ef5aa4697e79761656700dde9963b738a5380 authored over 4 years ago by Kevin Bonham <[email protected]>
Improved opening of datastore files (#13)

github.com/BioJulia/ReadDatastores.jl - d6bdae5dfbb701f9e8c8b4499511799314a81c01 authored over 4 years ago by Ben J. Ward <[email protected]>
Update RegistryCI

github.com/BioJulia/BioJuliaRegistry - 3fc3214035e2ad5881ea7c528eb840b917419926 authored over 4 years ago by Ben J. Ward <[email protected]>
PdbTool ref to docs

github.com/BioJulia/BioStructures.jl - 6e4ecac4f231cdfea8c02a1cd184b6b0f430e459 authored over 4 years ago by Joe Greener <[email protected]>
New version: BiobakeryUtils v0.3.2

UUID: fa5322f5-bd84-5069-834a-abf3230fb8f8
Repo: https://github.com/BioJulia/BiobakeryUtils.jl.g...

github.com/BioJulia/BioJuliaRegistry - 851c0c099efa6c6184742ac4931996c7f286b222 authored over 4 years ago by BioJuliaBot <[email protected]>
update benchmarks

github.com/BioJulia/PopGen.jl_archive - 36cf3b3e673e13263547f8a244729ec7fe26661a authored over 4 years ago by Pavel <[email protected]>
update benchmarks

github.com/BioJulia/PopGen.jl - 36cf3b3e673e13263547f8a244729ec7fe26661a authored over 4 years ago by Pavel <[email protected]>
Update nancycats.gen

github.com/BioJulia/PopGen.jl - fbf9374f0a8680ff1a6333b6023a248efc3e313b authored over 4 years ago by Pavel <[email protected]>
Update nancycats.gen

github.com/BioJulia/PopGen.jl_archive - fbf9374f0a8680ff1a6333b6023a248efc3e313b authored over 4 years ago by Pavel <[email protected]>
group changes

1. Removed old docs. 2. Added Utils.jl for general-use functions, like the new get_N(), which g...

github.com/BioJulia/PopGen.jl_archive - 8be564dd1c39a72fdb844ab82fa08be98e4a9df3 authored over 4 years ago by Pavel <[email protected]>
group changes

1. Removed old docs. 2. Added Utils.jl for general-use functions, like the new get_N(), which g...

github.com/BioJulia/PopGen.jl - 8be564dd1c39a72fdb844ab82fa08be98e4a9df3 authored over 4 years ago by Pavel <[email protected]>
Add draft multi-process minimizer table builder

github.com/BioJulia/KmerAnalysis.jl - d1fc931abd46cc79561cbd7a8ebc266928cd4fc2 authored over 4 years ago by Ben J. Ward <[email protected]>
Add docs

github.com/BioJulia/KmerAnalysis.jl - f44a21e85cbabc4d8e0e1f9823e72e4ddb1964e3 authored over 4 years ago by Ben J. Ward <[email protected]>
line endings in mmtf.jl

github.com/BioJulia/BioStructures.jl - b8cc531ac5758b9a63abc00eea856ea3d175509e authored over 4 years ago by Joe Greener <[email protected]>
Update Manipulate.jl

github.com/BioJulia/PopGen.jl - d1188c5ff702dea877ddbe3cb45734e1efc995b4 authored over 4 years ago by Pavel <[email protected]>
Update Manipulate.jl

github.com/BioJulia/PopGen.jl_archive - d1188c5ff702dea877ddbe3cb45734e1efc995b4 authored over 4 years ago by Pavel <[email protected]>