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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 remote-tracking branch 'origin/master'

github.com/BioJulia/KmerAnalysis.jl - f59c1afa511390e2a2bb71c5cb4e66d83c4264bb authored over 4 years ago by Ben J. Ward <[email protected]>
Update ReadDatastores version used

github.com/BioJulia/KmerAnalysis.jl - 7767fce3a231008509c2fa47728d3f9cb6a6b5a5 authored over 4 years ago by Ben J. Ward <[email protected]>
paper citation info

github.com/BioJulia/MMTF.jl - 41cce8e4575eda3cd8fc10c44f1b77edd21bc71b authored over 4 years ago by Joe Greener <[email protected]>
paper citation info

github.com/BioJulia/BioStructures.jl - 538b9f5cd917cf6359eb6884961c3c0e6cbe4019 authored over 4 years ago by Joe Greener <[email protected]>
Update CI and documentation for the general registry

- Julia LTS
- Name tweaks

github.com/BioJulia/GenomicFeatures.jl - 101e7927329fb075cfe7fcb91f97694036a73509 authored over 4 years ago by Ciarán O'Mara <[email protected]>
Add Benchmarks

- Local benchmark script

github.com/BioJulia/GenomicFeatures.jl - 20f418019af2e0d5af65c918a9dc291e6a9c3d36 authored over 4 years ago by Ciarán O'Mara <[email protected]>
Benchmark workflow

Conditionally posts benchmark results.

github.com/BioJulia/GenomicFeatures.jl - 481fe0d10669e168379b11d156cdca621e48aa4c authored over 4 years ago by Ciarán O'Mara <[email protected]>
Move code common used for benchmarks and tests into Utilities.jl

github.com/BioJulia/GenomicFeatures.jl - c10623f6a97f89e964bdc1d19c8f388dbdf362f2 authored over 4 years ago by Ciarán O'Mara <[email protected]>
Update Manipulate.jl

github.com/BioJulia/PopGen.jl_archive - a207bb42f1a7fede2d189ac740ce1a200c62a95e authored over 4 years ago by Pavel Dimens <[email protected]>
Update Manipulate.jl

github.com/BioJulia/PopGen.jl - a207bb42f1a7fede2d189ac740ce1a200c62a95e authored over 4 years ago by Pavel Dimens <[email protected]>
shrink exclude to feed into exclude!

github.com/BioJulia/PopGen.jl - a39c320f9af9e2aad23d36e77bc9417a4159c0ea authored over 4 years ago by Pavel Dimens <[email protected]>
shrink exclude to feed into exclude!

github.com/BioJulia/PopGen.jl_archive - a39c320f9af9e2aad23d36e77bc9417a4159c0ea authored over 4 years ago by Pavel Dimens <[email protected]>
less verbose show()

github.com/BioJulia/PopGen.jl_archive - d2b304954481b6f4192d975b30b7a72fa78dee25 authored over 4 years ago by Pavel Dimens <[email protected]>
less verbose show()

github.com/BioJulia/PopGen.jl - d2b304954481b6f4192d975b30b7a72fa78dee25 authored over 4 years ago by Pavel Dimens <[email protected]>
replace exclude_ with exclude and exclude!

github.com/BioJulia/PopGen.jl - 73a8adffe60bb00e596eafbefa4ba6ff08d75691 authored over 4 years ago by Pavel Dimens <[email protected]>
replace exclude_ with exclude and exclude!

github.com/BioJulia/PopGen.jl_archive - 73a8adffe60bb00e596eafbefa4ba6ff08d75691 authored over 4 years ago by Pavel Dimens <[email protected]>
add compat helper

github.com/BioJulia/MMTF.jl - ee5045a95cbbd5f7d38532943eda9f8b14829ac9 authored over 4 years ago by Joe Greener <[email protected]>
fix uuid

github.com/BioJulia/MMTF.jl - 2b6eeb69361e024db257e5ac6efd04158f9183f6 authored over 4 years ago by Joe Greener <[email protected]>
appveyor badge

github.com/BioJulia/MMTF.jl - 1ffd88597c3393228fe63e93494d68c81c41d058 authored over 4 years ago by Joe Greener <[email protected]>
Update readme

github.com/BioJulia/MMTF.jl - d6d007c4007410e9f5640ffd016616984bed773c authored over 4 years ago by Joe Greener <[email protected]>
Test on latest Julia

github.com/BioJulia/MMTF.jl - 978c37989fe11c32ec4c4d6d73fe683d0942f342 authored over 4 years ago by Joe Greener <[email protected]>
Remove REQUIRE

github.com/BioJulia/MMTF.jl - c6863fbf8e8ad182486d49920c7bbb1db5438f81 authored over 4 years ago by Joe Greener <[email protected]>
Merge pull request #5 from sethaxen/rmmanifest

Remove manifest and bump compats

github.com/BioJulia/MMTF.jl - ee36847b07eb01a656fdde3f951670662d10209b authored over 4 years ago by Joe Greener <[email protected]>
Increment version number

github.com/BioJulia/MMTF.jl - ac8c65e710809b76dbf9790f40657e39677771ca authored over 4 years ago by Seth Axen <[email protected]>
Bump MsgPack compat

github.com/BioJulia/MMTF.jl - 557f1a3bbc39b43014a557fbe0671f12a0686f2b authored over 4 years ago by Seth Axen <[email protected]>
Bump CodecZlib compat

github.com/BioJulia/MMTF.jl - f48535b9a279ca2a18e88ab26b489b9df2a5bb92 authored over 4 years ago by Seth Axen <[email protected]>
Add compat entries

github.com/BioJulia/MMTF.jl - 931f8f5573e87e95b93db6322b0737b354921b84 authored over 4 years ago by Seth Axen <[email protected]>
Remove Manifest.toml

github.com/BioJulia/MMTF.jl - 450a64dc00574334a179a73f70f74e5876774aa6 authored over 4 years ago by Seth Axen <[email protected]>
CompatHelper: bump compat for "ReadDatastores" to "0.4" (#4)

github.com/BioJulia/KmerAnalysis.jl - 6995f25913db8424f3f47dfaeb2a1821736a7ed7 authored over 4 years ago by github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
begin rewriting permutation test for fstats

github.com/BioJulia/PopGen.jl_archive - 761b49a62f8ca3ca057392a037da3afdb35a5268 authored over 4 years ago by Pavel Dimens <[email protected]>
begin rewriting permutation test for fstats

github.com/BioJulia/PopGen.jl - 761b49a62f8ca3ca057392a037da3afdb35a5268 authored over 4 years ago by Pavel Dimens <[email protected]>
add permutation methods

github.com/BioJulia/PopGen.jl - ae7b8a03117bbc775b81fd386c9c10a275f79641 authored over 4 years ago by Pavel Dimens <[email protected]>
add permutation methods

github.com/BioJulia/PopGen.jl_archive - ae7b8a03117bbc775b81fd386c9c10a275f79641 authored over 4 years ago by Pavel Dimens <[email protected]>
comment out unused math

github.com/BioJulia/PopGen.jl_archive - 59fb9e5e94bd0310fd9996e1cba773982a81145c authored over 4 years ago by Pavel Dimens <[email protected]>
comment out unused math

github.com/BioJulia/PopGen.jl - 59fb9e5e94bd0310fd9996e1cba773982a81145c authored over 4 years ago by Pavel Dimens <[email protected]>
better using specification

github.com/BioJulia/PopGen.jl - a9c33fb7a26f1cf4bf41df688078b867e7a88fd9 authored over 4 years ago by Pavel Dimens <[email protected]>
better using specification

github.com/BioJulia/PopGen.jl_archive - a9c33fb7a26f1cf4bf41df688078b867e7a88fd9 authored over 4 years ago by Pavel Dimens <[email protected]>
fix mixed ploidy printing

github.com/BioJulia/PopGen.jl_archive - eb0e8a5f7dd287506453b6cae55bcbd2138beb70 authored over 4 years ago by Pavel Dimens <[email protected]>
fix mixed ploidy printing

github.com/BioJulia/PopGen.jl - eb0e8a5f7dd287506453b6cae55bcbd2138beb70 authored over 4 years ago by Pavel Dimens <[email protected]>
CSV.read => CSV.File

github.com/BioJulia/PopGen.jl - 329aa86d17d8167f1a2a239bc9f057b4d2facfa9 authored over 4 years ago by Pavel Dimens <[email protected]>
CSV.read => CSV.File

github.com/BioJulia/PopGen.jl_archive - 329aa86d17d8167f1a2a239bc9f057b4d2facfa9 authored over 4 years ago by Pavel Dimens <[email protected]>
Update README.md

github.com/BioJulia/GenomeGraphs.jl - 66978436262121cad9f387ed9bdca26cadc22afe authored over 4 years ago by Ben J. Ward <[email protected]>
Update CompatHelper.yml

github.com/BioJulia/GenomeGraphs.jl - 206d56cb0dde59204921d6141c0c101791a946ea authored over 4 years ago by Ben J. Ward <[email protected]>
Support Julia LTS version (#29)

github.com/BioJulia/GenomeGraphs.jl - eadef2fc4ebb8af93d75ca6cfc9846ba8bcbde36 authored over 4 years ago by Ben J. Ward <[email protected]>
Update TagBot.yml

github.com/BioJulia/ReadDatastores.jl - e7d198c62bb55427ade170babc00cb70c7de308c authored over 4 years ago by Ben J. Ward <[email protected]>
Update Project.toml

github.com/BioJulia/ReadDatastores.jl - 26f6e24afb64ed4fb1a3b09f7d6c0792db02df45 authored over 4 years ago by Ben J. Ward <[email protected]>
Support Julia LTS versions (#15)

github.com/BioJulia/ReadDatastores.jl - b1713a5cecec0940ee73ccb87150a98f57f7d539 authored over 4 years ago by Ben J. Ward <[email protected]>
add fstats docstring

github.com/BioJulia/PopGen.jl_archive - 29ffc8ed91068e7eaad637d446fa4d3392ec51cb authored over 4 years ago by Pavel Dimens <[email protected]>
add fstats docstring

github.com/BioJulia/PopGen.jl - 29ffc8ed91068e7eaad637d446fa4d3392ec51cb authored over 4 years ago by Pavel Dimens <[email protected]>
add summarystats

github.com/BioJulia/PopGen.jl - 67f3e7aea4d2495a1206fc76a9e3d96abcea51f0 authored over 4 years ago by Pavel Dimens <[email protected]>
add summarystats

github.com/BioJulia/PopGen.jl_archive - 67f3e7aea4d2495a1206fc76a9e3d96abcea51f0 authored over 4 years ago by Pavel Dimens <[email protected]>
Update AlleleFreq.jl

github.com/BioJulia/PopGen.jl_archive - 4a2aa7a3deda8eb2a30fe123d156666c35d181d5 authored over 4 years ago by Pavel Dimens <[email protected]>
Update AlleleFreq.jl

github.com/BioJulia/PopGen.jl - 4a2aa7a3deda8eb2a30fe123d156666c35d181d5 authored over 4 years ago by Pavel Dimens <[email protected]>
add avg_allele_freq

this adds a function that returns a dictionary of the average allele frequencies across multuple...

github.com/BioJulia/PopGen.jl - 97fbf356258798b05b45c2add4757c35b61d83fd authored over 4 years ago by Pavel Dimens <[email protected]>
add avg_allele_freq

this adds a function that returns a dictionary of the average allele frequencies across multuple...

github.com/BioJulia/PopGen.jl_archive - 97fbf356258798b05b45c2add4757c35b61d83fd authored over 4 years ago by Pavel Dimens <[email protected]>
fix float conversion

github.com/BioJulia/PopGen.jl_archive - 73e611272e45181e8480ed9b72293818f1588502 authored over 4 years ago by Pavel Dimens <[email protected]>
fix float conversion

github.com/BioJulia/PopGen.jl - 73e611272e45181e8480ed9b72293818f1588502 authored over 4 years ago by Pavel Dimens <[email protected]>
extend nei het and fix reciprocal

github.com/BioJulia/PopGen.jl - 590bd6d7412f4040c9b68e14afa2db8f03318c01 authored over 4 years ago by Pavel Dimens <[email protected]>
extend nei het and fix reciprocal

github.com/BioJulia/PopGen.jl_archive - 590bd6d7412f4040c9b68e14afa2db8f03318c01 authored over 4 years ago by Pavel Dimens <[email protected]>
Update Project.toml

github.com/BioJulia/BioSequences.jl - 01fbc26dc6209e86ec13cdee5f8598469e98ff35 authored over 4 years ago by Ben J. Ward <[email protected]>
Update copying.jl (#109)

github.com/BioJulia/BioSequences.jl - 29d77d9f9a78c04703419090d7f92c4412a91b86 authored over 4 years ago by Ben J. Ward <[email protected]>
Update Project.toml

github.com/BioJulia/BioSequences.jl - f0848340fdcbb65ab65eb414a7d833d5f258ab4a authored over 4 years ago by Ben J. Ward <[email protected]>
Fixup addition with a BitIndex (#108)

github.com/BioJulia/BioSequences.jl - fb8b3a7e17c4b47f807206b3be129d1357aa08fc authored over 4 years ago by Ben J. Ward <[email protected]>
add genepop ibd output

github.com/BioJulia/PopGen.jl - 772f6d0e87a973b52899c5a33940228d79b17af6 authored over 4 years ago by Pavel Dimens <[email protected]>
add genepop ibd output

github.com/BioJulia/PopGen.jl_archive - 772f6d0e87a973b52899c5a33940228d79b17af6 authored over 4 years ago by Pavel Dimens <[email protected]>
test on Julia v1.0

github.com/BioJulia/BioStructures.jl - 1d934fb989c70bb720bab26dd09e5baa5456ab40 authored over 4 years ago by Joe Greener <[email protected]>
update docstrings

github.com/BioJulia/PopGen.jl - 4368180c37be6e89f078d488d4f4d75276bd0413 authored over 4 years ago by Pavel Dimens <[email protected]>
update docstrings

github.com/BioJulia/PopGen.jl_archive - 4368180c37be6e89f078d488d4f4d75276bd0413 authored over 4 years ago by Pavel Dimens <[email protected]>
add popdata2delimited

github.com/BioJulia/PopGen.jl_archive - 4c3f1cdf019d44ac106536c4cad98e6ba1552a78 authored over 4 years ago by Pavel Dimens <[email protected]>
add popdata2delimited

github.com/BioJulia/PopGen.jl - 4c3f1cdf019d44ac106536c4cad98e6ba1552a78 authored over 4 years ago by Pavel Dimens <[email protected]>
Update Project.toml

github.com/BioJulia/FASTX.jl - 345e3e935eb5795a28b43157211567dbc851fff1 authored over 4 years ago by Ben J. Ward <[email protected]>
Update index.md

github.com/BioJulia/FASTX.jl - 0f02681389bacc743833d9fabf111350c2e2b6ea authored over 4 years ago by Ben J. Ward <[email protected]>
Update README.md

github.com/BioJulia/FASTX.jl - 4c570fbf6bc37588c714d7083f526112d1b7e267 authored over 4 years ago by Ben J. Ward <[email protected]>
Support Julia LTS (#21)

github.com/BioJulia/FASTX.jl - 9c7285163ddec678a1b04ed612fc3761560649b2 authored over 4 years ago by Ben J. Ward <[email protected]>
Support LTS (#4)

github.com/BioJulia/FormatSpecimens.jl - 848829ed5472572187b8ae6ae2c6a933d3211b69 authored over 4 years ago by Ben J. Ward <[email protected]>
read_in => read_from

add `write_to`

github.com/BioJulia/PopGen.jl - 40cd934b1b4dcf05435de00a0b263d5089328ee0 authored over 4 years ago by Pavel Dimens <[email protected]>
read_in => read_from

add `write_to`

github.com/BioJulia/PopGen.jl_archive - 40cd934b1b4dcf05435de00a0b263d5089328ee0 authored over 4 years ago by Pavel Dimens <[email protected]>
Change from encode_copy! to copyto! as per change in BioSequences (#18)

github.com/BioJulia/FASTX.jl - 9a69972da599ffac513e8d10afd4c7dfabc2dcb0 authored over 4 years ago by Jakob Nybo Nissen <[email protected]>
Add StableRNGs Compat entry (#107)

ref https://github.com/BioJulia/BioSequences.jl/pull/106#issuecomment-638985043

github.com/BioJulia/BioSequences.jl - f8274b062999717042f1de9cc80b9fe1e46f7251 authored over 4 years ago by Kevin Bonham <[email protected]>
Update .gitignore

github.com/BioJulia/PopGen.jl - 4b62bd8565fbcdcb2480ac9accd924eef7821927 authored over 4 years ago by Pavel V. Dimens <[email protected]>
Update .gitignore

github.com/BioJulia/PopGen.jl_archive - 4b62bd8565fbcdcb2480ac9accd924eef7821927 authored over 4 years ago by Pavel V. Dimens <[email protected]>
Update Project.toml

github.com/BioJulia/BioSequences.jl - aef7d6689f9109be59a3070ffd2a0a3791508110 authored over 4 years ago by Ben J. Ward <[email protected]>
create genepop wrriter

github.com/BioJulia/PopGen.jl - 5c5ca48263436bff05a0eb96e7ae9541a7ba3a20 authored over 4 years ago by Pavel Dimens <[email protected]>
create genepop wrriter

github.com/BioJulia/PopGen.jl_archive - 5c5ca48263436bff05a0eb96e7ae9541a7ba3a20 authored over 4 years ago by Pavel Dimens <[email protected]>
Use stable RNG (#106)

github.com/BioJulia/BioSequences.jl - 07ffb8c07c75b8a2bf7505cda2e84d06995764b9 authored over 4 years ago by Jakob Nybo Nissen <[email protected]>
Fix reverse_complement orphan bug (#104)

github.com/BioJulia/BioSequences.jl - 22d54a99bd6592c18f6456b2c9c37fcf28286225 authored over 4 years ago by Jakob Nybo Nissen <[email protected]>
Support LTS (#101)

github.com/BioJulia/BioSequences.jl - 83adaefcbba6da8fcf367d6f763088a20f5af241 authored over 4 years ago by Ciarán O'Mara <[email protected]>
Re-add logical ops

github.com/BioJulia/BioSymbols.jl - ae96f92cfea5fca3b2127ef55dcbdac613800018 authored over 4 years ago by Jakob Nybo Nissen <[email protected]>
Move from reinterpret to encode

github.com/BioJulia/BioSymbols.jl - 7e6404e0f42cdf21fcd7f23ddf468679542397cd authored over 4 years ago by Jakob Nybo Nissen <[email protected]>
Remove biosymbol integer conversion

github.com/BioJulia/BioSymbols.jl - f9cac2f59ccf270e824d106ac715d2370567cba5 authored over 4 years ago by Jakob Nybo Nissen <[email protected]>
Update .gitignore

github.com/BioJulia/PopGen.jl_archive - 4853e012d883c6f8cf4d8c8604f737c8286bb10f authored over 4 years ago by Pavel Dimens <[email protected]>
Update .gitignore

github.com/BioJulia/PopGen.jl - 4853e012d883c6f8cf4d8c8604f737c8286bb10f authored over 4 years ago by Pavel Dimens <[email protected]>
Merge branch 'fstats' into dev

github.com/BioJulia/PopGen.jl - 850882ebe82547738dcb0e267f8ac78a78aff7b3 authored over 4 years ago by Pavel Dimens <[email protected]>
Merge branch 'fstats' into dev

github.com/BioJulia/PopGen.jl_archive - 850882ebe82547738dcb0e267f8ac78a78aff7b3 authored over 4 years ago by Pavel Dimens <[email protected]>
remove docs

and update logo

github.com/BioJulia/PopGen.jl_archive - 1e5ca7b44462762df2a76778fc389b9f132007e6 authored over 4 years ago by Pavel Dimens <[email protected]>
remove docs

and update logo

github.com/BioJulia/PopGen.jl - 1e5ca7b44462762df2a76778fc389b9f132007e6 authored over 4 years ago by Pavel Dimens <[email protected]>
Inbounds FASTQ parser (#20)

github.com/BioJulia/FASTX.jl - 4a0c465b9a364cd70b80506785b50b4ad11cdafd authored over 4 years ago by Jakob Nybo Nissen <[email protected]>
Add predicates

github.com/BioJulia/NTupleKmers.jl - b784f3402c2082d78a87226d6d3e52d4a5271f18 authored over 4 years ago by Ben J. Ward <[email protected]>
Implement BioSequences.jl style indexing

github.com/BioJulia/NTupleKmers.jl - fe583ce0f130f4197a57737b6a6970e4f4849ed7 authored over 4 years ago by Ben J. Ward <[email protected]>
Redesign the BitIndex and type traits

github.com/BioJulia/NTupleKmers.jl - b3de6e1cb9d018cb44edf6d1a14db63ac1d9c53e authored over 4 years ago by Ben J. Ward <[email protected]>