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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

Fix typo in genetic code show

github.com/BioJulia/BioSequences.jl - 218ba72d9e7aa19ef4a6459a67b470bf5a8a0788 authored over 3 years ago by Jakob Nybo Nissen <[email protected]>
Merge pull request #50 from alyst/reinstate_master

Prepare for minor release

github.com/BioJulia/BioAlignments.jl - 492cd5884b4a8094e003a4e28f0578cb468143f7 authored over 3 years ago by Jakob Nybo Nissen <[email protected]>
refer to "master" as "cutting edge" dev branch

also switch to "master" for CI documentation builds

fixes #49

github.com/BioJulia/BioAlignments.jl - ec443b4fd2b6768092c2d7cb49dbcb18f206f127 authored over 3 years ago by Alexey Stukalov <[email protected]>
Project.toml: remove julia 0.7 from compat

github.com/BioJulia/BioAlignments.jl - 65437b08e90a9f15c9cea3ce9125f3339b8f6a6a authored over 3 years ago by Alexey Stukalov <[email protected]>
README: use GH actions for build status badge

github.com/BioJulia/BioAlignments.jl - f4b47176215c1eb56f422d92a65499e4531cf8a9 authored over 3 years ago by Alexey Stukalov <[email protected]>
update CHANGELOG

github.com/BioJulia/BioAlignments.jl - 401bf3ff6759f3544b4cd879e5250b6d57f10d0e authored over 3 years ago by Alexey Stukalov <[email protected]>
update to release candidate

github.com/BioJulia/PopGen.jl - 81397e314dc89ddd8f30c279f51cd6347758ab38 authored over 3 years ago by Pavel Dimens <[email protected]>
parallelize pairwise FST methods

github.com/BioJulia/PopGen.jl - f22ae44ee026d15ab0b250a4cdd56219de698840 authored over 3 years ago by Pavel Dimens <[email protected]>
fix and organize pairwise fst

github.com/BioJulia/PopGen.jl - 72a4cad2fb858e5b85f3ef932fd92e38758d0dae authored over 3 years ago by Pavel Dimens <[email protected]>
add skip_methods

github.com/BioJulia/PopGen.jl - 517b6504f841db36f91e7ee0204d13bef2bf7bc3 authored over 3 years ago by Pavel Dimens <[email protected]>
rm quickstart

github.com/BioJulia/PopGen.jl - 5efdcc8ebc7a676259262c99a729b5cfd77a5e21 authored over 3 years ago by Pavel Dimens <[email protected]>
fix docstrings

github.com/BioJulia/PopGen.jl - 2b418b46e2b8f4ad55d652b7d0ff3f2e449d4269 authored over 3 years ago by Pavel Dimens <[email protected]>
Merge branch 'dev' of https://github.com/pdimens/PopGen.jl into dev

github.com/BioJulia/PopGen.jl - 49ada7c71f32978f6b8065056f279ecc4ea54136 authored over 3 years ago by Pavel Dimens <[email protected]>
Fix project

github.com/BioJulia/Automa.jl - 9ab54f6bae5811eb13abcc85310d81e48f2c261d authored over 3 years ago by = <=>
Merge pull request #61 from jakobnissen/fixf

Fix escape \f

github.com/BioJulia/Automa.jl - 3d8e70706eb2b6e0ce1b2de7176c9ee130e16145 authored over 3 years ago by Jakob Nybo Nissen <[email protected]>
Move to ScanByte

github.com/BioJulia/Automa.jl - 303ebb52446c2ba68d4a3684194e57856ef6bf8b authored over 3 years ago by Jakob Nybo Nissen <[email protected]>
Merge branch 'master' into develop

github.com/BioJulia/Indexes.jl - 3e9e2f0a248bc9bef30f4cd7a1819700db6dda7f authored over 3 years ago by Ciarán O’Mara <[email protected]>
Merge branch 'release/v0.1.3'

github.com/BioJulia/Indexes.jl - a331bed09178074b275a7d852c174c90f4fe3f46 authored over 3 years ago by Ciarán O’Mara <[email protected]>
Increment version

github.com/BioJulia/Indexes.jl - a9d8b83773d90ef3b919f760274f95dbd8dcb490 authored over 3 years ago by Ciarán O’Mara <[email protected]>
Migrate from BufferedStreams to TranscodingStreams

github.com/BioJulia/Indexes.jl - fe16d8bc219c4d8f0276374c7c3c8c3eaba90f5d authored over 3 years ago by Ciarán O’Mara <[email protected]>
Polyfil for bytesavailable

github.com/BioJulia/Indexes.jl - 7283c3af5c9b1d0eead5f2c8b557b73a03b7d161 authored over 3 years ago by Ciarán O'Mara <[email protected]>
Migrate from BioCore to BioGenerics

github.com/BioJulia/Indexes.jl - 9af395f766e0e8112504dd680d702baca2f92b40 authored over 3 years ago by Ciarán O’Mara <[email protected]>
Merge branch 'master' into develop

github.com/BioJulia/Indexes.jl - f34dc07d24278d2893f299519def407b4af15a81 authored over 3 years ago by Ciarán O’Mara <[email protected]>
Merge branch 'release/v0.1.2'

github.com/BioJulia/Indexes.jl - 1d90f6cafcad0bc67878a81aaf1892f4a23dff46 authored over 3 years ago by Ciarán O’Mara <[email protected]>
Increment version

github.com/BioJulia/Indexes.jl - bdd0298ce6177b9f7518be508ffe06be6c9cb66b authored over 3 years ago by Ciarán O’Mara <[email protected]>
Use accessors

github.com/BioJulia/Indexes.jl - c35a477e7b923f117eda37e092c506ee80f0d2d0 authored over 3 years ago by Ciarán O'Mara <[email protected]>
Merge pull request #44 from alyst/agn_pos

Add alignment string position support

github.com/BioJulia/BioAlignments.jl - bc9ad529766034f227c71454bb13e7f1354f2e5f authored over 3 years ago by Jakob Nybo Nissen <[email protected]>
Merge pull request #48 from alyst/fix_registry

Remove BioJuliaRegistry

github.com/BioJulia/BioAlignments.jl - 118c5ad3b614228ac2b67b418b7fb46ca07bbcd8 authored over 3 years ago by Jakob Nybo Nissen <[email protected]>
count_aligned(): optimize with alnpos

github.com/BioJulia/BioAlignments.jl - cc8237c48ad109036ed0f0da121f780447b7a6fa authored over 3 years ago by Alexey Stukalov <[email protected]>
alignment position support (seq2aln, ref2aln etc)

- add alnpos to each anchor
- add mapping to/from alnpos
- add alnpos support to traceback

github.com/BioJulia/BioAlignments.jl - 0156de451254f9547af2b8b3f3d6a321bd3d4132 authored over 3 years ago by Alexey Stukalov <[email protected]>
refactor seq2ref/ref2seq()

- add position getters for AlignmentAnchor
- convert findanchor() from generated function to nor...

github.com/BioJulia/BioAlignments.jl - eceb92d9b0346c53cd1d9015b0aed10bd24e43d9 authored over 3 years ago by Alexey Stukalov <[email protected]>
Alignment: expand docstring

github.com/BioJulia/BioAlignments.jl - 90513fbf4d229b4cf32f94297e703c5cb707b407 authored over 3 years ago by Alexey Stukalov <[email protected]>
count(pairwisealn): add @inbounds

github.com/BioJulia/BioAlignments.jl - d920daa9d4b210d5eead01a15d7821b8d847dc4c authored over 3 years ago by Alexey Stukalov <[email protected]>
check_aln_anchors(): optimize anchors access

github.com/BioJulia/BioAlignments.jl - ecc954332ae2e9ffe3d5cb4f46aa236bfbaa6cb2 authored over 3 years ago by Alexey Stukalov <[email protected]>
AlnAnchor: drop Tuple-based ctor (use splatting)

github.com/BioJulia/BioAlignments.jl - 8b0d70e055daf7bccc57b2df7dd14eaba1e7da0e authored over 3 years ago by Alexey Stukalov <[email protected]>
print(op): don't throw Exception, print ? instead

otherwise Anchors with invalid operation (and these anchors are
created temporarily during trace...

github.com/BioJulia/BioAlignments.jl - be5b72b64e80a1d8759dd4101d61a23c5c6e6e7d authored over 3 years ago by Alexey Stukalov <[email protected]>
TagBot.yml: don't use BioJuliaRegistry

also it seems TagBot key is not required

github.com/BioJulia/BioAlignments.jl - de41d911ddda6a64d6bc8fdcbecb8ed84458216b authored over 3 years ago by Alexey Stukalov <[email protected]>
CompatHelper: use Julia "1" and x64 arch

github.com/BioJulia/BioAlignments.jl - d830a532c9c1060384930ff097558d01510ca710 authored over 3 years ago by Alexey Stukalov <[email protected]>
TagBot.yml: correct when the action is being run

github.com/BioJulia/BioAlignments.jl - 09075ef5db5f0398a25c173f9d6d6b64b04e74b9 authored over 3 years ago by Alexey Stukalov <[email protected]>
README/index.md: remove BioJuliaRegistry mentions

github.com/BioJulia/BioAlignments.jl - 502858c46394a155f4c3ea865ec3a7bff5337027 authored over 3 years ago by Alexey Stukalov <[email protected]>
README/index.md: minor formatting corrections

github.com/BioJulia/BioAlignments.jl - 5b60898aa74f2d98bf2657e575e34ad3754f0682 authored over 3 years ago by Alexey Stukalov <[email protected]>
Merge pull request #47 from alyst/new_ci

New CI based on GH-actions

github.com/BioJulia/BioAlignments.jl - 3e3910c6a750da27f9cdcc74a9fa28b34bae4e8d authored over 3 years ago by Jakob Nybo Nissen <[email protected]>
ci: add windows-x64

github.com/BioJulia/BioAlignments.jl - f3dd0390f4fa8f1e6ab0e0f5f77d1f45c7f81e57 authored over 3 years ago by Alexey Stukalov <[email protected]>
runtests.jl: fix sequence type for julia nightly

github.com/BioJulia/BioAlignments.jl - cc6dc4952d56c4ee194d0fc6fce0bfd00f37a1c8 authored over 3 years ago by Alexey Stukalov <[email protected]>
remove older CI scripts

github.com/BioJulia/BioAlignments.jl - c2678bb6718365c0c9131eebd6a80f5061096358 authored over 3 years ago by Alexey Stukalov <[email protected]>
new CI based on GH-actions

* coverage script was removed since it should be handled by
julia-actions/julia-processcoverage@...

github.com/BioJulia/BioAlignments.jl - 56438d6223a0df60342ce1df0e97a57cd0dad1b9 authored over 3 years ago by Alexey Stukalov <[email protected]>
Fix escape \f

github.com/BioJulia/Automa.jl - a2904edfca2c8a2e844fcf0b9bdc7fbbfe47af83 authored over 3 years ago by Jakob Nybo Nissen <[email protected]>
Merge pull request #41 from jakobnissen/qualityiter

Add quality and sequence iterator

github.com/BioJulia/FASTX.jl - e72dcfe3053533a022db3adb4c3cb5fcc23c3dbd authored over 3 years ago by Jakob Nybo Nissen <[email protected]>
Merge branch 'release' into dev

github.com/BioJulia/PopGen.jl - 7ce0f81363322809cb990d15df6e421b0523b4e4 authored over 3 years ago by Pavel V. Dimens <[email protected]>
bump version number

github.com/BioJulia/PopGen.jl - 10572ca8ed87a83b7b1a09957013e37fcdd49864 authored over 3 years ago by Pavel Dimens <[email protected]>
Add parsing

github.com/BioJulia/SequenceVariation.jl - 642658f5920139fe4cb5e0bba6d16069c24793b3 authored over 3 years ago by Jakob Nybo Nissen <[email protected]>
Merge pull request #39 from jakobnissen/master

Change small lookup tables to Tuple

github.com/BioJulia/BioSymbols.jl - 5ab12d7e2a1c01eed6d02690a7f2ecdc131a7135 authored over 3 years ago by Jakob Nybo Nissen <[email protected]>
Merge pull request #40 from jakobnissen/fixinfer

Improve inferrability

github.com/BioJulia/BioSymbols.jl - 1092429f2381483274cd823adcd7eafb86907083 authored over 3 years ago by Jakob Nybo Nissen <[email protected]>
Improve inferrability

github.com/BioJulia/BioSymbols.jl - 18c5881d3f07b07b7a028abe48b05062368e3425 authored over 3 years ago by Jakob Nybo Nissen <[email protected]>
rename weircockerham

github.com/BioJulia/PopGen.jl - f12ae4182a05e61c74cdf6d689c258b0cf21f8c8 authored over 3 years ago by Pavel Dimens <[email protected]>
Merge 'dev' https://github.com/pdimens/PopGen.jl

github.com/BioJulia/PopGen.jl - df40119445ed3e2290372f00416f911cb868f3f3 authored over 3 years ago by Pavel Dimens <[email protected]>
update fstats

github.com/BioJulia/PopGen.jl - a572dcb7c7eb279db15345e30a01b1a74c08fd49 authored over 3 years ago by Pavel Dimens <[email protected]>
Switch to SumTypes

github.com/BioJulia/SequenceVariation.jl - 354f18e0e49abe9a45378ef47c8e5fce8781bd13 authored over 3 years ago by Jakob Nybo Nissen <[email protected]>
Start fixing

github.com/BioJulia/SequenceVariation.jl - 40749eb6f5eec175f11025eb756666a8694d8f0c authored over 3 years ago by Jakob Nybo Nissen <[email protected]>
update docstrings

github.com/BioJulia/PopGen.jl - 9d5d88a6c0933bb4a43200611bd81b004dd263ec authored over 3 years ago by Pavel Dimens <[email protected]>
more accurate testset

github.com/BioJulia/PopGen.jl - 0d0c0e4bd3ab9597352fe47b4db37a7dd0c14ea6 authored over 3 years ago by Pavel Dimens <[email protected]>
update io.jl tests for breaking gulfsharks

github.com/BioJulia/PopGen.jl - 0cbbeb84a843b040e67b1016d0af3c8c19f6b6f4 authored over 3 years ago by Pavel Dimens <[email protected]>
update manipulate tests for breaking populations

github.com/BioJulia/PopGen.jl - 47ba68000879c2b421e41ac4f809935f4e73a7e0 authored over 3 years ago by Pavel Dimens <[email protected]>
update and break populations behavior

github.com/BioJulia/PopGen.jl - cbbc769826c9c67cc79b866d27d15562ce431f5e authored over 3 years ago by Pavel Dimens <[email protected]>
update tests

github.com/BioJulia/PopGen.jl - 31dd07cdcf2ebb72d05790323b9d02b3eff1619a authored over 3 years ago by Pavel Dimens <[email protected]>
fix io

github.com/BioJulia/PopGen.jl - a03874c1ff6cb14754e2e0ce3f90dce6b6113cc0 authored over 3 years ago by Pavel Dimens <[email protected]>
fix docstring and module `using` calls

github.com/BioJulia/PopGen.jl - 1a4f67fff475b432d4974a357b1621b6b436f075 authored over 3 years ago by Pavel Dimens <[email protected]>
repair all IO and drop JLD2 support

github.com/BioJulia/PopGen.jl - a3cc93dac688cbb97492dd3e32021f8cb21bdc45 authored over 3 years ago by Pavel Dimens <[email protected]>
fix critical return error

github.com/BioJulia/PopGen.jl - 277f79021c4bc1274bbaaf1570c64f2af164c044 authored over 3 years ago by Pavel Dimens <[email protected]>
add missing Test dep

github.com/BioJulia/PopGen.jl - de81166430cc9f3221e044c084cf8d58aa07d309 authored over 3 years ago by Pavel Dimens <[email protected]>
update test deps

github.com/BioJulia/PopGen.jl - f5271f2b5575d9dde87fab3d1ffe4fa6481f4dd3 authored over 3 years ago by Pavel Dimens <[email protected]>
more housekeeping

github.com/BioJulia/PopGen.jl - 8e2b3f65bfafdcc17f54ba6d6ac0efefb22ed7b0 authored over 3 years ago by Pavel Dimens <[email protected]>
error message housekeeping

github.com/BioJulia/PopGen.jl - 45ee0828dec6aed8156f709665d38b443b84d23e authored over 3 years ago by Pavel Dimens <[email protected]>
add keep and keep!

github.com/BioJulia/PopGen.jl - bfef06aca26b173bbdfa3c4da77bb82f291f66f8 authored over 3 years ago by Pavel Dimens <[email protected]>
constrain dict

github.com/BioJulia/PopGen.jl - 838da9ba40817e17f09b86abb1703da6ca1f99f8 authored over 3 years ago by Pavel Dimens <[email protected]>
add missing and updated pools

github.com/BioJulia/PopGen.jl - 04f8c5f77b1c598e92848c39d4aeee97e65d4dc8 authored over 3 years ago by Pavel Dimens <[email protected]>
replace exclude function for parsimonious version

github.com/BioJulia/PopGen.jl - 73d60a8b8f2c2537551ac284060f7f9d954793a5 authored over 3 years ago by Pavel Dimens <[email protected]>
Add sequence iterator

github.com/BioJulia/FASTX.jl - 6b0f588dfdcd760627574074ae38b22966c1a0b4 authored over 3 years ago by Jakob Nybo Nissen <[email protected]>
Add quality iterator

github.com/BioJulia/FASTX.jl - 0754245539ce65850bc35d26b32fcd208c6a11e1 authored over 3 years ago by Jakob Nybo Nissen <[email protected]>
Fix dispatch

github.com/BioJulia/BioSequences.jl - 6b693c81eea96130d7a74014df727909bf65cf9c authored over 3 years ago by Jakob Nybo Nissen <[email protected]>
Merge branch 'dev' of https://github.com/pdimens/PopGen.jl into dev

github.com/BioJulia/PopGen.jl - c76c03f1ef5a0e6404c323823eaa41320d731b66 authored over 3 years ago by Pavel Dimens <[email protected]>
remove quickstart and rely on ?PopGen

github.com/BioJulia/PopGen.jl - 67e3cb4946336735af2a145c2dc6218f2de68c76 authored over 3 years ago by Pavel Dimens <[email protected]>
unrestrict types

github.com/BioJulia/PopGen.jl - 5801313796ed7fe528cb3654c934703c15f00fd5 authored over 3 years ago by Pavel Dimens <[email protected]>
Update pull_request_template.md

github.com/BioJulia/PopGen.jl - 3431f5986c71075d752f3d67fc10ee3ae75e1b97 authored over 3 years ago by Pavel V. Dimens <[email protected]>
Create pull_request_template.md

github.com/BioJulia/PopGen.jl - 2b5aa59c84343dd891df617e713c90943e246876 authored over 3 years ago by Pavel V. Dimens <[email protected]>
Update issue templates

github.com/BioJulia/PopGen.jl - 540e9758d0491912c386c50946e8a6b4bcdc45e5 authored over 3 years ago by Pavel V. Dimens <[email protected]>
Update issue templates

github.com/BioJulia/PopGen.jl - d78d685308ffc9240c56ac7c61a0f3e5ce5c9167 authored over 3 years ago by Pavel V. Dimens <[email protected]>
Move some indexing logic from LongSequence to BioSequence

github.com/BioJulia/BioSequences.jl - 09aef8fb72af0c427bd51399dad9704bd1829570 authored over 3 years ago by Jakob Nybo Nissen <[email protected]>
Allow indexing with all integers

github.com/BioJulia/BioSequences.jl - aeebe9a6b547e2b1ac3e98479b8a26f23821fd41 authored over 3 years ago by Jakob Nybo Nissen <[email protected]>
Merge pull request #120 from jakobnissen/seqview

Add sequence view

github.com/BioJulia/BioSequences.jl - 252720879620716f5f33a54e53ffcd9716706636 authored over 3 years ago by Jakob Nybo Nissen <[email protected]>
Fix tests for subseq

github.com/BioJulia/BioSequences.jl - 09d7e92cb9100df61b819a8e098439bbac7cae91 authored over 3 years ago by Jakob Nybo Nissen <[email protected]>
Merge pull request #132 from jakobnissen/deprminhash

Deprecate minhash

github.com/BioJulia/BioSequences.jl - ff6b93bd2e106f892c5f7c20627c3c5cb9e163a6 authored over 3 years ago by Jakob Nybo Nissen <[email protected]>
Merge pull request #131 from jakobnissen/optimtranslate

Refactor translation

github.com/BioJulia/BioSequences.jl - e1743d7836cd44c4df1c61f0bf20fda3e5a4d581 authored over 3 years ago by Jakob Nybo Nissen <[email protected]>
Deprecate minhash

github.com/BioJulia/BioSequences.jl - a85f6481cf64c64d6027d479db277fec4baac60a authored over 3 years ago by Jakob Nybo Nissen <[email protected]>
Optimize translation

github.com/BioJulia/BioSequences.jl - 0b2128db6b3664f51a58aeed0bace072b2dc2c99 authored over 3 years ago by Jakob Nybo Nissen <[email protected]>
wrap up weir-cockerham fst

github.com/BioJulia/PopGen.jl - ca525146c4e5496f2b6696ad15d614aa89b0989d authored over 3 years ago by Pavel Dimens <[email protected]>
finish calculation (still needs haploid vers)

github.com/BioJulia/PopGen.jl - 7a4e20bf422d64c980ccbba36a16f107d8a9456d authored over 3 years ago by Pavel Dimens <[email protected]>
better solution

github.com/BioJulia/PopGen.jl - 82d77eacb788879e410e41f9fee615d5ccb76b09 authored over 3 years ago by Pavel Dimens <[email protected]>
Merge branch 'master' into seqview

github.com/BioJulia/BioSequences.jl - c5b475b1d18dc0f1f0e725351d4e8415081e0423 authored over 3 years ago by Jakob Nybo Nissen <[email protected]>
constrain <:Signed to <:Integer

github.com/BioJulia/PopGen.jl - 741795615c2ff1e455f2de6d637a736e484de160 authored over 3 years ago by Pavel Dimens <[email protected]>