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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

So many changes

Edit df calculation in heterozygosity to n_exp_geno - n_obs_alleles. Split out Heterozygosity.jl...

github.com/BioJulia/PopGen.jl_archive - ec555f4b6d3bc18190a5d91cbee26d6c7414d544 authored over 4 years ago by Pavel Dimens <[email protected]>
So many changes

Edit df calculation in heterozygosity to n_exp_geno - n_obs_alleles. Split out Heterozygosity.jl...

github.com/BioJulia/PopGen.jl - ec555f4b6d3bc18190a5d91cbee26d6c7414d544 authored over 4 years ago by Pavel Dimens <[email protected]>
test with julia-1.4, update maintainers in README

github.com/BioJulia/SubstitutionModels.jl - 9233017509c2885cdd68eb7101e1718199151c20 authored over 4 years ago by Justin Angevaare <[email protected]>
small updates

github.com/BioJulia/PopGen.jl - 7841eea2e3cdd2598969a11d1204407ad12dfaea authored over 4 years ago by Pavel Dimens <[email protected]>
small updates

github.com/BioJulia/PopGen.jl_archive - 7841eea2e3cdd2598969a11d1204407ad12dfaea authored over 4 years ago by Pavel Dimens <[email protected]>
New version: XAM v0.2.1 (#61)

UUID: d759349c-bcba-11e9-07c2-5b90f8f05f7c
Repo: https://github.com/BioJulia/XAM.jl.git
Tree: 1a...

github.com/BioJulia/BioJuliaRegistry - a47b965fd6892a61aea7109fdaa46fe1ba46c91f authored over 4 years ago by Helix <[email protected]>
Use unsafe copy

github.com/BioJulia/XAM.jl - aec919c713b11cde218c92818a8dad4f448b6169 authored over 4 years ago by Ciarán O'Mara <[email protected]>
Merge branch 'hotfix/header'

github.com/BioJulia/XAM.jl - 6ae1180cfa1c9fc822f0a574ef825eecf3d5373b authored over 4 years ago by Ciarán O'Mara <[email protected]>
Merge branch 'master' into develop

github.com/BioJulia/XAM.jl - 429f69d84becac6411d84b5b1c1536be8741d934 authored over 4 years ago by Ciarán O'Mara <[email protected]>
Correct header parsing

github.com/BioJulia/XAM.jl - d0e2560ec4ba5f86aee9f3285304a9f9c16ec3fc authored over 4 years ago by Ciarán O'Mara <[email protected]>
Equality comparators

github.com/BioJulia/XAM.jl - e69c6de5867c94f9a2af5e1df2bdf064896eecdc authored over 4 years ago by Ciarán O'Mara <[email protected]>
Check header in roundtrip

github.com/BioJulia/XAM.jl - f6846edfb1eb4da1346756a7a73cd36b4fb2b4a0 authored over 4 years ago by Ciarán O'Mara <[email protected]>
Use broadcast

github.com/BioJulia/XAM.jl - cc2af1976bf0199b9da3f6ba0417285c7e8089da authored over 4 years ago by Ciarán O'Mara <[email protected]>
Use collect

github.com/BioJulia/XAM.jl - 08e253c297a82ecfdb598c01b7e037c3657f3392 authored over 4 years ago by Ciarán O'Mara <[email protected]>
Correct link

github.com/BioJulia/XAM.jl - 955cf8fbe2a46fcabea378eb596297599e0efc41 authored over 4 years ago by Ciarán O'Mara <[email protected]>
Increment version

github.com/BioJulia/XAM.jl - 031751f6b375cad59fc02c8550bbb599ce390666 authored over 4 years ago by Ciarán O'Mara <[email protected]>
chi sq fixes

Continuing the update for Chi Squared tests of hwe, added genotype obs/exp count functions, uniq...

github.com/BioJulia/PopGen.jl - 6810ddef9337b23c395b16cd394d03eeff1a8fcb authored over 4 years ago by Pavel <[email protected]>
chi sq fixes

Continuing the update for Chi Squared tests of hwe, added genotype obs/exp count functions, uniq...

github.com/BioJulia/PopGen.jl_archive - 6810ddef9337b23c395b16cd394d03eeff1a8fcb authored over 4 years ago by Pavel <[email protected]>
Update HardyWeinberg.jl

github.com/BioJulia/PopGen.jl_archive - f33ab563acc355bde2960e2dc8b3b4ddea7cabd9 authored over 4 years ago by Pavel <[email protected]>
Update HardyWeinberg.jl

github.com/BioJulia/PopGen.jl - f33ab563acc355bde2960e2dc8b3b4ddea7cabd9 authored over 4 years ago by Pavel <[email protected]>
fix allele_freq and add geno_freq_expected

fixed @async issue in allele_freq, along with moving expected genotype frequency calculations ou...

github.com/BioJulia/PopGen.jl - 6d53d55009e98ee7aee9300f7f9ea999e21d9df0 authored over 4 years ago by Pavel <[email protected]>
fix allele_freq and add geno_freq_expected

fixed @async issue in allele_freq, along with moving expected genotype frequency calculations ou...

github.com/BioJulia/PopGen.jl_archive - 6d53d55009e98ee7aee9300f7f9ea999e21d9df0 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_archive - 0f42bd9bd196c40d400074777c1310ffe3572e9a 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 - 0f42bd9bd196c40d400074777c1310ffe3572e9a authored over 4 years ago by Pavel <[email protected]>
Update Project.toml

github.com/BioJulia/PopGen.jl - 36008acb51906d890c639ea24a6145ff0e4e3079 authored over 4 years ago by Pavel <[email protected]>
Update Project.toml

github.com/BioJulia/PopGen.jl_archive - 36008acb51906d890c639ea24a6145ff0e4e3079 authored over 4 years ago by Pavel <[email protected]>
New version: XAM v0.2.0 (#59)

UUID: d759349c-bcba-11e9-07c2-5b90f8f05f7c
Repo: https://github.com/BioJulia/XAM.jl.git
Tree: 64...

github.com/BioJulia/BioJuliaRegistry - 00c0d150cd4e84418a9e942b99747bf7e0655bfd authored over 4 years ago by Helix <[email protected]>
Merge branch 'release/v0.2.0'

github.com/BioJulia/XAM.jl - c1397548450ebc373bc58e1fa91b862bbf97c4e9 authored over 4 years ago by Ciarán O'Mara <[email protected]>
Merge branch 'master' into develop

github.com/BioJulia/XAM.jl - 8279f545f5d9c6b575fb7f91c405cfbb776a0f22 authored over 4 years ago by Ciarán O'Mara <[email protected]>
Increment version

github.com/BioJulia/XAM.jl - 8702799593818ceaad2817a338e312a1b77d936b authored over 4 years ago by Ciarán O'Mara <[email protected]>
Merge branch 'feature/transcodingstreams' into develop

github.com/BioJulia/XAM.jl - 2aaab4d9ab53a1740b852e420ff8f42e6e7050e7 authored over 4 years ago by Ciarán O'Mara <[email protected]>
Update HardyWeinberg.jl

github.com/BioJulia/PopGen.jl - 17c4268b404941f87143732db92010e2348d8a29 authored over 4 years ago by Pavel V. Dimens <[email protected]>
Update HardyWeinberg.jl

github.com/BioJulia/PopGen.jl_archive - 17c4268b404941f87143732db92010e2348d8a29 authored over 4 years ago by Pavel V. Dimens <[email protected]>
continued updates for Heterozygosity

More patches/updates for the various heterozygosity function in HardyWeinberg.jl to work with th...

github.com/BioJulia/PopGen.jl_archive - de90ddb0a3b2b38c72b72bc7a4715aa92f13ef7c authored over 4 years ago by Pavel <[email protected]>
continued updates for Heterozygosity

More patches/updates for the various heterozygosity function in HardyWeinberg.jl to work with th...

github.com/BioJulia/PopGen.jl - de90ddb0a3b2b38c72b72bc7a4715aa92f13ef7c authored over 4 years ago by Pavel <[email protected]>
New version: XAM v0.1.1 (#58)

UUID: d759349c-bcba-11e9-07c2-5b90f8f05f7c
Repo: https://github.com/BioJulia/XAM.jl.git
Tree: c9...

github.com/BioJulia/BioJuliaRegistry - af8d2c9ba034d13582741c4d353fef834db30dd6 authored over 4 years ago by Helix <[email protected]>
Move isinteractive into machine

github.com/BioJulia/XAM.jl - 6cd89aba08cca53cc6888f6109edb7119907438e authored over 4 years ago by Ciarán O'Mara <[email protected]>
Quick fix for BioGenerics.ReaderHelper functions

This fix is likely to be replaced when migrating to TranscodingStreams.

github.com/BioJulia/XAM.jl - 365f7922fae84beea86a350e35887f3c54d8df18 authored over 4 years ago by Ciarán O'Mara <[email protected]>
Align emission symbols for TranscodingStreams

github.com/BioJulia/XAM.jl - 12db2c4ea84c1ba045f49ae2cbac7f6b518fe583 authored over 4 years ago by Ciarán O'Mara <[email protected]>
Migrate to BioGenerics

Basic find and replace.

github.com/BioJulia/XAM.jl - c4f3c4b0df70264cfba627263f9f7fb74c51666d authored over 4 years ago by Ciarán O'Mara <[email protected]>
Quick fix for BioCore.RecordHelper: unsafe_parse_decimal

github.com/BioJulia/XAM.jl - 2cad552f6308b28cd7a99aa3584da98716019bc4 authored over 4 years ago by Ciarán O'Mara <[email protected]>
Pipe into eval

github.com/BioJulia/XAM.jl - 892ad0d7dc8578fae4f9c24c4624561e5b8cfd54 authored over 4 years ago by Ciarán O'Mara <[email protected]>
Group Automa into readrecord.jl

github.com/BioJulia/XAM.jl - e63ce2e3986ada38e67f4e0b5477d8e541983299 authored over 4 years ago by Ciarán O'Mara <[email protected]>
Quick fix for BioCore.Ragel.State

This fix is likely to be replaced when migrating to TranscodingStreams.

github.com/BioJulia/XAM.jl - c59a1576755f109e989545e2510a433487b4ec3a authored over 4 years ago by Ciarán O'Mara <[email protected]>
Migrate from BufferedStreams to TranscodingStreams

github.com/BioJulia/XAM.jl - de56faf0667078ff20bb17747f77b0dd422af2d9 authored over 4 years ago by Ciarán O'Mara <[email protected]>
Flatten elseif

github.com/BioJulia/XAM.jl - 789cccbaff4c0a58fa6418c3ba0e90ce794114e7 authored over 4 years ago by Ciarán O'Mara <[email protected]>
Use accessor functions

github.com/BioJulia/XAM.jl - e8ad60b086d7a355718d0f4cf6a33a3bb4fd9a19 authored over 4 years ago by Ciarán O'Mara <[email protected]>
Preallocate

github.com/BioJulia/XAM.jl - b0069d6f27e19ab81f03024f56273c8897e1afdd authored over 4 years ago by Ciarán O'Mara <[email protected]>
Flatten returns

github.com/BioJulia/XAM.jl - ef99c703170e54e2e9873c13b47f8d46325fef25 authored over 4 years ago by Ciarán O'Mara <[email protected]>
Merge branch 'master' into develop

github.com/BioJulia/XAM.jl - 7a4d6d143d449ce458bed3e1f2eabf4b7f98a40d authored over 4 years ago by Ciarán O'Mara <[email protected]>
Merge branch 'hotfix/SAM'

github.com/BioJulia/XAM.jl - 5aca5f00111b5e220f637534d487485c308624f7 authored over 4 years ago by Ciarán O'Mara <[email protected]>
Flatten

github.com/BioJulia/XAM.jl - f272b410315c718bfbf76fecc82be37d07b91700 authored over 4 years ago by Ciarán O'Mara <[email protected]>
:white_check_mark: Enhanced unit test for rightposition (#37)

Added additional tests for SAM.Record and BAM.Record for `rightposition` (and implicitly...

github.com/BioJulia/XAM.jl - 6a33ac06a7a325de347950b8bb6a8f5beec782bb authored over 4 years ago by herbstk <[email protected]>
Increment version

github.com/BioJulia/XAM.jl - 6f03bef623cc52c7ce198c5b15e48a4d564b4715 authored over 4 years ago by Ciarán O'Mara <[email protected]>
:bug: Fix SAM.alignlength(record::Record)::Int (#37)

Fixes issue #37 by re-initializing `len` in `SAM.alignlength`.

github.com/BioJulia/XAM.jl - 8d14563f9d77cb0996ce6ab7839dc29d932e238f authored over 4 years ago by Konrad Herbst <[email protected]>
New version: Pseudoseq v0.2.0 (#57)

UUID: 5fa9f68e-f4b0-11e8-18b8-fb82dd3c6483
Repo: https://github.com/bioinfologics/Pseudoseq.jl....

github.com/BioJulia/BioJuliaRegistry - ad370d5e527a65411d001104076a18bc972978d8 authored over 4 years ago by Helix <[email protected]>
fix ioUtils, begin updates for heterozygosity

Added `hetero` function to control output when all genotypes of a locus in a population are miss...

github.com/BioJulia/PopGen.jl - 4a3764d3113a6916cfb0461473825bbbcb3063cd authored over 4 years ago by Pavel V. Dimens <[email protected]>
fix ioUtils, begin updates for heterozygosity

Added `hetero` function to control output when all genotypes of a locus in a population are miss...

github.com/BioJulia/PopGen.jl_archive - 4a3764d3113a6916cfb0461473825bbbcb3063cd 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 - c44707f3423cd36aaabbb56acb3a64085e4b9843 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 - c44707f3423cd36aaabbb56acb3a64085e4b9843 authored over 4 years ago by Pavel <[email protected]>
Update Project.toml

github.com/BioJulia/PopGen.jl - 550c0b4d3e08b298216a292609f1d07c642afe15 authored over 4 years ago by Pavel <[email protected]>
Update Project.toml

github.com/BioJulia/PopGen.jl_archive - 550c0b4d3e08b298216a292609f1d07c642afe15 authored over 4 years ago by Pavel <[email protected]>
Add the simple MerCount struct

github.com/BioJulia/KmerAnalysis.jl - 8e98ed3e979f13f5e28c8cd58c4f3bff81436cc8 authored over 4 years ago by Ben J. Ward <[email protected]>
Update juliaprimer.md

Minor spotfixes and clarifications

github.com/BioJulia/PopGen.jl - 0ae2890200a64610d00c34157627070efe1d4918 authored over 4 years ago by Pavel V. Dimens <[email protected]>
Update juliaprimer.md

Minor spotfixes and clarifications

github.com/BioJulia/PopGen.jl_archive - 0ae2890200a64610d00c34157627070efe1d4918 authored over 4 years ago by Pavel V. Dimens <[email protected]>
add determine_marker() and update delimited

added new function determine_marker() to ioUtils.jl, which is used to determine the marker type,...

github.com/BioJulia/PopGen.jl_archive - 8710a65e22856dd3ae0b86a8054905e56c247beb authored over 4 years ago by Pavel V. Dimens <[email protected]>
add determine_marker() and update delimited

added new function determine_marker() to ioUtils.jl, which is used to determine the marker type,...

github.com/BioJulia/PopGen.jl - 8710a65e22856dd3ae0b86a8054905e56c247beb authored over 4 years ago by Pavel V. Dimens <[email protected]>
update docs

github.com/BioJulia/PopGen.jl - 51fd0f571a3e84c156f78e22eb07f646e379af32 authored over 4 years ago by Pavel <[email protected]>
update docs

github.com/BioJulia/PopGen.jl_archive - 51fd0f571a3e84c156f78e22eb07f646e379af32 authored over 4 years ago by Pavel <[email protected]>
Update popobj_type.md

github.com/BioJulia/PopGen.jl_archive - d95345c48dfb6fedb7c5d9c0bb465a3b702f9f39 authored over 4 years ago by Pavel <[email protected]>
Update popobj_type.md

github.com/BioJulia/PopGen.jl - d95345c48dfb6fedb7c5d9c0bb465a3b702f9f39 authored over 4 years ago by Pavel <[email protected]>
update all the docs

github.com/BioJulia/PopGen.jl - d999702e7c563954d4565409b5b6f7204dc879b9 authored over 4 years ago by Pavel <[email protected]>
update all the docs

github.com/BioJulia/PopGen.jl_archive - d999702e7c563954d4565409b5b6f7204dc879b9 authored over 4 years ago by Pavel <[email protected]>
Add IndexedCounts

github.com/BioJulia/KmerAnalysis.jl - 94dd35af3f7828d2d98ea8d1aace41897e1577f0 authored over 4 years ago by Ben J. Ward <[email protected]>
update allele_freq and geno_freq

github.com/BioJulia/PopGen.jl - 16767f72f0be8aa4cdf929647d0b378860353bd0 authored over 4 years ago by Pavel <[email protected]>
update allele_freq and geno_freq

github.com/BioJulia/PopGen.jl_archive - 16767f72f0be8aa4cdf929647d0b378860353bd0 authored over 4 years ago by Pavel <[email protected]>
Add sticker

github.com/BioJulia/KmerAnalysis.jl - d0e09eb01af55e61cae7de3cb5e71de229f62cbc authored over 4 years ago by Ben J. Ward <[email protected]>
Add .gitignore and README

github.com/BioJulia/KmerAnalysis.jl - dc63574ecd01a898a8eba8de32010b0c3b1f0129 authored over 4 years ago by Ben J. Ward <[email protected]>
Add Project file and src file

github.com/BioJulia/KmerAnalysis.jl - 877c86cada2412dc96e0a254abc1fdc910ce0d77 authored over 4 years ago by Ben J. Ward <[email protected]>
CompatHelper: bump compat for "ReadDatastores" to "0.2" (#25)

Co-authored-by: Ben J. Ward <[email protected]>

github.com/BioJulia/GenomeGraphs.jl - 0966c2e25412bee1b195a3483d6690659e3b01b7 authored over 4 years ago by github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
New version: ReadDatastores v0.2.1 (#56)

UUID: 70a005b8-9d8a-11e9-0d98-c909fa2e52d2
Repo: https://github.com/BioJulia/ReadDatastores.jl.g...

github.com/BioJulia/BioJuliaRegistry - 376427a180c09d3f3eb72311bb1a3f5d36cb5c6d authored over 4 years ago by Helix <[email protected]>
Merge pull request #3 from JuliaTagBot/master

Install TagBot as a GitHub Action

github.com/BioJulia/GenomicAnnotations.jl - ba96a1afe6f637a082c594e196be8265900cf0df authored over 4 years ago by kdyrhage <[email protected]>
Export Datastorebuffer

github.com/BioJulia/ReadDatastores.jl - e902d27be69c72f6b20e2583d173185b8cad5738 authored over 4 years ago by Ben J. Ward <[email protected]>
Complete allele_freq

and add allele-freq-by-pop

github.com/BioJulia/PopGen.jl - cbfce6d9dbd46f91ef9ada4131f836a429237a70 authored over 4 years ago by Pavel <[email protected]>
Complete allele_freq

and add allele-freq-by-pop

github.com/BioJulia/PopGen.jl_archive - cbfce6d9dbd46f91ef9ada4131f836a429237a70 authored over 4 years ago by Pavel <[email protected]>
Update SummaryInfo.jl

github.com/BioJulia/PopGen.jl_archive - 82b581723c9dbe574a51a595d4ae3c81a3f5911e authored over 4 years ago by Pavel <[email protected]>
Update SummaryInfo.jl

github.com/BioJulia/PopGen.jl - 82b581723c9dbe574a51a595d4ae3c81a3f5911e authored over 4 years ago by Pavel <[email protected]>
update allele freq

add alleles(), allele_table(), update allele_avg

github.com/BioJulia/PopGen.jl - dab105854f655dc7e811c50f20621e8f1c5c73fa authored over 4 years ago by Pavel <[email protected]>
update allele freq

add alleles(), allele_table(), update allele_avg

github.com/BioJulia/PopGen.jl_archive - dab105854f655dc7e811c50f20621e8f1c5c73fa authored over 4 years ago by Pavel <[email protected]>
minor fixes

github.com/BioJulia/PopGen.jl_archive - 3de926eb750373b3eccbd1baaac36a619138ea78 authored over 4 years ago by Pavel <[email protected]>
minor fixes

github.com/BioJulia/PopGen.jl - 3de926eb750373b3eccbd1baaac36a619138ea78 authored over 4 years ago by Pavel <[email protected]>
remove @show_only

github.com/BioJulia/PopGen.jl - 4c0a471e7772caafdbe7c46daf265752d11ab029 authored over 4 years ago by Pavel <[email protected]>
remove @show_only

github.com/BioJulia/PopGen.jl_archive - 4c0a471e7772caafdbe7c46daf265752d11ab029 authored over 4 years ago by Pavel <[email protected]>
finish updating Manipulate to IndexedTables

github.com/BioJulia/PopGen.jl_archive - 8b5ceb888d52943cb748727795e4329b77bcb14a authored over 4 years ago by Pavel <[email protected]>
finish updating Manipulate to IndexedTables

github.com/BioJulia/PopGen.jl - 8b5ceb888d52943cb748727795e4329b77bcb14a authored over 4 years ago by Pavel <[email protected]>
Merge pull request #54 from BioJulia/registrator/microbiome/3bd8f0ae/v0.6.3

New version: Microbiome v0.6.3

github.com/BioJulia/BioJuliaRegistry - 383e308bf96b4a58ec370daf834c88e0c5e90445 authored over 4 years ago by Kevin Bonham <[email protected]>
New version: Microbiome v0.6.3

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

github.com/BioJulia/BioJuliaRegistry - 16640a2ee889c44def4c33f5bda5e46964474264 authored over 4 years ago by BioJuliaBot <[email protected]>
Initial commit

github.com/BioJulia/KmerAnalysis.jl - f064a361561724ab7bf3fe30be6c14df5d8aaee3 authored over 4 years ago by Ben J. Ward <[email protected]>
Fix Julia compat

github.com/BioJulia/MicrobiomePlots.jl - b7e4d49be9a7bb68442274f1099ed11c99b6ddbf authored over 4 years ago by Kevin Bonham <[email protected]>
Update julia version

github.com/BioJulia/MicrobiomePlots.jl - b9d9a9bdd7bea3703b5280ada5fc0bfb4273d03c authored over 4 years ago by Kevin Bonham <[email protected]>