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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

Add files via upload

github.com/BioJulia/PopGen.jl_archive - 0044d6292b52edc3b078feedca41595af8d3722e authored over 4 years ago by Pavel V. Dimens <[email protected]>
Add files via upload

github.com/BioJulia/PopGen.jl - 0044d6292b52edc3b078feedca41595af8d3722e authored over 4 years ago by Pavel V. Dimens <[email protected]>
Add files via upload

github.com/BioJulia/PopGen.jl - 2d30186a40fbaaa10bfa1d880ba6a2a2fa86c8a2 authored over 4 years ago by Pavel V. Dimens <[email protected]>
Add files via upload

github.com/BioJulia/PopGen.jl_archive - 2d30186a40fbaaa10bfa1d880ba6a2a2fa86c8a2 authored over 4 years ago by Pavel V. Dimens <[email protected]>
Seq-Lang blog post

github.com/BioJulia/biojulia.github.io - d784053b00d2d9bc2c823e1adc9487d69838e355 authored over 4 years ago by Ben J. Ward <[email protected]>
Exporting readgff and printgff

github.com/BioJulia/GenomicAnnotations.jl - 885a224e700af8d40f1f8efb98cc1ca304eb112d authored over 4 years ago by Karl Dyrhage <[email protected]>
Added support for trailing semicolons, and for multivalue attributes

github.com/BioJulia/GenomicAnnotations.jl - 00c5736e0c7269a74b24e961307536503e688263 authored over 4 years ago by Karl Dyrhage <[email protected]>
Added GFF parser

github.com/BioJulia/GenomicAnnotations.jl - fd0c1979f7e24a7d51b99f210195c88861708365 authored over 4 years ago by Karl Dyrhage <[email protected]>
Simplified genes_special_cases!()

github.com/BioJulia/GenomicAnnotations.jl - 965b0443f5fe7e86c0caae248a02aabdc9bd7246 authored over 4 years ago by Karl Dyrhage <[email protected]>
Remove SAM and BAM IO from documentation

github.com/BioJulia/BioAlignments.jl - d32d39626c84fbdc54f4293f58198faadaf60f99 authored over 4 years ago by Ciarán O'Mara <[email protected]>
Remove SAM and BAM

SAM and BAM code has been moved to https://github.com/BioJulia/XAM.jl.

github.com/BioJulia/BioAlignments.jl - a7f9f1620803a5cfd2de1546277f1175f626de5e authored over 4 years ago by Ciarán O'Mara <[email protected]>
Added up/downstream() and neighbour()

github.com/BioJulia/GenomicAnnotations.jl - a6b555b59c94698968282b3494346c22e28c28c1 authored over 4 years ago by Karl Dyrhage <[email protected]>
CompatHelper: bump compat for "Automa" to "0.8" (#40)

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

github.com/BioJulia/BioAlignments.jl - 09b7fd950750127024e8860e01f07e6639a91cb1 authored over 4 years ago by github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Update an email address

github.com/BioJulia/BioAlignments.jl - 7a3801289a9564acb24c1e364fe68c01cbd332e3 authored over 4 years ago by Ben J. Ward <[email protected]>
Fix julia compat line

github.com/BioJulia/BioAlignments.jl - 3d5439983b02ec67b204e5062fd93b16e907cea2 authored over 4 years ago by Ben J. Ward <[email protected]>
Release/v1.0.1 (#39)

* Update .gitignore

* Remove obsolete house keeping files

Code of conduct and contributing...

github.com/BioJulia/BioAlignments.jl - 4219d6522a976d6b92406cd30e23c4cc3d588602 authored over 4 years ago by Ciarán O'Mara <[email protected]>
summary() touchups

github.com/BioJulia/PopGen.jl_archive - d8ba022c4f139272525cb8a2cad4040c93469c24 authored almost 5 years ago by Pavel <[email protected]>
summary() touchups

github.com/BioJulia/PopGen.jl - d8ba022c4f139272525cb8a2cad4040c93469c24 authored almost 5 years ago by Pavel <[email protected]>
un-break gulfsharks

Very silly minor mistake ammended

github.com/BioJulia/PopGen.jl - b1704923762ff4c756b68dd41c5392afc650f1b0 authored almost 5 years ago by Pavel <[email protected]>
un-break gulfsharks

Very silly minor mistake ammended

github.com/BioJulia/PopGen.jl_archive - b1704923762ff4c756b68dd41c5392afc650f1b0 authored almost 5 years ago by Pavel <[email protected]>
fix docstrings and improve summary()

github.com/BioJulia/PopGen.jl_archive - 262cbb2808b64cda629a287061d577a39fbf0c66 authored almost 5 years ago by Pavel <[email protected]>
fix docstrings and improve summary()

github.com/BioJulia/PopGen.jl - 262cbb2808b64cda629a287061d577a39fbf0c66 authored almost 5 years ago by Pavel <[email protected]>
bump version to fix docs build

github.com/BioJulia/BioStructures.jl - 615a0d0833511a7587893e1aa3cf2f19a98c4b9d authored almost 5 years ago by Joe Greener <[email protected]>
fix doc build

github.com/BioJulia/BioStructures.jl - 767f3d7e9fdb4e5d2a15c4a9297a2d30e8721970 authored almost 5 years ago by Joe Greener <[email protected]>
Document and improve performance of resize! (#92)

* Document copy! and resize, improve resize! perf

* More tests of copy

github.com/BioJulia/BioSequences.jl - 762e309b872c5994be90ca1c3715c1d6882e1af3 authored almost 5 years ago by Jakob Nybo Nissen <[email protected]>
Add original authors

github.com/BioJulia/Indexes.jl - 5735676b2cc7d79eac868d0c51fe730e42fef56a authored almost 5 years ago by Ciarán O'Mara <[email protected]>
Generated files

github.com/BioJulia/Indexes.jl - fc06a7fee6c3f68e41b89e0e93ec3d95e08a97a8 authored almost 5 years ago by Ciarán O'Mara <[email protected]>
Initial commit

github.com/BioJulia/Indexes.jl - 0cf19e747da7d2822605df9cb550acf7d53fda7c authored almost 5 years ago by Ciarán O'Mara <[email protected]>
test on Julia 1.3

github.com/BioJulia/BioStructures.jl - cd83050764cb985567a991708305a187652d7e05 authored almost 5 years ago by Joe Greener <[email protected]>
correct error type thrown

github.com/BioJulia/BioStructures.jl - d62769ddceb6c88c69d5d6dadd255d12c5a09d00 authored almost 5 years ago by Joe Greener <[email protected]>
fix write function interpolation

github.com/BioJulia/BioStructures.jl - 62a2fab234aa1c2f27fbb64afe8649be58706828 authored almost 5 years ago by Joe Greener <[email protected]>
benchmark suite

github.com/BioJulia/BioStructures.jl - feac3012c50defea4c54e1472f3bcabfce060133 authored almost 5 years ago by Joe Greener <[email protected]>
update news, bump version

github.com/BioJulia/BioStructures.jl - 99dd1d7fbdb16ce7661e894a27c221a146aafa55 authored almost 5 years ago by Joe Greener <[email protected]>
suggest mmCIF/MMTF on PDB download fail

github.com/BioJulia/BioStructures.jl - a021cf0d1452ffa9582ad92d2617d53e7b5405e0 authored almost 5 years ago by Joe Greener <[email protected]>
Revamb copy! and copyto! interface

github.com/BioJulia/BioSequences.jl - 6a80f8e8cb603337a7efd1e14629c3bee0fc7cc1 authored almost 5 years ago by Jakob Nybo Nissen <[email protected]>
Update Project.toml

github.com/BioJulia/SubstitutionModels.jl - 4326e44b204505e47039cd4b08bd76fd94099718 authored almost 5 years ago by Justin Angevaare <[email protected]>
Merge pull request #24 from BioJulia/julia-one

Support BioSymbols 3.x to enable Julia 1.0 to pass

github.com/BioJulia/SubstitutionModels.jl - be880220bbc63a9e54d1bc32578ed539a5f8333e authored almost 5 years ago by Justin Angevaare <[email protected]>
Support BioSymbols 3.x to enable Julia 1.0 to pass?

github.com/BioJulia/SubstitutionModels.jl - 4404eb34f90dd105bc834b01ead6c94cbfbced77 authored almost 5 years ago by Justin Angevaare <[email protected]>
Merge pull request #23 from BioJulia/compathelper/new_version/2020-01-19-01-04-50-082-1406933593

CompatHelper: add new compat entry for "BioSymbols" at version "4.0"

github.com/BioJulia/SubstitutionModels.jl - 72c41548781e2ca356e9bf58365ecc3e21807fa4 authored almost 5 years ago by Justin Angevaare <[email protected]>
Merge branch 'master' into compathelper/new_version/2020-01-19-01-04-50-082-1406933593

github.com/BioJulia/SubstitutionModels.jl - f45775c07e8ec270c91b1aa64ffcca0a7dddc757 authored almost 5 years ago by Justin Angevaare <[email protected]>
Merge pull request #22 from BioJulia/compathelper/new_version/2020-01-19-01-04-44-795-2211115710

CompatHelper: add new compat entry for "StaticArrays" at version "0.12"

github.com/BioJulia/SubstitutionModels.jl - ef2b0c4d1e184961528ea662951e108b79cf85f2 authored almost 5 years ago by Justin Angevaare <[email protected]>
Create TagBot.yml

github.com/BioJulia/SubstitutionModels.jl - 44d0d417442fbb0181f0143a4fe6c1c9c52dc9a3 authored almost 5 years ago by Justin Angevaare <[email protected]>
Create docs.yml

github.com/BioJulia/SubstitutionModels.jl - fa5b3395c2ef9cdf64b459ae9c9f2cf44f05aa17 authored almost 5 years ago by Justin Angevaare <[email protected]>
add BioJuliaRegistry, 1.3 testing

github.com/BioJulia/SubstitutionModels.jl - ff780913771ebbf70c01bd389f4f5c3fd15362ef authored almost 5 years ago by Justin Angevaare <[email protected]>
CompatHelper: add new compat entry for "BioSymbols" at version "4.0"

github.com/BioJulia/SubstitutionModels.jl - 237a76ff028db2de3fed5e095b8abdf011efd5f0 authored almost 5 years ago by github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
CompatHelper: add new compat entry for "StaticArrays" at version "0.12"

github.com/BioJulia/SubstitutionModels.jl - 2ce7a357a0bbab1dfa2fa1a6a91a2a308f67029a authored almost 5 years ago by github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Update CompatHelper.yml

Add BioJulia repository

github.com/BioJulia/SubstitutionModels.jl - da1e2794b8c4164980ff188a4662ee3d83d42b18 authored almost 5 years ago by Justin Angevaare <[email protected]>
Create CompatHelper.yml

github.com/BioJulia/SubstitutionModels.jl - 4f1dbc742281142122846429e134c9c188c4bbc1 authored almost 5 years ago by Justin Angevaare <[email protected]>
Misc fixes (#93)

github.com/BioJulia/BioSequences.jl - bd7dd9bfc3228303ac8700dc81a7cb0c4d7f6d1c authored almost 5 years ago by Jakob Nybo Nissen <[email protected]>
allow writing of empty containers

github.com/BioJulia/BioStructures.jl - c98ec2ad2a2642dd7eab3d34de123abd7d4ae814 authored almost 5 years ago by Joe Greener <[email protected]>
remove redundant writepdb method

github.com/BioJulia/BioStructures.jl - 7cdf3dff49e10800e7d9ed56397f97619f254021 authored almost 5 years ago by Joe Greener <[email protected]>
remove redundant writemmcif method

github.com/BioJulia/BioStructures.jl - 00bb860a07f058564a168ad3e1f9a68ac1864147 authored almost 5 years ago by Joe Greener <[email protected]>
restrict downloadable types

github.com/BioJulia/BioStructures.jl - d4a2146c0df1a980bb50c6ff2612053a5d738541 authored almost 5 years ago by Joe Greener <[email protected]>
remove double line breaks

github.com/BioJulia/BioStructures.jl - 4101b459bb607e734cfb245f161d0b2676219664 authored almost 5 years ago by Joe Greener <[email protected]>
MMTF docs

github.com/BioJulia/BioStructures.jl - 57c23716bf4775a6cadbc79963a447974b694338 authored almost 5 years ago by Joe Greener <[email protected]>
Examples as separate docs section

github.com/BioJulia/BioStructures.jl - d827e4e3892aa545388db2909b464e8e647851d2 authored almost 5 years ago by Joe Greener <[email protected]>
switch writemmtf to atom list loop

github.com/BioJulia/BioStructures.jl - 25d95192ccc600efb100167a089c8f844004a626 authored almost 5 years ago by Joe Greener <[email protected]>
New version: Microbiome v0.6.1 (#37)

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

github.com/BioJulia/BioJuliaRegistry - ba539db23180201852cf9f89c020f2472e3bc208 authored almost 5 years ago by Helix <[email protected]>
CompatHelper: bump compat for "Colors" to "0.11"

github.com/BioJulia/MicrobiomePlots.jl - a0a9c208bc831f105188cea9d806ff76799cdc33 authored almost 5 years ago by github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Faster printing (#91)

github.com/BioJulia/BioSequences.jl - 1f6706a6b04ffb070b03a0b0268206c83573512e authored almost 5 years ago by Jakob Nybo Nissen <[email protected]>
add compat helper

github.com/BioJulia/MicrobiomePlots.jl - 0baf9ad8fea1f95cda70a016f2bdc82cd9ebe4d3 authored almost 5 years ago by Kevin Bonham <[email protected]>
Merge pull request #4 from BioJulia/updates

Updates

github.com/BioJulia/MicrobiomePlots.jl - e8173807b49476938587713c151a596503c6f414 authored almost 5 years ago by Kevin Bonham <[email protected]>
New package: GenomeGraphs v0.1.0 (#36)

UUID: 3aa97884-90e5-11e8-2134-af657ec4f203
Repo: https://github.com/BioJulia/GenomeGraphs.jl.gi...

github.com/BioJulia/BioJuliaRegistry - 4c146bb0774afd439639eef21c95e978e537a7a2 authored almost 5 years ago by Helix <[email protected]>
Add MerTools submodule (#18)

github.com/BioJulia/GenomeGraphs.jl - fff259b93f2817cb8179501f35bacb895eed2e40 authored almost 5 years ago by Ben J. Ward <[email protected]>
Update the documentation setup

github.com/BioJulia/GenomeGraphs.jl - 655dd31260964248fd6a534a3a30de0aaa259c41 authored almost 5 years ago by Ben J. Ward <[email protected]>
Introduce Graphs submodule

github.com/BioJulia/GenomeGraphs.jl - a0afae92f5b8773696fafa21fd4ed66598d7ece1 authored almost 5 years ago by Ben J. Ward <[email protected]>
Implement draft of perfect circle resolution for the dbg constructor (#16)

Perfect circles don't have ends and so the kmers involved in them don't get incorporated into
a...

github.com/BioJulia/GenomeGraphs.jl - f974941d03d225d5b70c764d2396e3d6bc66ca28 authored almost 5 years ago by Ben J. Ward <[email protected]>
Cleanup clutter and edit project files

github.com/BioJulia/GenomeGraphs.jl - e98a83a846e72983f80590a4efba20cbd8eb7819 authored almost 5 years ago by Ben J. Ward <[email protected]>
Merge tip-clipping from GSoC into GenomeGraphs framework (#15)

github.com/BioJulia/GenomeGraphs.jl - 9ea3cb30beabcb23b475d261b14591b70a584335 authored almost 5 years ago by Ben J. Ward <[email protected]>
Add the basic NodeView type

github.com/BioJulia/GenomeGraphs.jl - 8b412b464e6883fab57da4ce7a3fe3f6bf9c9999 authored almost 5 years ago by Ben J. Ward <[email protected]>
Rename BioSequenceGraphs to GenomeGraphs

github.com/BioJulia/GenomeGraphs.jl - b001fbbfa22f45ea96b1e33a254918b10a8b3218 authored almost 5 years ago by Ben J. Ward <[email protected]>
Add GraphIndexes API manual page

Minor fixes to project files

github.com/BioJulia/GenomeGraphs.jl - 5d27a2e3b9510f24007090f2bd502e38255329c8 authored almost 5 years ago by Ben J. Ward <[email protected]>
Update the documentation setup

github.com/BioJulia/GenomeGraphs.jl - d97e1211e42f9280afbfc8a9badb1ec93ca7129e authored almost 5 years ago by Ben J. Ward <[email protected]>
Add a UniqueMerIndex

The UniqueMerIndex indexes unique mers in a graph, to the node and position in the node
at which...

github.com/BioJulia/GenomeGraphs.jl - 377bb0d4f0e381c94fa3c6a229ab26b8207dbfe3 authored almost 5 years ago by Ben J. Ward <[email protected]>
Add new compat entry for "FASTX" (#20)

github.com/BioJulia/GenomeGraphs.jl - 6a7199e29d67a337eea20839b3d7e799efdd5e30 authored almost 5 years ago by github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Add mer count datastores

github.com/BioJulia/GenomeGraphs.jl - 53882385da1a8e8d29ab038ed6417326b73a0a1e authored almost 5 years ago by Ben J. Ward <[email protected]>
Add new compat entry for "ReadDatastores" (#21)

github.com/BioJulia/GenomeGraphs.jl - 7d5c8b40d09e21a9cdddfc238753af9c71343dac authored almost 5 years ago by github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Create GraphIndexes submodule

github.com/BioJulia/GenomeGraphs.jl - e5bbb7ed58356f393981d5ee8e96f4f3cb5503ef authored almost 5 years ago by Ben J. Ward <[email protected]>
Add a first rough draft of the dbg process

It currently does no error correction or tip clipping

Support BigMers for dbg process

github.com/BioJulia/GenomeGraphs.jl - c88ad7d7a205d2fd360ec81a921a6693b1260365 authored almost 5 years ago by Ben J. Ward <[email protected]>
Generated files

github.com/BioJulia/XAM.jl - 07c0f925e624ede0068951e6e915a55aabf01581 authored almost 5 years ago by Ciarán O'Mara <[email protected]>
Brief description

github.com/BioJulia/XAM.jl - c8d7ea0524b7a48a1152c7dad54888c3f4607ca4 authored almost 5 years ago by Ciarán O'Mara <[email protected]>
Initial commit

github.com/BioJulia/XAM.jl - a8133f431608b36fa0574e3ab2d392900f5d5a79 authored almost 5 years ago by Ciarán O'Mara <[email protected]>
Update .travis.yml

github.com/BioJulia/BioJuliaRegistry - a980ddfa270283549b535b47f2ebb81fc296ea92 authored almost 5 years ago by Ben J. Ward <[email protected]>
Don't test Windows

github.com/BioJulia/ReadDatastores.jl - 1569bc5afcd5380a29e62df4979d50eb00fce208 authored almost 5 years ago by Ben J. Ward <[email protected]>
Add GitHub actions

github.com/BioJulia/ReadDatastores.jl - c9217da91cca03154291940d304a5e39012fe4d3 authored almost 5 years ago by Ben J. Ward <[email protected]>
Implement generic methods for commonly used functions and export them (#11)

* Implement generic methods for commonly used functions and export them

* Remove generic meth...

github.com/BioJulia/FASTX.jl - c7ca87cbfab14c0f08085402bdc33e380a379169 authored almost 5 years ago by Harry Scholes <[email protected]>
CompatHelper: bump compat for "Automa" to "0.8" (#16)

github.com/BioJulia/FASTX.jl - db1a910d3e0932fe8f00838cb26bf02d9ac4a4d4 authored almost 5 years ago by github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
CompatHelper: add new compat entry for "Combinatorics" at version "1.0" (#89)

github.com/BioJulia/BioSequences.jl - 5beeaeaf89f321fbc6a8a75fef818c52ab859b82 authored almost 5 years ago by github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
CompatHelper: add new compat entry for "BioGenerics" at version "0.1" (#90)

github.com/BioJulia/BioSequences.jl - 9329b55625a9d340431f19447f3ee5acc9f303ba authored almost 5 years ago by github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Merge branch 'master' of github.com:BioJulia/FASTX.jl

github.com/BioJulia/FASTX.jl - 6d48e3904c9e4e7f154e0868d578b2d737bfa57f authored almost 5 years ago by Ben J. Ward <[email protected]>
Add CompatHelper

github.com/BioJulia/FASTX.jl - 808a0b45c79e56cd37f3747382c5659d2dafa0f4 authored almost 5 years ago by Ben J. Ward <[email protected]>
Add the CompatHelper

github.com/BioJulia/BioSequences.jl - 59b3f7d86746b3ec9bef19cb993d5561e771c6a3 authored almost 5 years ago by Ben J. Ward <[email protected]>
Fix orphan! bug (#88)

* Fix orphan! bug

* Optimize resize! of LongSequence

github.com/BioJulia/BioSequences.jl - dad9fa8c1e8a219750031d62e72a8ed65f089c7a authored almost 5 years ago by Jakob Nybo Nissen <[email protected]>
Add TagBot

github.com/BioJulia/BioSequences.jl - 83ef24489f36c7a214b7a0f7ecb1bfd3492c94d4 authored almost 5 years ago by Ben J. Ward <[email protected]>
Faster reverse! of LongSequence (#84)

* Faster, simpler sequence reversion

* Review 1: Faster reversion

* SIMD reversion, remove...

github.com/BioJulia/BioSequences.jl - 9d6decb0c2ba5d437cdbb5b48f93c72413131e3d authored almost 5 years ago by Jakob Nybo Nissen <[email protected]>
Add copy! method to LongSequence (#87)

* Add copy! method to LongSequence

* Add seq to seq copy! method

github.com/BioJulia/BioSequences.jl - 2c84165b937c16b05380e0797d66e834349f41c0 authored almost 5 years ago by Jakob Nybo Nissen <[email protected]>
quick FASTA.identifier(record) example (#15)

to save 30mins of pain

github.com/BioJulia/FASTX.jl - 6485a52ca5479aa64ca35a001534b210f8128fc4 authored almost 5 years ago by dehann <[email protected]>
Use the registered version of RegistryCI.jl (#34)

github.com/BioJulia/BioJuliaRegistry - 65369c7d5398bce7a74ed27c4c46be11f719062d authored almost 5 years ago by Dilum Aluthge <[email protected]>
New version: BioSymbols v4.0.3 (#33)

UUID: 3c28c6f8-a34d-59c4-9654-267d177fcfa9
Repo: https://github.com/BioJulia/BioSymbols.jl.git
T...

github.com/BioJulia/BioJuliaRegistry - 117e559aadf727ba3f31ce058e38b00c29b6d884 authored almost 5 years ago by Helix <[email protected]>
Update Project.toml

github.com/BioJulia/BioSymbols.jl - 1a394fa15a73e62a75230a1853acbe87d081dad4 authored almost 5 years ago by Ben J. Ward <[email protected]>