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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

Tidy method signature types

github.com/BioJulia/GenomicFeatures.jl - 6870d9f6c8e5a266115a81c6165300f276d17a14 authored almost 3 years ago by Ciarán O'Mara <[email protected]>
Workflow maintenance

github.com/BioJulia/GenomicFeatures.jl - 2d731eac84bdb7bfb2876858f7d13757a12922a6 authored almost 3 years ago by Ciarán O'Mara <[email protected]>
Rename `OverlapIterator` types

github.com/BioJulia/GenomicFeatures.jl - 343e8b72f77172be3cc911294b4d34eb344fadbe authored almost 3 years ago by Ciarán O'Mara <[email protected]>
Add workflow for downstream tests

github.com/BioJulia/GenomicFeatures.jl - cd0052aa08c6a02205a7a8e21494214215b4783a authored almost 3 years ago by Ciarán O'Mara <[email protected]>
Tweak IntervalCollection equivalency method

github.com/BioJulia/GenomicFeatures.jl - e0e933d7be303bda55a00b352d6f6706ca4fdd14 authored almost 3 years ago by Ciarán O’Mara <[email protected]>
Use accessor functions when handling intervals

github.com/BioJulia/GenomicFeatures.jl - ce5d26ec038adff79c4f1f65bd908c3750407399 authored almost 3 years ago by Ciarán O'Mara <[email protected]>
Update chat links

github.com/BioJulia/GenomicFeatures.jl - f8895bbe5894eaa411744a2efa5d4a8f543063ba authored almost 3 years ago by Ciarán O'Mara <[email protected]>
Tweak push! method

Use get! method with default.

github.com/BioJulia/GenomicFeatures.jl - 86c12e93101f3cfe8b54c98266a26200c3b79170 authored almost 3 years ago by Ciarán O’Mara <[email protected]>
Use argument types

github.com/BioJulia/GenomicFeatures.jl - 44b4f9fbcbfb7e42b34881ebae666d9bf0a3be0d authored almost 3 years ago by Ciarán O'Mara <[email protected]>
CompatHelper: add new compat entry for PyCall at version 1, (keep existing compat)

github.com/BioJulia/BioMakie.jl - 59302f1faa29ec04ee908bd33c2977e480e7d012 authored almost 3 years ago by CompatHelper Julia <[email protected]>
CompatHelper: add new compat entry for Conda at version 1, (keep existing compat)

github.com/BioJulia/BioMakie.jl - 5cb90b7d9346672e5a53557e0293c39f4574209b authored almost 3 years ago by CompatHelper Julia <[email protected]>
Update README.md

github.com/BioJulia/BioMakie.jl - 3a31ab9dc54c716f3adaab07ca691005891a8b95 authored almost 3 years ago by Dan Kool <[email protected]>
Add files via upload

github.com/BioJulia/BioMakie.jl - 62ee1c4a1753615b9bd0a01fe880768da414b9b7 authored almost 3 years ago by Dan Kool <[email protected]>
Add files via upload

github.com/BioJulia/BioMakie.jl - df5a447d10d3966d04b6ad2dbf421e8bbfca4d9d authored almost 3 years ago by Dan Kool <[email protected]>
Update README.md

github.com/BioJulia/BioMakie.jl - 2f27214860577e9b4e0ddd0f8c873e9e4400e1b8 authored almost 3 years ago by Dan Kool <[email protected]>
Merge pull request #386 from kool7d/dev

Dev

github.com/BioJulia/BioMakie.jl - 65a1cb53e2d972ef841f4c40aa1e22fda04ce83a authored almost 3 years ago by Dan Kool <[email protected]>
fixsome1

github.com/BioJulia/BioMakie.jl - 75a860fddbdd76166d8684577dc8cd4ac1e7b2d7 authored almost 3 years ago by kool7d <[email protected]>
Fixed reorder bug

github.com/BioJulia/GenomicAnnotations.jl - 5a0c14a2ca2b9c021da2c14a7ba72612a5f8e69a authored almost 3 years ago by Karl Dyrhage <[email protected]>
CompatHelper: bump compat for Underscores to 3, (keep existing compat)

github.com/BioJulia/BioMakie.jl - 83520d1864d36295a63071336db6011614b2f22e authored almost 3 years ago by CompatHelper Julia <[email protected]>
add WAT to water residue names

github.com/BioJulia/BioStructures.jl - 3d54777ca04651b9a896d2a1decd78be57fbf64c authored almost 3 years ago by Joe Greener <[email protected]>
make convertcoord more flexible

github.com/BioJulia/PopGenCore.jl - 0fe9ad6d2b9df65b3a6df271a07c02096981b860 authored almost 3 years ago by Pavel Dimens <[email protected]>
Update Project.toml

github.com/BioJulia/PopGen.jl - ff3bce46fcc6ce44661eca02d15120c015a8f2c7 authored almost 3 years ago by Pavel V. Dimens <[email protected]>
Add workflow for downstream tests (#49)

github.com/BioJulia/BioSymbols.jl - 9228385bf9ed51fbcf2611315d8ed49daf1f71b1 authored almost 3 years ago by Ciarán O'Mara <[email protected]>
Merge branch 'master-bak'

github.com/BioJulia/BioSequences.jl - 6a91d5f308ad085d12623a9f296b6c04a96ac475 authored almost 3 years ago by Ben J. Ward <[email protected]>
Add workflow for downstream tests (#192)

github.com/BioJulia/BioSequences.jl - 6d65c17a45d2347a05c06e19867710987e78e88e authored almost 3 years ago by Ciarán O'Mara <[email protected]>
Test bonanza for v3 (#203)

Add more tests and fix various small bugs

github.com/BioJulia/BioSequences.jl - cd6caac61b0651fc5a7800d5743b49b4d36c83cd authored almost 3 years ago by Jakob Nybo Nissen <[email protected]>
Add `has_interface` function (#202)

Add `BioSequences.has_interface` function

github.com/BioJulia/BioSequences.jl - 832fb7c28f0f25cf385ee4ec2acb4eb18af484c3 authored almost 3 years ago by Jakob Nybo Nissen <[email protected]>
Rename stringbyte and avoid pirating BioSymbols (#200)

* Rename the un-released method `stringbyte(::Alphabet, ::UInt8)` to `ascii_encode`
* Remove th...

github.com/BioJulia/BioSequences.jl - fdad21d49ac11fa1460ab986bb23c88ade4b87d3 authored almost 3 years ago by Jakob Nybo Nissen <[email protected]>
Add stringbyte function (#48)

Add stringbyte function

github.com/BioJulia/BioSymbols.jl - c8e893b3577763a0e65cf0807ca4fc3f0c2e85f2 authored almost 3 years ago by Jakob Nybo Nissen <[email protected]>
Remove sequence conversion to/from String and Vector (#196)

* Remove sequence conversion to/from String and Vector

github.com/BioJulia/BioSequences.jl - 11bedfed009de4a12420f90b81e363ad85300284 authored almost 3 years ago by Jakob Nybo Nissen <[email protected]>
fix calls to _ishet

github.com/BioJulia/PopGen.jl - b8dfe9e7366f73ed797dc794b36cc5fbd0471a2c authored almost 3 years ago by Pavel Dimens <[email protected]>
Merge branch 'dev' of https://github.com/BioJulia/PopGenCore.jl into dev

github.com/BioJulia/PopGenCore.jl - 151f98ed86212afbeb0d7241c4ad5bda05220267 authored almost 3 years ago by Pavel Dimens <[email protected]>
add all the _ishXX methods

github.com/BioJulia/PopGenCore.jl - 910be1924dec403dc0510327d80458177645f290 authored almost 3 years ago by Pavel Dimens <[email protected]>
Update PopDataWrappers.jl

github.com/BioJulia/PopGenCore.jl - edda414c08ed6751bbed12151bb40e6681366bcb authored almost 3 years ago by Pavel V. Dimens <[email protected]>
Update Iterators.jl

github.com/BioJulia/PopGenCore.jl - ef7edfe9082ab17a258fb957db398872493683ce authored almost 3 years ago by Pavel V. Dimens <[email protected]>
export _isXXX

github.com/BioJulia/PopGenCore.jl - 12060cdcff5615800f4a9f7ff1f79ca9b7f603c7 authored almost 3 years ago by Pavel Dimens <[email protected]>
update ishet to _ishet

github.com/BioJulia/PopGen.jl - 09e9b793b6be5e8a148d18fcd68d0e6eecc25cae authored almost 3 years ago by Pavel Dimens <[email protected]>
update phrasing

github.com/BioJulia/PopGenCore.jl - f0059901dadbed3a3a1cd4d4c274998f3a5b6970 authored almost 3 years ago by Pavel Dimens <[email protected]>
Simplified Locus API

github.com/BioJulia/GenomicAnnotations.jl - 198d5d1f78399cc7a30f5a671a15322e2bf6c182 authored almost 3 years ago by Karl Dyrhage <[email protected]>
Added reorder

github.com/BioJulia/GenomicAnnotations.jl - 6bb75b6acc47c05cb1c68441a4a456f2fd165600 authored almost 3 years ago by Karl Dyrhage <[email protected]>
wording upates

github.com/BioJulia/PopGenCore.jl - 54ca9f7215baf12e7a644cb52126ec77b136758c authored almost 3 years ago by Pavel Dimens <[email protected]>
export sampleinfo! and locusinfo!

github.com/BioJulia/PopGenCore.jl - a44df0d01c919f26d4230e4bae2e2eec31c24fd2 authored almost 3 years ago by Pavel Dimens <[email protected]>
revert all lattitude to latitude

github.com/BioJulia/PopGenCore.jl - 3125ac932d6636fc870b3ad639eb098a3d8850d5 authored almost 3 years ago by Pavel Dimens <[email protected]>
convert all latitude to lattitude

github.com/BioJulia/PopGenCore.jl - 778f6604d5c0659805ff91d474c3e2c82484fb2f authored almost 3 years ago by Pavel Dimens <[email protected]>
overlooked issues

github.com/BioJulia/PopGenCore.jl - 0c456cad2a0132612e72c91a1b99d4f689f98793 authored almost 3 years ago by Pavel Dimens <[email protected]>
fix new locationdata! and genotype tests

github.com/BioJulia/PopGenCore.jl - 4e278e5314cc91f8e291f367e9c31b459419887d authored almost 3 years ago by Pavel Dimens <[email protected]>
rename locations => locationdata

github.com/BioJulia/PopGenCore.jl - 0ce33b0a64404c720d64b74a9962dcbf5616414e authored almost 3 years ago by Pavel Dimens <[email protected]>
address some methods

github.com/BioJulia/PopGenCore.jl - 26d48c8f590a7eb2d25ce665425239f0be27b7af authored almost 3 years ago by Pavel Dimens <[email protected]>
CompatHelper: bump compat for Pluto to 0.17, (keep existing compat)

github.com/BioJulia/BioMakie.jl - 5dfac5b7ca396e09dee707ca2a47d48566c3e5b2 authored almost 3 years ago by CompatHelper Julia <[email protected]>
rm nightly from tests

github.com/BioJulia/PopGen.jl - fa4157d4ca4b0f9ae5462f24f124b02a518efdf2 authored almost 3 years ago by Pavel Dimens <[email protected]>
rm nightly from tests

github.com/BioJulia/PopGenCore.jl - 718ebb8c2430f6bee441af9ee6796df80c44e1bc authored almost 3 years ago by Pavel Dimens <[email protected]>
update dep calls

github.com/BioJulia/PopGen.jl - 9743066abdf516faa0299a6a6682feb39ff747c7 authored almost 3 years ago by Pavel Dimens <[email protected]>
Merge branch 'dev' of https://github.com/BioJulia/PopGenCore.jl into dev

github.com/BioJulia/PopGenCore.jl - 1cbbef82568fef49733bc3a2decb7d5bcecb3c8e authored almost 3 years ago by Pavel Dimens <[email protected]>
unique hwe testmodule name

github.com/BioJulia/PopGen.jl - e1e55fe65d2b171906d07dff15f3c8c9fab36899 authored almost 3 years ago by Pavel Dimens <[email protected]>
update some tests with new syntax

github.com/BioJulia/PopGen.jl - 968c2b780e32232ebc18dc8c5353d4d1511c022d authored almost 3 years ago by Pavel Dimens <[email protected]>
rm empty test

github.com/BioJulia/PopGenCore.jl - 4f35b3856654e2b9c6ba79e7fc44b989d9a456f7 authored almost 3 years ago by Pavel Dimens <[email protected]>
update core compat

github.com/BioJulia/PopGen.jl - 28a185a976d730462c44028bb9a49725d375be4d authored almost 3 years ago by Pavel Dimens <[email protected]>
Update Project.toml

github.com/BioJulia/PopGenCore.jl - 3befa49ade84cec3033cb5e426bf4d7f734261bb authored almost 3 years ago by Pavel V. Dimens <[email protected]>
Clarify comparison to sequences in docs (#201)

github.com/BioJulia/BioSequences.jl - 4da3a8a2d3bb248c6e681d9f9e0755364adafa0b authored almost 3 years ago by Jakob Nybo Nissen <[email protected]>
downstream updates

github.com/BioJulia/PopGen.jl - c8fe85ab9c116988228b7277d522f6895287fa1d authored almost 3 years ago by Pavel Dimens <[email protected]>
Merge branch 'dev' of https://github.com/BioJulia/PopGen.jl into dev

github.com/BioJulia/PopGen.jl - 78ae0c26a8fbfa5f8b0b6425cf62417f7e8f893b authored almost 3 years ago by Pavel Dimens <[email protected]>
update downstream underscore removal

github.com/BioJulia/PopGen.jl - 86e8716912a6d1166ee5be81fd18166b14509bae authored almost 3 years ago by Pavel Dimens <[email protected]>
more standardization

github.com/BioJulia/PopGenCore.jl - aaa479738a95f55d20637648e6f4f9972b0b4128 authored almost 3 years ago by Pavel Dimens <[email protected]>
fix tests

github.com/BioJulia/PopGenCore.jl - d004a61deafaf50625cdd7a164fd6b0da5a187da authored almost 3 years ago by Pavel Dimens <[email protected]>
update a lot of changes

github.com/BioJulia/PopGenCore.jl - 1172879fea227011b8460edb2720ccb9b89edeb4 authored almost 3 years ago by Pavel Dimens <[email protected]>
remove all mid-function underscores

github.com/BioJulia/PopGenCore.jl - 578f688c39e2902d925d4342336a26fd1a00f2b0 authored almost 3 years ago by Pavel Dimens <[email protected]>
add wrappers

github.com/BioJulia/PopGenCore.jl - 84435382831ee30e688d9d8ec8879b243df72415 authored almost 3 years ago by Pavel Dimens <[email protected]>
Allow chain id to be assigned with chainid!() (#35)

* Allow chain id to be assigned with chainid!()

Adds two function for assigning the chainid, ...

github.com/BioJulia/BioStructures.jl - 74a643a9014d55e8a878ebc9844efd1998185bf5 authored almost 3 years ago by Nate Guerin <[email protected]>
Create Project.toml

github.com/BioJulia/PopGen.jl - 134a3cdb85f7c6c365a134aaf3f4b8c2b6a1cdd4 authored about 3 years ago by Pavel V. Dimens <[email protected]>
typo

github.com/BioJulia/PopGen.jl - fbb9d53eb02c6745ed1ed582734cb6073dc8b672 authored about 3 years ago by Pavel Dimens <[email protected]>
standardize naming conventions with underscore

github.com/BioJulia/PopGen.jl - 266207f7479e6ff0ca5836059f10b0a11046a43f authored about 3 years ago by Pavel Dimens <[email protected]>
add vscode stuff to gitignore

github.com/BioJulia/PopGen.jl - 6ba942ae9c8e8724c04df28655b49d7d205086b6 authored about 3 years ago by Pavel Dimens <[email protected]>
remove unneeded tomls from test

github.com/BioJulia/PopGen.jl - a022c13e4dc38068b1502b077d1da42c4f27be2d authored about 3 years ago by Pavel Dimens <[email protected]>
move data to Core

github.com/BioJulia/PopGen.jl - 8f81af9ff58e48649283cb1ee639d39edb1b1bc1 authored about 3 years ago by Pavel Dimens <[email protected]>
Remove mention of Gitter on README.md

github.com/BioJulia/FASTX.jl - eb0bda0c80969800ccced725c919a99ed247e58b authored about 3 years ago by Jakob Nybo Nissen <[email protected]>
Remove mention of Gitter from README.md

github.com/BioJulia/XAM.jl - 30d61bd79c4254138b21bf19299e8a664291de12 authored about 3 years ago by Jakob Nybo Nissen <[email protected]>
Add parsing of BioSequence, simplify some printing (#194)

github.com/BioJulia/BioSequences.jl - 00491c0e337046e4cb294302e338f459379a9fc6 authored about 3 years ago by Jakob Nybo Nissen <[email protected]>
Improve docstrings (#193)

github.com/BioJulia/BioSequences.jl - 34c49253cec2c9aecdcece8a08692c796cace452 authored about 3 years ago by Jakob Nybo Nissen <[email protected]>
Fix REPL blocks in docs (#197)

* Fix REPL blocks in docs
* Fix ambiguities in doctests

github.com/BioJulia/BioSequences.jl - 6846a04eda7b44ce09d45df18df0dcb7933def21 authored about 3 years ago by Jakob Nybo Nissen <[email protected]>
Improve documentation of flag function

github.com/BioJulia/XAM.jl - a72fcf47cbfef82ee296ca28dff95e2a8ef7ad2b authored about 3 years ago by Jakob Nybo Nissen <[email protected]>
Merge branch 'exports'

github.com/BioJulia/FASTX.jl - 38878439351f08ec63a0c4057d39688b426fe7fd authored about 3 years ago by Jakob Nybo Nissen <[email protected]>
Export all user-facing functions

github.com/BioJulia/FASTX.jl - fba10715a74c184071074a136a7071d7e92de682 authored about 3 years ago by Jakob Nybo Nissen <[email protected]>
??

github.com/BioJulia/BioMakie.jl - f4df27c77b2304aa2819942dedb1c9a85f2662c3 authored about 3 years ago by kool7d <[email protected]>
Merge pull request #47 from jamiecm17/docstring_JM

Add docstring to describe functionality

github.com/BioJulia/BioSymbols.jl - f07b9d70ba24bfdfa55087075c38c88372c41ff8 authored about 3 years ago by Kevin Bonham <[email protected]>
Functions in unordered list

github.com/BioJulia/BioSymbols.jl - 94aecb27fbdd267e7e9ddeafafe74b93cc38c1a0 authored about 3 years ago by jamiecm17 <[email protected]>
Shortened BioSymbols docstring

github.com/BioJulia/BioSymbols.jl - 60d47c7c97d729c76ecd011e9b6cf80c834e8b3b authored about 3 years ago by jamiecm17 <[email protected]>
Add docstring to describe functionality

github.com/BioJulia/BioSymbols.jl - faf14092a6853d5431916fbb8dbc998e447d15e7 authored about 3 years ago by jamiecm17 <[email protected]>
Update downstream.yml

github.com/BioJulia/PopGenCore.jl - ff7df19dfb367d3f2a9ea65e9d9fa9868a70d2cd authored about 3 years ago by Pavel V. Dimens <[email protected]>
Create downstream.yml

github.com/BioJulia/PopGenCore.jl - e8563162af50c6e5ad89a5aec303a6958239b17d authored about 3 years ago by Pavel V. Dimens <[email protected]>
CompatHelper: bump compat for GraphMakie to 0.3, (keep existing compat)

github.com/BioJulia/BioMakie.jl - 2833db0a885ae5e1f0ee3cfab095bbd521a427dc authored about 3 years ago by CompatHelper Julia <[email protected]>
Improve docstrings and changelog slightly (#191)

github.com/BioJulia/BioSequences.jl - 04a016cb6b7232d678281563237e1de0106f698b authored about 3 years ago by Jakob Nybo Nissen <[email protected]>
add extra fields to popdatainfo show

github.com/BioJulia/PopGenCore.jl - fee32d78ead6778084cc3e65d7180bbf60f6f794 authored about 3 years ago by Pavel Dimens <[email protected]>
change popdatainfo show method

github.com/BioJulia/PopGenCore.jl - 1b2a9531c46497b624d263cf03db8006688b4377 authored about 3 years ago by Pavel Dimens <[email protected]>
undo last commit

github.com/BioJulia/PopGenCore.jl - 6d2858fccfee1d7375c64dc68b5ee9e1b3b32fcd authored about 3 years ago by Pavel Dimens <[email protected]>
Update Manipulate.jl

github.com/BioJulia/PopGenCore.jl - 60a5f2c8e948df1cd0b4948ca694fe5e152b1c98 authored about 3 years ago by Pavel V. Dimens <[email protected]>
add Random

github.com/BioJulia/PopGen.jl - 931efe2022a1d979455afc289324d3b2abddc038 authored about 3 years ago by Pavel Dimens <[email protected]>
restore Random: shuffle

github.com/BioJulia/PopGen.jl - 1c4179d2db42108e6e6dfdd24d52ce3e3418d311 authored about 3 years ago by Pavel Dimens <[email protected]>
more overlooked typos

github.com/BioJulia/PopGen.jl - a0d9249fae39fcb48084b6349cbb49010d693cb3 authored about 3 years ago by Pavel Dimens <[email protected]>
update fst internals with _

github.com/BioJulia/PopGen.jl - ac1bf2ab19cfd86ad5ffb422d38273ffcaab0deb authored about 3 years ago by Pavel Dimens <[email protected]>
remove old name, update module

github.com/BioJulia/PopGen.jl - 9dca1671dd7e47c889933c6831558cc843f3ad0a authored about 3 years ago by Pavel Dimens <[email protected]>