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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

wishful thinking port added to scratch

github.com/BioJulia/PopGen.jl - 19979a6ce0c5f12ccd26a3651f27d2025795ceda authored almost 4 years ago by Pavel Dimens <[email protected]>
optimize geno/allele freq methods using StatsBase

github.com/BioJulia/PopGen.jl_archive - 36fcce224a8ccb806148f3b784f40b7a7aae175a authored almost 4 years ago by Pavel Dimens <[email protected]>
optimize geno/allele freq methods using StatsBase

github.com/BioJulia/PopGen.jl - 36fcce224a8ccb806148f3b784f40b7a7aae175a authored almost 4 years ago by Pavel Dimens <[email protected]>
Fix RC for seq with unused data (#128)

github.com/BioJulia/BioSequences.jl - 1cfc0aa5eecd38ee02bbd23ec9b24d1832223fe3 authored almost 4 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 - aa555a44718b42c517397acad1b7de00e063ab6d authored almost 4 years ago by Pavel Dimens <[email protected]>
Merge branch 'dev' of https://github.com/pdimens/PopGen.jl into dev

github.com/BioJulia/PopGen.jl_archive - aa555a44718b42c517397acad1b7de00e063ab6d authored almost 4 years ago by Pavel Dimens <[email protected]>
fix typo bug in function definition

github.com/BioJulia/PopGen.jl_archive - eda4a4b07c96f900ed6ea9b63eb5119ff90cfedd authored almost 4 years ago by Pavel Dimens <[email protected]>
fix typo bug in function definition

github.com/BioJulia/PopGen.jl - eda4a4b07c96f900ed6ea9b63eb5119ff90cfedd authored almost 4 years ago by Pavel Dimens <[email protected]>
clean up fstats code/bugs

github.com/BioJulia/PopGen.jl_archive - 10deac8981f5ab0e7786d253edc6edb01eb1bf87 authored almost 4 years ago by Pavel Dimens <[email protected]>
clean up fstats code/bugs

github.com/BioJulia/PopGen.jl - 10deac8981f5ab0e7786d253edc6edb01eb1bf87 authored almost 4 years ago by Pavel Dimens <[email protected]>
simplify perm code

github.com/BioJulia/PopGen.jl - 8ad2dc929d6620ce7df1ebf31d9f28281d20c0b4 authored almost 4 years ago by Pavel Dimens <[email protected]>
simplify perm code

github.com/BioJulia/PopGen.jl_archive - 8ad2dc929d6620ce7df1ebf31d9f28281d20c0b4 authored almost 4 years ago by Pavel Dimens <[email protected]>
Base.show flexibility

github.com/BioJulia/PopGen.jl - 0500b48a9c41eec1487cef2f5c3834e8ebb64ff5 authored almost 4 years ago by Pavel Dimens <[email protected]>
Base.show flexibility

github.com/BioJulia/PopGen.jl_archive - 0500b48a9c41eec1487cef2f5c3834e8ebb64ff5 authored almost 4 years ago by Pavel Dimens <[email protected]>
Merge branch 'dev' of https://github.com/pdimens/PopGen.jl into dev

github.com/BioJulia/PopGen.jl - f424bd823734b7f9b423d5e1565fcfcf60238434 authored almost 4 years ago by Pavel Dimens <[email protected]>
Merge branch 'dev' of https://github.com/pdimens/PopGen.jl into dev

github.com/BioJulia/PopGen.jl_archive - f424bd823734b7f9b423d5e1565fcfcf60238434 authored almost 4 years ago by Pavel Dimens <[email protected]>
sidechain centroid docs example

github.com/BioJulia/BioStructures.jl - 3f62456290d33a35caf4f5a048766949e8aced21 authored almost 4 years ago by Joe Greener <[email protected]>
fix rename

github.com/BioJulia/PopGen.jl_archive - 0fb45cd789aff612379e84642d9443e1295c0f38 authored almost 4 years ago by Pavel Dimens <[email protected]>
fix rename

github.com/BioJulia/PopGen.jl - 0fb45cd789aff612379e84642d9443e1295c0f38 authored almost 4 years ago by Pavel Dimens <[email protected]>
Merge branch 'dev' of https://github.com/pdimens/PopGen.jl into dev

github.com/BioJulia/PopGen.jl_archive - d6ae516f9a6cf3f37ce0ca8858199edebaf46d0b authored almost 4 years ago by Pavel Dimens <[email protected]>
Merge branch 'dev' of https://github.com/pdimens/PopGen.jl into dev

github.com/BioJulia/PopGen.jl - d6ae516f9a6cf3f37ce0ca8858199edebaf46d0b authored almost 4 years ago by Pavel Dimens <[email protected]>
replace popdata2____ as methods

github.com/BioJulia/PopGen.jl_archive - ba11037197f14b713a6694620ebd379fb687c34e authored almost 4 years ago by Pavel Dimens <[email protected]>
replace popdata2____ as methods

github.com/BioJulia/PopGen.jl - ba11037197f14b713a6694620ebd379fb687c34e authored almost 4 years ago by Pavel Dimens <[email protected]>
Add do syntax to AbstractFormattedIO built from other IO objects

github.com/BioJulia/BioGenerics.jl - 8f1f13ff4645f4c87f0bc6b632cd4d436af9581d authored almost 4 years ago by Jakob Nybo Nissen <[email protected]>
Add Base.show flexibility

github.com/BioJulia/PopGen.jl_archive - 96d6f1089887167c05ab833941dca233a2e2367b authored almost 4 years ago by Pavel Dimens <[email protected]>
Add Base.show flexibility

github.com/BioJulia/PopGen.jl - 96d6f1089887167c05ab833941dca233a2e2367b authored almost 4 years ago by Pavel Dimens <[email protected]>
run CI every week with cron job

github.com/BioJulia/MMTF.jl - e58f1478d45ea111ffe58b4eee62c10caded8289 authored almost 4 years ago by Joe Greener <[email protected]>
bump version

github.com/BioJulia/BioStructures.jl - 2b9ac8d921ff34fe7887ce0f7de6e093a7f6bb86 authored almost 4 years ago by Joe Greener <[email protected]>
run CI every week with cron job

github.com/BioJulia/BioStructures.jl - a475a1e8412104a8fbb18f8530d5c9fe7593b81b authored almost 4 years ago by Joe Greener <[email protected]>
move CI from Travis/AppVeyor to GitHub Actions

github.com/BioJulia/MMTF.jl - 5da121ffc6ab9913bd2b3337a3b0395145b718b4 authored almost 4 years ago by Joe Greener <[email protected]>
update CompatHelper

github.com/BioJulia/MMTF.jl - 0be118f865d6bf1022efd01962c8e32969d7bba6 authored almost 4 years ago by Joe Greener <[email protected]>
update CompatHelper

github.com/BioJulia/BioStructures.jl - 17ee6342fd3d828110f33d32a0b804856f738101 authored almost 4 years ago by Joe Greener <[email protected]>
CI status badge

github.com/BioJulia/BioStructures.jl - 11b9ee8ad66bafaadc7c4c35733605921e8fd6af authored almost 4 years ago by Joe Greener <[email protected]>
move CI from Travis/AppVeyor to GitHub Actions

github.com/BioJulia/BioStructures.jl - befc591ea2b54644507309a6697950509e91c6e3 authored almost 4 years ago by Joe Greener <[email protected]>
paper link

github.com/BioJulia/MMTF.jl - c98041b4f51f9b2ce7cd28d6e4e518dbda1e294c authored almost 4 years ago by Joe Greener <[email protected]>
citation file

github.com/BioJulia/MMTF.jl - 640d90095caa9a6e43b2dee51fd570f87495ef83 authored almost 4 years ago by Joe Greener <[email protected]>
paper PDF

github.com/BioJulia/BioStructures.jl - 21f76c843dc962333d0b69e449bf41b5cef98517 authored almost 4 years ago by Joe Greener <[email protected]>
citation file

github.com/BioJulia/BioStructures.jl - c8bb017071f710e5f89d439de9dd4b2b611cf9c9 authored almost 4 years ago by Joe Greener <[email protected]>
Improve SIMD loop for LLVM11

github.com/BioJulia/Automa.jl - 3c63a5b831b825c3546b833cd00722b44e36c074 authored almost 4 years ago by Jakob Nybo Nissen <[email protected]>
Add comments

github.com/BioJulia/Automa.jl - 9ff2d4244e5768880d80d9553c2d3ad1d9e3c192 authored almost 4 years ago by Jakob Nybo Nissen <[email protected]>
Force LLVM to use vptest

github.com/BioJulia/Automa.jl - 3d2c6bf5e089cd9353a4d12f75078a13f105cc71 authored almost 4 years ago by Jakob Nybo Nissen <[email protected]>
Improve test coverage

github.com/BioJulia/Automa.jl - 3cf0e073af943bc6edf5d27bcd79687765b369fd authored almost 4 years ago by Jakob Nybo Nissen <[email protected]>
Improve SIMD tests

github.com/BioJulia/Automa.jl - 3f72597d7ac99e73c706ae69e96900eff719ddf2 authored almost 4 years ago by Jakob Nybo Nissen <[email protected]>
Jump through more hoops to make LLVM compile the SIMD loop

github.com/BioJulia/Automa.jl - ebfb7e88abaa42718a2cd95889ddcb44111f02a4 authored almost 4 years ago by Jakob Nybo Nissen <[email protected]>
Merge branch 'simd' of github.com:jakobnissen/Automa.jl into simd

github.com/BioJulia/Automa.jl - 5ee92e70da0ad013c50df83b90b3fb3eca332c51 authored almost 4 years ago by Jakob Nybo Nissen <[email protected]>
Add more tests

github.com/BioJulia/Automa.jl - 14966093eed3c2a2db1ec0a6e065504332117977 authored almost 4 years ago by Jakob Nybo Nissen <[email protected]>
add PooledArrays to test deps

github.com/BioJulia/PopGen.jl - 03adc111a076f317617754d2b33813520e749da8 authored almost 4 years ago by Pavel Dimens <[email protected]>
add PooledArrays to test deps

github.com/BioJulia/PopGen.jl_archive - 03adc111a076f317617754d2b33813520e749da8 authored almost 4 years ago by Pavel Dimens <[email protected]>
revert meta creation

github.com/BioJulia/PopGen.jl - a305a9bee633f2d3ab5b200704743a68dd6c106c authored almost 4 years ago by Pavel Dimens <[email protected]>
revert meta creation

github.com/BioJulia/PopGen.jl_archive - a305a9bee633f2d3ab5b200704743a68dd6c106c authored almost 4 years ago by Pavel Dimens <[email protected]>
actually add Test to project.toml

github.com/BioJulia/PopGen.jl_archive - 5d84856b88d8aa62ea02b438453ba216cc5a7f21 authored almost 4 years ago by Pavel Dimens <[email protected]>
actually add Test to project.toml

github.com/BioJulia/PopGen.jl - 5d84856b88d8aa62ea02b438453ba216cc5a7f21 authored almost 4 years ago by Pavel Dimens <[email protected]>
Merge branch 'dev' of https://github.com/pdimens/PopGen.jl into dev

github.com/BioJulia/PopGen.jl - f1fba544a4c897c0b816a34bba3450356e62fde6 authored almost 4 years ago by Pavel Dimens <[email protected]>
Merge branch 'dev' of https://github.com/pdimens/PopGen.jl into dev

github.com/BioJulia/PopGen.jl_archive - f1fba544a4c897c0b816a34bba3450356e62fde6 authored almost 4 years ago by Pavel Dimens <[email protected]>
add geneticvariation/gzip test deps

github.com/BioJulia/PopGen.jl - ba15bf02f364a4949a29a0fdd95c0f9dff7d2235 authored almost 4 years ago by Pavel Dimens <[email protected]>
add geneticvariation/gzip test deps

github.com/BioJulia/PopGen.jl_archive - ba15bf02f364a4949a29a0fdd95c0f9dff7d2235 authored almost 4 years ago by Pavel Dimens <[email protected]>
Merge pull request #51 from pdimens/compathelper/new_version/2020-12-12-00-52-16-869-2184825279

CompatHelper: add new compat entry for "RandomNumbers" at version "1.4"

github.com/BioJulia/PopGen.jl - 624afb8ee4490223b6d9ecae45d721c11dc4ecc8 authored almost 4 years ago by Pavel V. Dimens <[email protected]>
Merge pull request #51 from pdimens/compathelper/new_version/2020-12-12-00-52-16-869-2184825279

CompatHelper: add new compat entry for "RandomNumbers" at version "1.4"

github.com/BioJulia/PopGen.jl_archive - 624afb8ee4490223b6d9ecae45d721c11dc4ecc8 authored almost 4 years ago by Pavel V. Dimens <[email protected]>
add more tests

github.com/BioJulia/PopGen.jl_archive - c16d5db7cd3486cbaa50af3c3332bfd058640b19 authored almost 4 years ago by Pavel Dimens <[email protected]>
add more tests

github.com/BioJulia/PopGen.jl - c16d5db7cd3486cbaa50af3c3332bfd058640b19 authored almost 4 years ago by Pavel Dimens <[email protected]>
replace manual creation with generate_meta

github.com/BioJulia/PopGen.jl - e470c48cc96ddeb3ed0efeac86a0985601882724 authored almost 4 years ago by Pavel Dimens <[email protected]>
replace manual creation with generate_meta

github.com/BioJulia/PopGen.jl_archive - e470c48cc96ddeb3ed0efeac86a0985601882724 authored almost 4 years ago by Pavel Dimens <[email protected]>
rename missing to missing_data

github.com/BioJulia/PopGen.jl_archive - 11f8611a59dce1a87fdc231085ceee0e2f3bdc4f authored almost 4 years ago by Pavel Dimens <[email protected]>
rename missing to missing_data

github.com/BioJulia/PopGen.jl - 11f8611a59dce1a87fdc231085ceee0e2f3bdc4f authored almost 4 years ago by Pavel Dimens <[email protected]>
Improve inferrability of haszerolayout

github.com/BioJulia/Automa.jl - 2d1342b81c12bd7c73290f49b17c13fac586bd19 authored almost 4 years ago by Jakob Nybo Nissen <[email protected]>
add generate_meta

github.com/BioJulia/PopGen.jl - 4067dc988fb7b70aa18c7ffe537bbf3d322db969 authored almost 4 years ago by Pavel Dimens <[email protected]>
add generate_meta

github.com/BioJulia/PopGen.jl_archive - 4067dc988fb7b70aa18c7ffe537bbf3d322db969 authored almost 4 years ago by Pavel Dimens <[email protected]>
make robust against missings

github.com/BioJulia/PopGen.jl - f16db7e0baba167bdeb839743f676d3cd7f5c546 authored almost 4 years ago by Pavel Dimens <[email protected]>
make robust against missings

github.com/BioJulia/PopGen.jl_archive - f16db7e0baba167bdeb839743f676d3cd7f5c546 authored almost 4 years ago by Pavel Dimens <[email protected]>
fixed DataFrames v0.22 syntax deprecation bug

github.com/BioJulia/PopGen.jl - 2d3b98ce290dd2879f467fdc24fdc4450f733e8e authored almost 4 years ago by Pavel Dimens <[email protected]>
fixed DataFrames v0.22 syntax deprecation bug

github.com/BioJulia/PopGen.jl_archive - 2d3b98ce290dd2879f467fdc24fdc4450f733e8e authored almost 4 years ago by Pavel Dimens <[email protected]>
update tests for get_genotypes api change

github.com/BioJulia/PopGen.jl_archive - b1b0da0d76ed9f5e80a725da06969e05f5cf7a12 authored almost 4 years ago by Pavel Dimens <[email protected]>
update tests for get_genotypes api change

github.com/BioJulia/PopGen.jl - b1b0da0d76ed9f5e80a725da06969e05f5cf7a12 authored almost 4 years ago by Pavel Dimens <[email protected]>
fix occurences of deprecated sharks/cats datasets

github.com/BioJulia/PopGen.jl_archive - b17dac1e37130cf924330e92159bd3da7ab02a16 authored almost 4 years ago by Pavel Dimens <[email protected]>
fix occurences of deprecated sharks/cats datasets

github.com/BioJulia/PopGen.jl - b17dac1e37130cf924330e92159bd3da7ab02a16 authored almost 4 years ago by Pavel Dimens <[email protected]>
CompatHelper: add new compat entry for "RandomNumbers" at version "1.4"

github.com/BioJulia/PopGen.jl - b42d593582e7bdc023616a225bcc849482d1b846 authored almost 4 years ago by github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
CompatHelper: add new compat entry for "RandomNumbers" at version "1.4"

github.com/BioJulia/PopGen.jl_archive - b42d593582e7bdc023616a225bcc849482d1b846 authored almost 4 years ago by github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
clean completed todos, bugfix

github.com/BioJulia/PopGen.jl_archive - 69c9abff378b424478b15ad9bb037dcd7d9e563e authored almost 4 years ago by Pavel Dimens <[email protected]>
clean completed todos, bugfix

github.com/BioJulia/PopGen.jl - 69c9abff378b424478b15ad9bb037dcd7d9e563e authored almost 4 years ago by Pavel Dimens <[email protected]>
make richness() kwarg consistent

github.com/BioJulia/PopGen.jl - 879e0bbb058a87f2d4e4c040cfd2731b66454e97 authored almost 4 years ago by Pavel Dimens <[email protected]>
make richness() kwarg consistent

github.com/BioJulia/PopGen.jl_archive - 879e0bbb058a87f2d4e4c040cfd2731b66454e97 authored almost 4 years ago by Pavel Dimens <[email protected]>
add X_freqtable functions

github.com/BioJulia/PopGen.jl_archive - 855db6dbfa1ce4784fe8e05818c1113da2de022f authored almost 4 years ago by Pavel Dimens <[email protected]>
add X_freqtable functions

github.com/BioJulia/PopGen.jl - 855db6dbfa1ce4784fe8e05818c1113da2de022f authored almost 4 years ago by Pavel Dimens <[email protected]>
posthoc MT => Xorshift

github.com/BioJulia/PopGen.jl - a6775b729b94755005412f150659f4e4b091c808 authored almost 4 years ago by Pavel Dimens <[email protected]>
posthoc MT => Xorshift

github.com/BioJulia/PopGen.jl_archive - a6775b729b94755005412f150659f4e4b091c808 authored almost 4 years ago by Pavel Dimens <[email protected]>
add RandomNumbers.jl and replace MT w/ Xorshift

github.com/BioJulia/PopGen.jl - a9970f761303dffe1241503e1fa59f0c2fc90e8a authored almost 4 years ago by Pavel Dimens <[email protected]>
add RandomNumbers.jl and replace MT w/ Xorshift

github.com/BioJulia/PopGen.jl_archive - a9970f761303dffe1241503e1fa59f0c2fc90e8a authored almost 4 years ago by Pavel Dimens <[email protected]>
Merge branch 'dev' of https://github.com/pdimens/PopGen.jl into dev

github.com/BioJulia/PopGen.jl - 25ab16a4ad6dbde99cf077fa98c2293d355b8a6e authored almost 4 years ago by Pavel Dimens <[email protected]>
Merge branch 'dev' of https://github.com/pdimens/PopGen.jl into dev

github.com/BioJulia/PopGen.jl_archive - 25ab16a4ad6dbde99cf077fa98c2293d355b8a6e authored almost 4 years ago by Pavel Dimens <[email protected]>
fix dataset macros

github.com/BioJulia/PopGen.jl_archive - 116e631166ed2e690fe3b2f8586f8faaeedc0710 authored almost 4 years ago by Pavel Dimens <[email protected]>
fix dataset macros

github.com/BioJulia/PopGen.jl - 116e631166ed2e690fe3b2f8586f8faaeedc0710 authored almost 4 years ago by Pavel Dimens <[email protected]>
Merge pull request #50 from pdimens/compathelper/new_version/2020-11-28-00-43-49-199-1751520

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

github.com/BioJulia/PopGen.jl - 5edc10f7a7b6f13446452d2573b1155f1210398b authored almost 4 years ago by Pavel V. Dimens <[email protected]>
Merge pull request #50 from pdimens/compathelper/new_version/2020-11-28-00-43-49-199-1751520

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

github.com/BioJulia/PopGen.jl_archive - 5edc10f7a7b6f13446452d2573b1155f1210398b authored almost 4 years ago by Pavel V. Dimens <[email protected]>
add relatedness_posthoc

github.com/BioJulia/PopGen.jl - de6f598678d87efe547ecb335ba7009e0f62151f authored almost 4 years ago by Pavel Dimens <[email protected]>
add relatedness_posthoc

github.com/BioJulia/PopGen.jl_archive - de6f598678d87efe547ecb335ba7009e0f62151f authored almost 4 years ago by Pavel Dimens <[email protected]>
CompatHelper: bump compat for "StaticArrays" to "1.0"

github.com/BioJulia/PopGen.jl_archive - ceacd79d6843784db876073fb78e4e5957901ba2 authored almost 4 years ago by github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
CompatHelper: bump compat for "StaticArrays" to "1.0"

github.com/BioJulia/PopGen.jl - ceacd79d6843784db876073fb78e4e5957901ba2 authored almost 4 years ago by github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Updated version

github.com/BioJulia/GenomicAnnotations.jl - 9db8a0bce94ed0a7b787354a56ba2808da633bf9 authored almost 4 years ago by Karl Dyrhage <[email protected]>
Backwards compatibility

github.com/BioJulia/GenomicAnnotations.jl - d805abdb8118a105a7dd81028524427565c2d2f7 authored almost 4 years ago by Karl Dyrhage <[email protected]>
Updated for Dataframes >0.20

github.com/BioJulia/GenomicAnnotations.jl - 64a0adc832de5c4e2ee52ff97f2ea48a69dfc66c authored almost 4 years ago by Karl Dyrhage <[email protected]>