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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

Continuous Integration

github.com/BioJulia/Indexes.jl - f92eefd480f2189de6167831364a18cd4a06c8c2 authored over 4 years ago by Ciarán O'Mara <[email protected]>
Update Manipulate.jl

github.com/BioJulia/PopGen.jl - be4a63fc44cf029557739120065a9117eccda470 authored over 4 years ago by Pavel V. Dimens <[email protected]>
Update Manipulate.jl

github.com/BioJulia/PopGen.jl_archive - be4a63fc44cf029557739120065a9117eccda470 authored over 4 years ago by Pavel V. Dimens <[email protected]>
start pecking away at Manipulate.jl

github.com/BioJulia/PopGen.jl - 11024d1346c78aa2c61b015ed2b043fabf47d582 authored over 4 years ago by Pavel V. Dimens <[email protected]>
start pecking away at Manipulate.jl

github.com/BioJulia/PopGen.jl_archive - 11024d1346c78aa2c61b015ed2b043fabf47d582 authored over 4 years ago by Pavel V. Dimens <[email protected]>
wrap up new popgen import

github.com/BioJulia/PopGen.jl_archive - 4274873373eebcb7c309fc2ad55f5cbd7dcd1ff5 authored over 4 years ago by Pavel V. Dimens <[email protected]>
wrap up new popgen import

github.com/BioJulia/PopGen.jl - 4274873373eebcb7c309fc2ad55f5cbd7dcd1ff5 authored over 4 years ago by Pavel V. Dimens <[email protected]>
Update readgen_new.jl

github.com/BioJulia/PopGen.jl_archive - b7f37e23931dbec5309e6aac2eee7c491d4c6d1e authored over 4 years ago by Pavel V. Dimens <[email protected]>
Update readgen_new.jl

github.com/BioJulia/PopGen.jl - b7f37e23931dbec5309e6aac2eee7c491d4c6d1e authored over 4 years ago by Pavel V. Dimens <[email protected]>
Update readgen_new.jl

github.com/BioJulia/PopGen.jl - 26e04c5d3d37aa9280f1bfb9af310d0acc21c3f2 authored over 4 years ago by Pavel V. Dimens <[email protected]>
Update readgen_new.jl

github.com/BioJulia/PopGen.jl_archive - 26e04c5d3d37aa9280f1bfb9af310d0acc21c3f2 authored over 4 years ago by Pavel V. Dimens <[email protected]>
Update readgen_new.jl

github.com/BioJulia/PopGen.jl_archive - d4b985cbe478cd7e2bce32f3e59880466a02dd6d authored over 4 years ago by Pavel V. Dimens <[email protected]>
Update readgen_new.jl

github.com/BioJulia/PopGen.jl - d4b985cbe478cd7e2bce32f3e59880466a02dd6d authored over 4 years ago by Pavel V. Dimens <[email protected]>
Merge branch 'pdimens' of https://github.com/pdimens/PopGen.jl into pdimens

github.com/BioJulia/PopGen.jl_archive - 6df239c6353f092abad4335d66a4ab636e5d71c7 authored over 4 years ago by Pavel V. Dimens <[email protected]>
Merge branch 'pdimens' of https://github.com/pdimens/PopGen.jl into pdimens

github.com/BioJulia/PopGen.jl - 6df239c6353f092abad4335d66a4ab636e5d71c7 authored over 4 years ago by Pavel V. Dimens <[email protected]>
get workable genepop reader

Needs to be optimized for speed/memory at row merge section

github.com/BioJulia/PopGen.jl - e33cb4e242e2db22d652f96a24776563a9f0862b authored over 4 years ago by Pavel V. Dimens <[email protected]>
get workable genepop reader

Needs to be optimized for speed/memory at row merge section

github.com/BioJulia/PopGen.jl_archive - e33cb4e242e2db22d652f96a24776563a9f0862b authored over 4 years ago by Pavel V. Dimens <[email protected]>
Merge branch 'pdimens' of https://github.com/pdimens/PopGen.jl into pdimens

github.com/BioJulia/PopGen.jl_archive - 45e712264e381884ef448003be2fdfd96d827882 authored over 4 years ago by Pavel <[email protected]>
Merge branch 'pdimens' of https://github.com/pdimens/PopGen.jl into pdimens

github.com/BioJulia/PopGen.jl - 45e712264e381884ef448003be2fdfd96d827882 authored over 4 years ago by Pavel <[email protected]>
Update orcid.png

github.com/BioJulia/PopGen.jl - b16b20ba896ddbf14a4bb58f54a7af052af81b94 authored over 4 years ago by Pavel <[email protected]>
Update orcid.png

github.com/BioJulia/PopGen.jl_archive - b16b20ba896ddbf14a4bb58f54a7af052af81b94 authored over 4 years ago by Pavel <[email protected]>
Merge branch 'pdimens' of https://github.com/pdimens/PopGen.jl into pdimens

github.com/BioJulia/PopGen.jl - 21a43e31f939a77380f4d19b3210dc06f85e8e58 authored over 4 years ago by Pavel V. Dimens <[email protected]>
Merge branch 'pdimens' of https://github.com/pdimens/PopGen.jl into pdimens

github.com/BioJulia/PopGen.jl_archive - 21a43e31f939a77380f4d19b3210dc06f85e8e58 authored over 4 years ago by Pavel V. Dimens <[email protected]>
fix nancycats ID's

github.com/BioJulia/PopGen.jl_archive - 21280634a4128b9bfd9b1b42fa11859289ccbd2e authored over 4 years ago by Pavel V. Dimens <[email protected]>
fix nancycats ID's

github.com/BioJulia/PopGen.jl - 21280634a4128b9bfd9b1b42fa11859289ccbd2e authored over 4 years ago by Pavel V. Dimens <[email protected]>
Merge pull request #98 from BioJulia/benjward/patch

Syntax error fix

github.com/BioJulia/BioSequences.jl - a5654f2654d179dd6b523a288c496830b6903d28 authored over 4 years ago by Ben J. Ward <[email protected]>
New package: BioAlignments v2.0.0 (#43)

UUID: 00701ae9-d1dc-5365-b64a-a3a3ebf5695e
Repo: https://github.com/BioJulia/BioAlignments.jl.g...

github.com/BioJulia/BioJuliaRegistry - a4518d9ec6f14061b23b0472865d81e037e71b45 authored over 4 years ago by Helix <[email protected]>
Fixup doctest

github.com/BioJulia/BioAlignments.jl - 6e7cdd0f2cf21e8dacbd1cf1fa9a2d80be2fcc3f authored over 4 years ago by Ben J. Ward <[email protected]>
Fixup docs again

github.com/BioJulia/BioAlignments.jl - 20e9e28443a35b4654a6522a4449efa9e5518a2f authored over 4 years ago by Ben J. Ward <[email protected]>
Fixup doctests

github.com/BioJulia/BioAlignments.jl - cffbb05812713799ca06fdb8be1213768500a4a8 authored over 4 years ago by Ben J. Ward <[email protected]>
Fixup docs Project.toml

github.com/BioJulia/BioAlignments.jl - d223cae84073b43a3e670fba5bd38af0e46457f8 authored over 4 years ago by Ben J. Ward <[email protected]>
Fixup docs makefile

github.com/BioJulia/BioAlignments.jl - 12843b164c1a97c96ccf47306a5a8b8cc7801676 authored over 4 years ago by Ben J. Ward <[email protected]>
Update logo and add Funding file

github.com/BioJulia/BioAlignments.jl - e2aa3cf1e258265adcbb03b8b972e26a75f08b5b authored over 4 years ago by Ben J. Ward <[email protected]>
Add TagBot

github.com/BioJulia/BioAlignments.jl - a3bc19f608d2abbd056852f62aa2ea8d2bc7da8c authored over 4 years ago by Ben J. Ward <[email protected]>
Increment version (#41)

github.com/BioJulia/BioAlignments.jl - 1f96df7554f570f4472c1c188b7fded8672f4911 authored over 4 years ago by Ciarán O'Mara <[email protected]>
New package: GenomicFeatures v2.0.0 (#42)

UUID: 899a7d2d-5c61-547b-bef9-6698a8d05446
Repo: https://github.com/BioJulia/GenomicFeatures.jl...

github.com/BioJulia/BioJuliaRegistry - 7861109132c9bf118f026dfa5402f4ee73f16c55 authored over 4 years ago by Helix <[email protected]>
Merge branch 'master' into benjward/patch

github.com/BioJulia/BioSequences.jl - a99c4db280a0cd31b464c26cd060641fd696a251 authored over 4 years ago by Ben J. Ward <[email protected]>
New version: Microbiome v0.6.2 (#41)

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

github.com/BioJulia/BioJuliaRegistry - a4045fbad0927e0465ff6810ce88b33828239734 authored over 4 years ago by Helix <[email protected]>
Merge branch 'pdimens' of https://github.com/pdimens/PopGen.jl into pdimens

github.com/BioJulia/PopGen.jl_archive - 6c5edf20d6d0e12de385a8d411d985e80aa06d9a authored over 4 years ago by Pavel <[email protected]>
Merge branch 'pdimens' of https://github.com/pdimens/PopGen.jl into pdimens

github.com/BioJulia/PopGen.jl - 6c5edf20d6d0e12de385a8d411d985e80aa06d9a authored over 4 years ago by Pavel <[email protected]>
Update install_carbon.png

github.com/BioJulia/PopGen.jl_archive - 273b93b1829e6e3d3ae8dc5b237884ee6c84a23f authored over 4 years ago by Pavel <[email protected]>
Update install_carbon.png

github.com/BioJulia/PopGen.jl - 273b93b1829e6e3d3ae8dc5b237884ee6c84a23f authored over 4 years ago by Pavel <[email protected]>
New version: BioSequences v2.0.1 (#40)

UUID: 7e6ae17a-c86d-528c-b3b9-7f778a29fe59
Repo: https://github.com/BioJulia/BioSequences.jl.git...

github.com/BioJulia/BioJuliaRegistry - 09649a44bd14d1da014ac2555ac79c888ce7f561 authored over 4 years ago by Helix <[email protected]>
Update change-log and add Compat entries to Project file

github.com/BioJulia/BioSequences.jl - ef486fe1a85d980a5ba1edd754290ab335556133 authored over 4 years ago by Ben J. Ward <[email protected]>
Have travis ci test on v1.3

github.com/BioJulia/BioSequences.jl - f673b0690a1d801633dabb99a915c91410da6f5b authored over 4 years ago by Ben J. Ward <[email protected]>
Increase version number

github.com/BioJulia/BioSequences.jl - 2cb9037973c4f55dd596b21399a4ba769051d8cc authored over 4 years ago by Ben J. Ward <[email protected]>
Fix syntax error

github.com/BioJulia/BioSequences.jl - bcaad8563a101410a25204587f22833b20391eda authored over 4 years ago by Ben J. Ward <[email protected]>
Merge pull request #6 from BioJulia/compathelper/new_version/2020-01-17-19-07-11-150-1718366901

CompatHelper: bump compat for "Colors" to "0.11"

github.com/BioJulia/MicrobiomePlots.jl - 256c721a3e98971cf99aee3e06706381f89ed399 authored over 4 years ago by Kevin Bonham <[email protected]>
Update HardyWeinberg.jl

github.com/BioJulia/PopGen.jl - f285d1592267ad9ddd4f89326e2c601cdbf6f406 authored over 4 years ago by Pavel V. Dimens <[email protected]>
Update HardyWeinberg.jl

github.com/BioJulia/PopGen.jl_archive - f285d1592267ad9ddd4f89326e2c601cdbf6f406 authored over 4 years ago by Pavel V. Dimens <[email protected]>
create ishet() functions for super fast heterozygosity

github.com/BioJulia/PopGen.jl_archive - 3be1ef5abbb24294b3ce137ac25fba742e07c4d8 authored over 4 years ago by Pavel V. Dimens <[email protected]>
create ishet() functions for super fast heterozygosity

github.com/BioJulia/PopGen.jl - 3be1ef5abbb24294b3ce137ac25fba742e07c4d8 authored over 4 years ago by Pavel V. Dimens <[email protected]>
Merge branch 'tsbugfix'

github.com/BioJulia/FASTX.jl - 3b0a452d311dbb62ef203f4132fb424e9a68996a authored over 4 years ago by Ben J. Ward <[email protected]>
New version: FASTX v1.1.1 (#38)

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

github.com/BioJulia/BioJuliaRegistry - 77ef50349f058232c40728faf55137e64ec42fd6 authored over 4 years ago by Helix <[email protected]>
Use symbols for names instead of strings (#10)

github.com/BioJulia/ReadDatastores.jl - ad0de834565428973fce5eb0345fe4865ee64482 authored over 4 years ago by Ben J. Ward <[email protected]>
Add julia 1.3 to travis

github.com/BioJulia/FASTX.jl - 30f4dda1b12d2cfd7b63699068969664fdf78683 authored over 4 years ago by Ben J. Ward <[email protected]>
Add TagBot

github.com/BioJulia/FASTX.jl - 8ba5c816c2d109f18e6025918addae6a7bf2e3fc authored over 4 years ago by Ben J. Ward <[email protected]>
Update Project.toml version number

github.com/BioJulia/FASTX.jl - 03c04ce512cfece0540a64259d0931589e1edbba authored over 4 years ago by Ben J. Ward <[email protected]>
Improve performance of bit-parallel counting methods (#96)

github.com/BioJulia/BioSequences.jl - cf26ba9524d3a4bf3cdac5ac3a8a92adda380b07 authored over 4 years ago by Ben J. Ward <[email protected]>
Update newtypes_JDB.jl

github.com/BioJulia/PopGen.jl_archive - 86ec47cb68256131c65204a084b956fd02bc5a92 authored over 4 years ago by Pavel V. Dimens <[email protected]>
Update newtypes_JDB.jl

github.com/BioJulia/PopGen.jl - 86ec47cb68256131c65204a084b956fd02bc5a92 authored over 4 years ago by Pavel V. Dimens <[email protected]>
Update newtypes_JDB.jl

github.com/BioJulia/PopGen.jl_archive - 23a2222f48bfb410fd192fe8e73a2a929382224c authored over 4 years ago by Pavel V. Dimens <[email protected]>
Update newtypes_JDB.jl

github.com/BioJulia/PopGen.jl - 23a2222f48bfb410fd192fe8e73a2a929382224c authored over 4 years ago by Pavel V. Dimens <[email protected]>
Update newtypes_JDB.jl

github.com/BioJulia/PopGen.jl - bbf881ab97ded05880957ebbaa5aed75c6ffd0bd authored over 4 years ago by Pavel V. Dimens <[email protected]>
Update newtypes_JDB.jl

github.com/BioJulia/PopGen.jl_archive - bbf881ab97ded05880957ebbaa5aed75c6ffd0bd authored over 4 years ago by Pavel V. Dimens <[email protected]>
Update PopObj.jl

github.com/BioJulia/PopGen.jl_archive - 5379d654556fa3c0b13123664957d6fa22172e90 authored over 4 years ago by Pavel V. Dimens <[email protected]>
Update PopObj.jl

github.com/BioJulia/PopGen.jl - 5379d654556fa3c0b13123664957d6fa22172e90 authored over 4 years ago by Pavel V. Dimens <[email protected]>
Update PopGen.jl

github.com/BioJulia/PopGen.jl - f4f894cdc75d652da34e281720e9bdc093f7682f authored over 4 years ago by Pavel V. Dimens <[email protected]>
Update PopGen.jl

github.com/BioJulia/PopGen.jl_archive - f4f894cdc75d652da34e281720e9bdc093f7682f authored over 4 years ago by Pavel V. Dimens <[email protected]>
update show

github.com/BioJulia/PopGen.jl_archive - a553793e65039cb2325f902305909bb8a6699673 authored over 4 years ago by Pavel V. Dimens <[email protected]>
update show

github.com/BioJulia/PopGen.jl - a553793e65039cb2325f902305909bb8a6699673 authored over 4 years ago by Pavel V. Dimens <[email protected]>
don't strip space unless required to

github.com/BioJulia/BioStructures.jl - 65e9e4c7ab1988639e8f7843c90c2a7e228231b2 authored over 4 years ago by Joe Greener <[email protected]>
speed up dihedral angle calculation

github.com/BioJulia/BioStructures.jl - 284963fb334e90a056a9874bda4675e93db4ec53 authored over 4 years ago by Joe Greener <[email protected]>
speed up sequence extraction

github.com/BioJulia/BioStructures.jl - 314ac2bc474a99483dedb453ee11a7be4afbb4e4 authored over 4 years ago by Joe Greener <[email protected]>
speed up defaultmodel

github.com/BioJulia/BioStructures.jl - bcdf935ea84e10fda305e78cda1b647cab20e88c authored over 4 years ago by Joe Greener <[email protected]>
more benchmarks

github.com/BioJulia/BioStructures.jl - 67b238de20ce22bf2da9f683bee099d3f431b5a9 authored over 4 years ago by Joe Greener <[email protected]>
Install TagBot as a GitHub Action

github.com/BioJulia/GenomicAnnotations.jl - 85bf86452dc55590c2cee0bd7f50c84e743a57fc authored over 4 years ago by Julia TagBot <[email protected]>
Update PopGen.jl

github.com/BioJulia/PopGen.jl - c541bf2566175d23ce1ce421433693108b122173 authored over 4 years ago by Jason Selwyn <[email protected]>
Update PopGen.jl

github.com/BioJulia/PopGen.jl_archive - c541bf2566175d23ce1ce421433693108b122173 authored over 4 years ago by Jason Selwyn <[email protected]>
Update PairwiseRelatedness.jl

github.com/BioJulia/PopGen.jl_archive - 61abdf4f7d4dead505eee6ee96b30a8c4856d00b authored over 4 years ago by Jason Selwyn <[email protected]>
Update PairwiseRelatedness.jl

github.com/BioJulia/PopGen.jl - 61abdf4f7d4dead505eee6ee96b30a8c4856d00b authored over 4 years ago by Jason Selwyn <[email protected]>
Update PairwiseRelatedness.jl

multi-threaded

github.com/BioJulia/PopGen.jl_archive - 1a5fb4e0c2c08bc077510b062dd3bc5a19a42822 authored over 4 years ago by Jason Selwyn <[email protected]>
Update PairwiseRelatedness.jl

multi-threaded

github.com/BioJulia/PopGen.jl - 1a5fb4e0c2c08bc077510b062dd3bc5a19a42822 authored over 4 years ago by Jason Selwyn <[email protected]>
separate collect functions for speed

github.com/BioJulia/BioStructures.jl - 04931333559fd37087f92267cbb1840883613863 authored over 4 years ago by Joe Greener <[email protected]>
speed up mmCIF read/write

github.com/BioJulia/BioStructures.jl - 8d91f1b7affec7306d3004b9aaebfc62cec7d923 authored over 4 years ago by Joe Greener <[email protected]>
Update PairwiseRelatedness.jl

github.com/BioJulia/PopGen.jl_archive - 4591a8a05b580570748119e47e56a09ddccb73c0 authored over 4 years ago by Jason Selwyn <[email protected]>
Update PairwiseRelatedness.jl

github.com/BioJulia/PopGen.jl - 4591a8a05b580570748119e47e56a09ddccb73c0 authored over 4 years ago by Jason Selwyn <[email protected]>
Merge branch 'dev' of https://github.com/pdimens/PopGen.jl into dev

github.com/BioJulia/PopGen.jl - 5536daeff0abf0403600f5aedea0e3e98212e834 authored over 4 years ago by Jason Selwyn <[email protected]>
Merge branch 'dev' of https://github.com/pdimens/PopGen.jl into dev

github.com/BioJulia/PopGen.jl_archive - 5536daeff0abf0403600f5aedea0e3e98212e834 authored over 4 years ago by Jason Selwyn <[email protected]>
Update PairwiseRelatedness.jl

github.com/BioJulia/PopGen.jl_archive - 1a0e153dd78c9f3bd445803a94bf006b40bd99b7 authored over 4 years ago by Jason Selwyn <[email protected]>
Update PairwiseRelatedness.jl

github.com/BioJulia/PopGen.jl - 1a0e153dd78c9f3bd445803a94bf006b40bd99b7 authored over 4 years ago by Jason Selwyn <[email protected]>
add convenience types and Base.show() overload for it

github.com/BioJulia/PopGen.jl - 4502aca411ca88f3495da54dea9a964ae61cc431 authored over 4 years ago by Pavel <[email protected]>
add convenience types and Base.show() overload for it

github.com/BioJulia/PopGen.jl_archive - 4502aca411ca88f3495da54dea9a964ae61cc431 authored over 4 years ago by Pavel <[email protected]>
Merge branch 'master' into pdimens

github.com/BioJulia/PopGen.jl - d1c568816abfcc157f43e4ebaac1adc492fd4e08 authored over 4 years ago by Pavel <[email protected]>
Merge branch 'master' into pdimens

github.com/BioJulia/PopGen.jl_archive - d1c568816abfcc157f43e4ebaac1adc492fd4e08 authored over 4 years ago by Pavel <[email protected]>
add condition to genepop() to purge trailing whitespace columns

replace populations!() with 4 different methods and update docstring accordingly

github.com/BioJulia/PopGen.jl - b78dc27d20aa615e1f5839eb6ce8352cd5d8cca4 authored over 4 years ago by Pavel <[email protected]>
add condition to genepop() to purge trailing whitespace columns

replace populations!() with 4 different methods and update docstring accordingly

github.com/BioJulia/PopGen.jl_archive - b78dc27d20aa615e1f5839eb6ce8352cd5d8cca4 authored over 4 years ago by Pavel <[email protected]>
Update PairwiseRelatedness.jl

github.com/BioJulia/PopGen.jl_archive - 2021032a75145244b76313fc6cad1a739e2c50a7 authored over 4 years ago by jdselwyn <[email protected]>
Update PairwiseRelatedness.jl

github.com/BioJulia/PopGen.jl - 2021032a75145244b76313fc6cad1a739e2c50a7 authored over 4 years ago by jdselwyn <[email protected]>
Merge branch 'pdimens' of https://github.com/pdimens/PopGen.jl into pdimens

github.com/BioJulia/PopGen.jl - c09158e604b8899cf4db19a8d2c00c668a7529d1 authored over 4 years ago by Pavel <[email protected]>