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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

Merge branch 'master' into develop

github.com/BioJulia/GenomicFeatures.jl - 5a2e8484ba8d34d86db049ed7d636263156ad9c6 authored over 3 years ago by Ciarán O’Mara <[email protected]>
Removed CodecZlib dependency

github.com/BioJulia/GenomicAnnotations.jl - 60fc0e023dd41a1fe27f23bf56da165d696f825f authored over 3 years ago by Karl Dyrhage <[email protected]>
Updated version number to v0.3.0

github.com/BioJulia/GenomicAnnotations.jl - e636a883ee573e1fce6d8ac1045f025ba9a089bc authored over 3 years ago by Karl Dyrhage <[email protected]>
Removed CodecZlib dependency

github.com/BioJulia/GenomicAnnotations.jl - f7a85b42b3b357ca9a665a3acd667b8516e89af1 authored over 3 years ago by Karl Dyrhage <[email protected]>
Change escape sequence in @genes to $

github.com/BioJulia/GenomicAnnotations.jl - 36aa5bf1d95a56d218a67bb326b5b111f3c73911 authored over 3 years ago by Karl Dyrhage <[email protected]>
Revert BioSequences.sequence extension

github.com/BioJulia/GenomicAnnotations.jl - c383b3e53243f5a12f2efade3605d59274a7511d authored over 3 years ago by Karl Dyrhage <[email protected]>
Add range and strand specification (#1)

github.com/BioJulia/BioFetch.jl - e3a12a02dcf0e9f69b519800f9776ae93e68f272 authored over 3 years ago by Nicholas Bauer <[email protected]>
bump version

github.com/BioJulia/BioStructures.jl - fe63347dac5927743a0a0469141ff2bf14b9ca9c authored over 3 years ago by Joe Greener <[email protected]>
docstring for read

github.com/BioJulia/BioStructures.jl - 693bda7c18a7a3b23e19ef64aeed0382425a0716 authored over 3 years ago by Joe Greener <[email protected]>
MMTF compat bounds

github.com/BioJulia/BioStructures.jl - db027b06970061b0afe6197ce45b5bdfc6d33516 authored over 3 years ago by Joe Greener <[email protected]>
export Base functions for API docstrings

github.com/BioJulia/BioStructures.jl - ae2cea405f1e3e33f219d3b687b2e1a9c5ce0ce8 authored over 3 years ago by Joe Greener <[email protected]>
use Downloads, require Julia 1.3

github.com/BioJulia/MMTF.jl - 71ceec63927ebcec7deacffeed63c5b27e0cf98f authored over 3 years ago by Joe Greener <[email protected]>
docstring for read

github.com/BioJulia/BioStructures.jl - a98cda824b5c914de88730c9a27cba3293a68abd authored over 3 years ago by Joe Greener <[email protected]>
use Downloads package

github.com/BioJulia/BioStructures.jl - 777b90297feba80ea456fbb616d30bcd12481ed1 authored over 3 years ago by Joe Greener <[email protected]>
residue sorting sorts hetero last

github.com/BioJulia/BioStructures.jl - fb6f87cf3054cd1ebb7f8b9a51caf92a9607cb3c authored over 3 years ago by Joe Greener <[email protected]>
add Aqua to tests

github.com/BioJulia/BioStructures.jl - d71b0edf2a84e6ffda0dcca367e631edb188561d authored over 3 years ago by Joe Greener <[email protected]>
Fix ambiguity

github.com/BioJulia/FASTX.jl - ab3a1b58fa88c551368fcbd65323d2cf88996b66 authored over 3 years ago by Jakob Nybo Nissen <[email protected]>
Allow trailing newlines for FASTQ files

github.com/BioJulia/FASTX.jl - 8c4bfc3e49c406d1a3287cd54669be0c51ee47b6 authored over 3 years ago by Jakob Nybo Nissen <[email protected]>
CompatHelper: bump compat for "MultipleTesting" to "0.5"

github.com/BioJulia/PopGen.jl - d2175708b7f5a3127cc905513641cea9864340e9 authored over 3 years ago by github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Update README.md

github.com/BioJulia/BioFetch.jl - f9726bda52eb47cf5c86bf0b9299fc31b553ae41 authored over 3 years ago by Nicholas Bauer <[email protected]>
Update README.md

github.com/BioJulia/BioFetch.jl - c98f469e678790a671b443276e760649058edd4d authored over 3 years ago by Nicholas Bauer <[email protected]>
Create LICENSE

github.com/BioJulia/BioFetch.jl - 91d7e84d0670319bbb9d9e7992b4d903ec47b3f0 authored over 3 years ago by Nicholas Bauer <[email protected]>
Create ci.yml

github.com/BioJulia/BioFetch.jl - 25f951d3ed3e8b2e51144e069eabb78450fe711d authored over 3 years ago by Nicholas Bauer <[email protected]>
Basic tests

github.com/BioJulia/BioFetch.jl - 7f63b97bf7227c7b1260f8dcbdd600250adde850 authored over 3 years ago by Nicholas Bauer <[email protected]>
Make GenBank work, refinements

github.com/BioJulia/BioFetch.jl - 03230423773bebb7ac6d9dc055864ea2124b0f89 authored over 3 years ago by Nicholas Bauer <[email protected]>
Update README.md

github.com/BioJulia/BioFetch.jl - 579a1ded0f0491b3aef6f5ea39e9d36cf4f761ae authored over 3 years ago by Nicholas Bauer <[email protected]>
Update README.md

github.com/BioJulia/BioFetch.jl - 367fd93d3cbd0d38fe2c0f527dc6f50c5afd982e authored over 3 years ago by Nicholas Bauer <[email protected]>
Adjust for fact that some single queries return multiple sequences.

github.com/BioJulia/BioFetch.jl - 68b9fb3ae0f73672b590aed5ef28d5be50dcc9be authored over 3 years ago by Nicholas Bauer <[email protected]>
Add using for EBIProteins

github.com/BioJulia/BioFetch.jl - 055690da7d1725891279358d8d10729fcbc51f8d authored over 3 years ago by Nicholas Bauer <[email protected]>
Fix proteins, remove gb for now

github.com/BioJulia/BioFetch.jl - 1502a2a643878db8c5aaad4904e6974864f51ca4 authored over 3 years ago by Nicholas Bauer <[email protected]>
single-sequence version

github.com/BioJulia/BioFetch.jl - a8d6a9b3625fdc89d5a2a7c2f290c0d40af95429 authored over 3 years ago by Nicholas Bauer <[email protected]>
Fixes and diagnostics

github.com/BioJulia/BioFetch.jl - 21981fc39c0d9bfe7f3a9a782f27fb11c2e4f35f authored over 3 years ago by Nicholas Bauer <[email protected]>
Fixes

github.com/BioJulia/BioFetch.jl - 9e691a173c0533c627bd16161d975bbaf8c926e6 authored over 3 years ago by Nicholas Bauer <[email protected]>
Added Project info

github.com/BioJulia/BioFetch.jl - 3033d8833a7ec761669117c054ab3f0867bf4199 authored over 3 years ago by Nicholas Bauer <[email protected]>
Added doc

github.com/BioJulia/BioFetch.jl - 7f8f9fc5aea0dea63df95c76c0aed6efbab1cbd6 authored over 3 years ago by Nicholas Bauer <[email protected]>
Added EBI UniProt and Ensembl

github.com/BioJulia/BioFetch.jl - 1c2603aebc42bc27235cc0163db1e35925e13065 authored over 3 years ago by Nicholas Bauer <[email protected]>
Refined interface to infer database for NCBI

github.com/BioJulia/BioFetch.jl - b0bac7f694e930dd55aaa7e6e745741f0ded994a authored over 3 years ago by Nicholas Bauer <[email protected]>
Merge pull request #44 from jakobnissen/noautoma

Removed Automa parsing

github.com/BioJulia/BioSymbols.jl - 54bff1aba4799cb7b96f23090c92a7f6ed470284 authored over 3 years ago by Jakob Nybo Nissen <[email protected]>
Removed Automa parsing

github.com/BioJulia/BioSymbols.jl - 460ad173a376e172619be9f6ca5af83115eb7239 authored over 3 years ago by Jakob Nybo Nissen <[email protected]>
Update Project.toml

github.com/BioJulia/PopGen.jl - 86f53c183c2c7be9f937ae429a459e0a921cbea5 authored over 3 years ago by Pavel V. Dimens <[email protected]>
Merge pull request #70 from BioJulia/compathelper/new_version/2021-05-05-00-57-21-811-2670172845

CompatHelper: bump compat for "DataFrames" to "1.1"

github.com/BioJulia/PopGen.jl - 88edb124dc2d8d19b9c53654fc1a783b488aa400 authored over 3 years ago by Pavel V. Dimens <[email protected]>
Merge branch 'dev' into compathelper/new_version/2021-05-05-00-57-21-811-2670172845

github.com/BioJulia/PopGen.jl - ec03584046fb99576b9b0bc87634a298d044ea67 authored over 3 years ago by Pavel V. Dimens <[email protected]>
Merge pull request #69 from BioJulia/compathelper/new_version/2021-05-03-01-04-10-729-4110009785

CompatHelper: bump compat for "Distributions" to "0.25"

github.com/BioJulia/PopGen.jl - 345ca7ce3c6d46a80d10c153793455d2afaba97c authored over 3 years ago by Pavel V. Dimens <[email protected]>
Merge branch 'dev' into compathelper/new_version/2021-05-03-01-04-10-729-4110009785

github.com/BioJulia/PopGen.jl - 8a5030e6116e0ae4b8646fc9635a9845889bef3e authored over 3 years ago by Pavel V. Dimens <[email protected]>
Merge pull request #68 from BioJulia/compathelper/new_version/2021-04-22-00-20-10-428-571431155

CompatHelper: bump compat for "DataFrames" to "1.0"

github.com/BioJulia/PopGen.jl - c26060b542e4fef50ca3c53634f0f18238e3479f authored over 3 years ago by Pavel V. Dimens <[email protected]>
CompatHelper: bump compat for "DataFrames" to "1.1"

github.com/BioJulia/PopGen.jl - 3c124212c38668e520c246ba4fe549f020f24fb7 authored over 3 years ago by github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
CompatHelper: bump compat for "Distributions" to "0.25"

github.com/BioJulia/PopGen.jl - ff93b24d3f90a1332363e39384fe3f037e089d0a authored over 3 years ago by github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Extend BioSequences.sequence()

github.com/BioJulia/GenomicAnnotations.jl - fab65622e79ec06e022d4b17b59631a649dbcdfe authored over 3 years ago by Karl Dyrhage <[email protected]>
Merge pull request #79 from jakobnissen/fixexecute

Fix execute (issue 78)

github.com/BioJulia/Automa.jl - 9f06021b77bfe3c9f4b7ada88ea754afa26f2e91 authored over 3 years ago by Jakob Nybo Nissen <[email protected]>
Fix execute (issue 78)

github.com/BioJulia/Automa.jl - f8bae2beac226113b2813ad7aeeaa72ddd64d303 authored over 3 years ago by Jakob Nybo Nissen <[email protected]>
Changed version to v0.2.4

github.com/BioJulia/GenomicAnnotations.jl - 67a2f78d3512523453ae933c0aab119a128674d9 authored over 3 years ago by Karl Dyrhage <[email protected]>
Merge pull request #153 from jakobnissen/readme

Remove financial backing and Gitter from README

github.com/BioJulia/BioSequences.jl - 08a67d75d9e2005caa32a6f300c20092d521c431 authored over 3 years ago by Jakob Nybo Nissen <[email protected]>
Updated DataFrame version

github.com/BioJulia/GenomicAnnotations.jl - 373df1d69ae02c371cdaa8d12f0076679a1d407e authored over 3 years ago by Karl Dyrhage <[email protected]>
Remove IndexableBitVector dependency (#159)

github.com/BioJulia/BioSequences.jl - d95fa67b6f4d4e3400bd4f19e4e33e6218e00f5d authored over 3 years ago by Ben J. Ward <[email protected]>
Remove Combinatorics dependency (#158)

github.com/BioJulia/BioSequences.jl - 80a1c3567d95eb09fb760368511cb9d7fd8410d3 authored over 3 years ago by Ben J. Ward <[email protected]>
Remove BioGenerics dependency (#157)

* Remove BioGenerics dependency

* Remove kmer string literals from documentation

github.com/BioJulia/BioSequences.jl - 1bc7932c58724a78f6afd3dba3e096dca431bdb6 authored over 3 years ago by Ben J. Ward <[email protected]>
Remove sprintf (#156)

github.com/BioJulia/BioSequences.jl - 287c0b7ee47449604910c25e30be126dccd589ac authored over 3 years ago by Ben J. Ward <[email protected]>
Remove kmer documentation

github.com/BioJulia/BioSequences.jl - 0f0a2921643fa8910141bbce9439edc4d40e14a8 authored over 3 years ago by Ben J. Ward <[email protected]>
Remove Kmers (#121)

* Remove Kmers

* Get all tests to pass without RNACodon or DNACodon

github.com/BioJulia/BioSequences.jl - 8cf14bcb2bcba8af1c8e6c624df3c8517e3b53e2 authored over 3 years ago by Ben J. Ward <[email protected]>
gitignore

github.com/BioJulia/GenomicAnnotations.jl - 93c9c61ad1251fcf0d664b0a35e7301647898b00 authored over 3 years ago by Karl Dyrhage <[email protected]>
bump version

github.com/BioJulia/BioStructures.jl - cf24e65799ce4f4fdc1854ee34adbd4382425937 authored over 3 years ago by Joe Greener <[email protected]>
CompatHelper: bump compat for "DataFrames" to "1.0" (#30)

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

github.com/BioJulia/BioStructures.jl - a6ce70fbeb284ae9ed454306052c989268b5084a authored over 3 years ago by github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
CompatHelper: bump compat for "DataFrames" to "1.0"

github.com/BioJulia/PopGen.jl - 39f3e6c06c8de4bd9cbf72b739fd80f4d430e1da authored over 3 years ago by github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Merge pull request #45 from jakobnissen/fixheader

Fix header code

github.com/BioJulia/FASTX.jl - e9202ba134e05070a047b916e02e77b0df1a1696 authored over 3 years ago by Jakob Nybo Nissen <[email protected]>
Fix header code

github.com/BioJulia/FASTX.jl - 7d98cbcd20f3c7421fae8d1a900eb807b4d8f0ff authored over 3 years ago by Jakob Nybo Nissen <[email protected]>
Add join and join! for BioSequence (#134)

* Allow indexing with all integers

* Move some indexing logic from LongSequence to BioSequenc...

github.com/BioJulia/BioSequences.jl - c92a5f4773a2296826f131e03dc7e3faf2c02e3d authored over 3 years ago by Jakob Nybo Nissen <[email protected]>
Update CHANGELOG.md

github.com/BioJulia/BioServices.jl - af0868519a81124a33a8172f1996378bcb2d2bc3 authored over 3 years ago by Kevin Bonham <[email protected]>
Update CHANGELOG.md

github.com/BioJulia/BioServices.jl - 42fe4ac8cb4c193d6be523a56dfb540f61a0ec03 authored over 3 years ago by Kevin Bonham <[email protected]>
WIP: Add EMBL-EBI Proteins REST API (#37)

* Implemented proteins and features calls, renamed module

* Added EBIProteins REST API

github.com/BioJulia/BioServices.jl - 21a5a45470eef4a9e495e0ef27e0f750639837f8 authored over 3 years ago by Nicholas Bauer <[email protected]>
update license links (#41)

github.com/BioJulia/BioServices.jl - c6fff96a32987cf5b13a509424b78d2f275359b2 authored over 3 years ago by Kevin Bonham <[email protected]>
close #31. docs for xmldict and lightxml (#33)

github.com/BioJulia/BioServices.jl - de95593d50a47f8beaac12fe6c4d5fff7d56df0b authored over 3 years ago by august <[email protected]>
Updated documentation links (#39)

github.com/BioJulia/BioServices.jl - a5fd297ba1f574a170601d42f2b3f0a068e48a30 authored over 3 years ago by Nicholas Bauer <[email protected]>
Modernize docs and CI (#36)

* setup github actions, remove travis, appveyor

* cleanup docs code

* bump major version -...

github.com/BioJulia/BioServices.jl - 436f095b01370e2911d53a13c6abc694ccd6fe17 authored over 3 years ago by Kevin Bonham <[email protected]>
Updated version

github.com/BioJulia/GenomicAnnotations.jl - ae0fba3e4928efbdf4dbb5c76c2105412a595fd0 authored over 3 years ago by Karl Dyrhage <[email protected]>
Updated documenter URL

github.com/BioJulia/GenomicAnnotations.jl - 1a8f9eb723dcef9387f6e326e349473c53e5e982 authored over 3 years ago by Karl Dyrhage <[email protected]>
Added GFF.Writer docstring

github.com/BioJulia/GenomicAnnotations.jl - 3c6131b240b0ed3498b85265832db263b04768b2 authored over 3 years ago by Karl Dyrhage <[email protected]>
Removed stable doc link

github.com/BioJulia/GenomicAnnotations.jl - 0a8e3a6598505abc251ad095cc3f363903e906e3 authored over 3 years ago by Karl Dyrhage <[email protected]>
Removed incorrect example

github.com/BioJulia/GenomicAnnotations.jl - 80beffe2e902f1e61f17d9f25d3e49180c359253 authored over 3 years ago by Karl Dyrhage <[email protected]>
Fixed trailing empty line bug

github.com/BioJulia/GenomicAnnotations.jl - f33b802fdc96f821fa61da9e0067c25f7eee6216 authored over 3 years ago by Karl Dyrhage <[email protected]>
src/GenBank/reader.jl

github.com/BioJulia/GenomicAnnotations.jl - 601ec819e6724471ae16fa69061e955a8442837b authored over 3 years ago by Karl Dyrhage <[email protected]>
Merge branch 'hotfix/issue-34'

github.com/BioJulia/XAM.jl - 22667dc7afe68a76cd5cdbc22c65b77c0ddf15b3 authored over 3 years ago by Ciarán O’Mara <[email protected]>
Merge branch 'master' into develop

github.com/BioJulia/XAM.jl - 5bd793bc5fe388b09008fde9f0c2dc25187d4684 authored over 3 years ago by Ciarán O’Mara <[email protected]>
Cater for blank sam files

github.com/BioJulia/XAM.jl - c423694f296075e11317f961561744bb60ec664a authored over 3 years ago by Ciarán O’Mara <[email protected]>
Adjust for Automa 0.8.1

Defines an unambiguous state machine.
https://github.com/BioJulia/Automa.jl/pull/49.

github.com/BioJulia/XAM.jl - 64f371e1e479b07d7d14621b0bd23ad040087842 authored over 3 years ago by Ciarán O’Mara <[email protected]>
move conditionals to Conditionals.jl

github.com/BioJulia/PopGen.jl - 770d213ea4aa1361882ae017b3175e38bf243709 authored over 3 years ago by Pavel Dimens <[email protected]>
bump version

github.com/BioJulia/PopGen.jl - 084b9a7232ebf0f454efbef4ad1a647181868b52 authored over 3 years ago by Pavel Dimens <[email protected]>
fix hudson_fst typo

github.com/BioJulia/PopGen.jl - a8133cd0a11b1d5273e1e8a10b0a27f79c474c62 authored over 3 years ago by Pavel Dimens <[email protected]>
clean up TODO comments

github.com/BioJulia/PopGen.jl - 186af8fc9fdae003bf9954ad50de785d00264661 authored over 3 years ago by Pavel Dimens <[email protected]>
Update Project.toml

github.com/BioJulia/PopGen.jl - 9f3bf243fa0ff22bacf929b3748e9b6cfeb93820 authored over 3 years ago by Pavel V. Dimens <[email protected]>
Update FstMethods.jl

github.com/BioJulia/PopGen.jl - ee8a1a427b891db7a7b56aa0a9d01e40ed931395 authored over 3 years ago by Pavel V. Dimens <[email protected]>
bump version to 0.6.0

github.com/BioJulia/PopGen.jl - 1338b9b56550e23e7e2da882974cd902d9525db1 authored over 3 years ago by Pavel Dimens <[email protected]>
remove deprecated map(fn, gdf) calls

github.com/BioJulia/PopGen.jl - 898956b29ac7990b6a211c95e65188dd832775b3 authored over 3 years ago by Pavel Dimens <[email protected]>
vcf io kwarg consistency

github.com/BioJulia/PopGen.jl - dd0b0701bdab80900350ad0b64d30e353a3c295d authored over 3 years ago by Pavel Dimens <[email protected]>
swap out vcf test file

github.com/BioJulia/PopGen.jl - d8dacbe95975c7ba71edde447e35fc02a9201d5a authored over 3 years ago by Pavel Dimens <[email protected]>
add Hudson pairwise FST

github.com/BioJulia/PopGen.jl - 380f6a8a97285211c67426a664f6871060d6e4c0 authored over 3 years ago by Pavel Dimens <[email protected]>
make drop_monomorphic faster

github.com/BioJulia/PopGen.jl - 724cc5bc4eadb964a5153bc833026b33e4f6dcf3 authored over 3 years ago by Pavel Dimens <[email protected]>
Merge branch 'release/v0.2.0'

github.com/BioJulia/Indexes.jl - ccba7adc69f497437bd47a8384506d7aab75a30a authored over 3 years ago by Ciarán O’Mara <[email protected]>
Merge branch 'master' into develop

github.com/BioJulia/Indexes.jl - e62f6c8c31c6a25079e8dfa71b8add53d0750b82 authored over 3 years ago by Ciarán O’Mara <[email protected]>
Increment version

github.com/BioJulia/Indexes.jl - f9347a1cafc0cdaaf559a817207816d0fbdbed7d authored over 3 years ago by Ciarán O’Mara <[email protected]>
Adjust test matrix

The Indexes package uses the Artifacts framework, which is first available in Julia v1.3.

github.com/BioJulia/Indexes.jl - a1d9eaa70d82c399cc90840643735d1ccb24425e authored over 3 years ago by Ciarán O’Mara <[email protected]>