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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

Correct username in README.md

github.com/BioJulia/Kmers.jl - b5713baea348a50d0a99eb5519c489bdb7c63096 authored over 7 years ago by Kevin Murray <[email protected]>
Update README.md

github.com/BioJulia/Kmers.jl - aecdd9416e228a211a5af408aa5d987c0bffe88d authored over 7 years ago by Ben J. Ward <[email protected]>
Create README.md

github.com/BioJulia/Kmers.jl - cef8a7a9a08ae5ae5b17a2a5e76d0398ff54fedc authored over 7 years ago by Ben J. Ward <[email protected]>
Initial commit

github.com/BioJulia/Kmers.jl - 48cb7e518e9ea69fd367c5fef35ec7e902e9169d authored over 7 years ago by Ben J. Ward <[email protected]>
rename some accessor functions of GFF3 (#450)

github.com/BioJulia/Bio.jl - 48f297c507ceb787a7720f6ce918e1599ee401fa authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
add more FASTQ constructors (#451)

github.com/BioJulia/Bio.jl - eebd0e0601f8a28ff8279896f6d8fb41799789ca authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
add FASTQ module (#448)

github.com/BioJulia/Bio.jl - a4b978f057943f0fa28d567dc7619bf7d0e410d1 authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
fix doctests (#449)

github.com/BioJulia/Bio.jl - 37eb550f9c546a1149504cbde35032fa924a66d9 authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
add linewrap tags in FASTQ (#20)

github.com/BioJulia/BioFmtSpecimens - 49311feb1e5a88af140fe76f3e4a268271a3b9cc authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
add kmer_str macro to allow kmer string literals (#446)

github.com/BioJulia/Bio.jl - ccb05de6d756b7771e0c4872ed8092d94f98c725 authored over 7 years ago by Kevin Murray <[email protected]>
add SAM and BAM modules (#440)

github.com/BioJulia/Bio.jl - 621123a2ed1a9b4f6ae933c06fd12e41b809d990 authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Minor doc edits

github.com/BioJulia/BioServices.jl - 03847a6c6319dfdbba36222de51e74879b7c4ef0 authored over 7 years ago by Ben J. Ward <[email protected]>
Merge remote-tracking branch 'origin/master'

github.com/BioJulia/Contributing - 135118a70cdb69fd576c9a913ad6cf862f60fb2e authored over 7 years ago by Ben J. Ward <[email protected]>
Added the contributor covenant

github.com/BioJulia/Contributing - 5cd0f1e22cf521e45818bb7855a57424e8b02058 authored over 7 years ago by Ben J. Ward <[email protected]>
Edited make

github.com/BioJulia/BioServices.jl - ebcf3b0a0aa41bc9dc2c52f31a10b91b2978a9fb authored over 7 years ago by Ben J. Ward <[email protected]>
Added Requests to the require file.

github.com/BioJulia/BioServices.jl - cb05e2dbbb93f465d550963827489ed25e7f00a6 authored over 7 years ago by Ben J. Ward <[email protected]>
use BioSymbols.jl (#443)

github.com/BioJulia/Bio.jl - 235c90c0e089b46d7fa9bf6897e6893dbcfecf5a authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Use Bio.Seq.mismatches in demulitplexer (#445)

Removes the less optimised hamming_distance function created for this package.

github.com/BioJulia/Bio.jl - 04e15a345e07b52c7c77341fa2d11d35ef52f809 authored over 7 years ago by Kevin Murray <[email protected]>
update docs (#8)

github.com/BioJulia/BioSymbols.jl - da0fb8f37acf6776e6b77a406dc46281b772797d authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Update NEWS.md (#444)

github.com/BioJulia/Bio.jl - 19976bd0d325ef59e181f7386c4dd317c5726d83 authored over 7 years ago by Ben J. Ward <[email protected]>
Edited require

github.com/BioJulia/BioServices.jl - 0c806057ee7045091e7d53f605b377050bbfa411 authored over 7 years ago by Ben J. Ward <[email protected]>
Create README.md

github.com/BioJulia/BioServices.jl - 2b8f180bbcf4d2915b9bf733eb5ceab3594c3e74 authored over 7 years ago by Ben J. Ward <[email protected]>
Added first set of files

github.com/BioJulia/BioServices.jl - 05b10936926339cbe0ef297c452713cc60987df8 authored over 7 years ago by Ben J. Ward <[email protected]>
Initial commit

github.com/BioJulia/BioServices.jl - a60650dd07145c5830f13b5a750dafb34ff1f5a2 authored over 7 years ago by Ben J. Ward <[email protected]>
Initial commit

github.com/BioJulia/BioTools.jl - d945378e38a20f0172a506144d9b4e5eed0e90ab authored over 7 years ago by Ben J. Ward <[email protected]>
fix package name in docs (#7)

github.com/BioJulia/BioSymbols.jl - 9dc6576df1e84a549fbd59e1734f8515201cbcbf authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
export the ACGTN constant (#442)

github.com/BioJulia/Bio.jl - 16ae2e70d13004e3ee7012a0567b5bdbf4a924e7 authored over 7 years ago by Kevin Murray <[email protected]>
Fix to make.jl in docs

github.com/BioJulia/BioSymbols.jl - f70c1ca7824173b69f073c0b3f2fc6e25f4803d0 authored over 7 years ago by Ben J. Ward <[email protected]>
export ACGTN and ACGUN (#6)

github.com/BioJulia/BioSymbols.jl - 0dbbf631fa67904446e5c341fda2a5a033163227 authored over 7 years ago by Ben J. Ward <[email protected]>
fix compare when tagging not-latest version (#24)

github.com/BioJulia/attobot - cb41c4fc86193098530339a9774fabbad1b1e058 authored over 7 years ago by Simon Byrne <[email protected]>
do not print newlines in sequence by default (#441)

github.com/BioJulia/Bio.jl - 472fff302c1b651b2f24deb97553113a82fe223b authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Deconstruct Phylo (#438)

github.com/BioJulia/Bio.jl - 7782a111468e1e186dfee41880f8112a1be1ac9f authored over 7 years ago by Ben J. Ward <[email protected]>
Removed compat from src

github.com/BioJulia/Phylogenies.jl - ca021549dc4ce15560f4c64f8c32835aa891ad57 authored over 7 years ago by Ben J. Ward <[email protected]>
Added distributions

github.com/BioJulia/Phylogenies.jl - 281490eba32aac4e9788577fe4c4725bfc7b797e authored over 7 years ago by Ben J. Ward <[email protected]>
Remove compat

github.com/BioJulia/Phylogenies.jl - cb9ea094d07c27559b681a779d9d87950e3e6f8a authored over 7 years ago by Ben J. Ward <[email protected]>
Edit to docs

github.com/BioJulia/Phylogenies.jl - 10557ba30207c316963052e06a15f97471eb40f1 authored over 7 years ago by Ben J. Ward <[email protected]>
Update manpages

github.com/BioJulia/Phylogenies.jl - 7ff23a8700603d420d5a547db85c03a477cf6fc2 authored over 7 years ago by Ben J. Ward <[email protected]>
Added readme

github.com/BioJulia/Phylogenies.jl - 75c227d5101799181e1176a67f5d06947ba88b28 authored over 7 years ago by Ben J. Ward <[email protected]>
Update compat

github.com/BioJulia/Phylogenies.jl - 8607f0769f880e265cad85706a2b372f73b9ac77 authored over 7 years ago by Ben J. Ward <[email protected]>
Update mkdocs.yml

github.com/BioJulia/Contributing - acbd5ae28a11f533d45d1d422464897caa0a6e03 authored over 7 years ago by Ben J. Ward <[email protected]>
Moved pull requests to policy

github.com/BioJulia/Contributing - 65776975412afec7abe09664ab8c53ef5e6973e4 authored over 7 years ago by Ben J. Ward <[email protected]>
Moved docs to a policy folder

github.com/BioJulia/Contributing - f9f3ca3a9edde9f7ed752595d12ee43090076e00 authored over 7 years ago by Ben J. Ward <[email protected]>
Add travis and appveyor configuration

github.com/BioJulia/Phylogenies.jl - 89bd70e3fd242982c01045936c0ac67d495776eb authored over 7 years ago by Ben J. Ward <[email protected]>
Added tests and docs.

github.com/BioJulia/Phylogenies.jl - a0c6ae8de50427c1a8de80e651d19b0bc99c56d2 authored over 7 years ago by Ben J. Ward <[email protected]>
Minor changes to mkdocs and types.md (#5)

github.com/BioJulia/BioSymbols.jl - 71cc62f1f3b670d5c2fd2c8af5719e66d7031d93 authored over 7 years ago by Ben J. Ward <[email protected]>
restructure files in type-centric way (#4)

github.com/BioJulia/BioSymbols.jl - ba23a9ad2b4a9d9e01b0556e5ae633d319352c65 authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
improve test coverage (#3)

github.com/BioJulia/BioSymbols.jl - e6b9fdac756529f52212d082b3a79184faf7142d authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
add a converage badge to README.md (#2)

github.com/BioJulia/BioSymbols.jl - 7b3e8b241e7ed04b1fb556059c3c49a9aa0aa9e8 authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
move 2bit tools under Bio.Seq.TwoBit (#431)

github.com/BioJulia/Bio.jl - 4b9dbb1fae2906db7eed646f6028ac68cdf8f421 authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
add VCF and BCF modules (#433)

github.com/BioJulia/Bio.jl - 52835822483ad1e97e1255b660a4898605906faa authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
remove takebuf_string from tests (#1)

github.com/BioJulia/BioSymbols.jl - 07306d673924abae16e327e289358fa2b20600c0 authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
speed up Bio.Structure parsing (#430)

* typo fix

* parse functions for each part of PDB line

* tests for new parsing functions

github.com/BioJulia/Bio.jl - 55417e8a577af2231d0a3c91fca478ee3f31e77c authored over 7 years ago by Joe Greener <[email protected]>
Added off-boarding guidelines

github.com/BioJulia/Contributing - 733deb707e1b04a9be8839b40d2674f0db7d4537 authored over 7 years ago by Ben J. Ward <[email protected]>
Update to the mkdocs config file.

github.com/BioJulia/Contributing - a0b51d75038fe0abd7dcf24392d4e74106fcd027 authored over 7 years ago by Ben J. Ward <[email protected]>
Genomic Distances using MASH (#415)

* begin MASH

* add minhash + tests

* add some documentation to minhash

* add functions ...

github.com/BioJulia/Bio.jl - e49e34324114ab1d548104417a2850c2a9bae495 authored over 7 years ago by Kevin Bonham <[email protected]>
ABIF Reader (#353)

* Implement ABIF Reader

* Basic reader for ABIF File Format - Applied Biosystems

* http://...

github.com/BioJulia/Bio.jl - 032087b8f0df7fc7b3bb76d81038692022e4d4b0 authored over 7 years ago by Marcio Giaxa Marinheiro <[email protected]>
rewrite BED (#418)

github.com/BioJulia/Bio.jl - 999cb1dac0fc399ca45542672f1d645ad3318d85 authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
fix some Bio.Var tests (#432)

github.com/BioJulia/Bio.jl - 725fc9eb9381ec75675547d8157fd6a3efd3d2d6 authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
implement eachoverlap (and remove intersect) (#426)

github.com/BioJulia/Bio.jl - 2aebb141d9ba66629e8aab71084bbd6c51c72803 authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Add description() and identifier() to FASTA export (#428)

github.com/BioJulia/Bio.jl - 96bd4573f327f720ba519cc5a91cec660e200918 authored over 7 years ago by Kevin Bonham <[email protected]>
update README

github.com/BioJulia/IntervalTrees.jl - 1f1bb8b510e508a1f8969f7e0ebde5968ecdbfd6 authored over 7 years ago by Kenta Sato <[email protected]>
support Julia v0.6 and drop Julia 0.4 (#24)

github.com/BioJulia/IntervalTrees.jl - 600a3f9d94aefce06cbe2900fece7f96f8256604 authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Added src files

Added IO, Ragel, ReaderHelper, StringFields

Added ds_store to gitignore

github.com/BioJulia/BioCore.jl - 21948e23605d8bc2172d596521ceb527e2656e14 authored over 7 years ago by Ben J. Ward <[email protected]>
readme commit

github.com/BioJulia/Community-Issues - bb66310cec151bad7e0b20fc7a47f59713f1cf14 authored over 7 years ago by Ben J. Ward <[email protected]>
Added src folder

github.com/BioJulia/Phylogenies.jl - 03f01b1ffd6e5195d56910cd43813b8af29c395f authored over 7 years ago by Ben J. Ward <[email protected]>
Added compat minimum version

Rename of package

Minor test fixes

Rename

Minor change to file header

github.com/BioJulia/BioSymbols.jl - c87580388b10088e044a899a98038b24e65717e5 authored over 7 years ago by Ben J. Ward <[email protected]>
Changed BiologicalSymbols to BioSymbols

github.com/BioJulia/assets - d695373072e63f3b8b538441ec569612ca75ff02 authored over 7 years ago by Ben J. Ward <[email protected]>
add string ending to version regex, fixes #20

github.com/BioJulia/attobot - c7ef73120f00cbd915c68736dd6f8dea4deb4ac2 authored over 7 years ago by Simon Byrne <[email protected]>
Initial commit

github.com/BioJulia/Phylogenies.jl - 29ef45c9c5fe122104fe30e4acf68d5c79069bc0 authored over 7 years ago by Ben J. Ward <[email protected]>
Corrected readme typo

github.com/BioJulia/BioSymbols.jl - dfe07e28ff3304b6e33bbac121f97aa456a82d9d authored over 7 years ago by Ben J. Ward <[email protected]>
Revert "Corrected readme typo"

This reverts commit f192cf0e59a1b8fff76b4bc62d62cc2659984bc3.

github.com/BioJulia/BioSymbols.jl - 2cbfb1d22b126be6694a3a73f8e49486d51f0728 authored over 7 years ago by Ben J. Ward <[email protected]>
Added nucleic acids, amino acids, and setup integrations & docs

Edited docbuilding

Corrected some docs

Corrected make.jl

Corrected doctests

Added docs ...

github.com/BioJulia/BioSymbols.jl - 7e236aaefcf0cc3d998b8db77fa5f7cfe7cfde9f authored over 7 years ago by Ben J. Ward <[email protected]>
Moved NucleicAcids assets to BiologicalSymbols assets.

github.com/BioJulia/assets - 7b4167f178bd4273d96d4bce2790deb1721cea18 authored over 7 years ago by Ben J. Ward <[email protected]>
Initial commit

github.com/BioJulia/BioSymbols.jl - 5c788968f011edfaa408d9b02cf14cabdc8d441f authored over 7 years ago by Ben J. Ward <[email protected]>
Edited Nucleotide branding names

github.com/BioJulia/assets - c325c99d936abf9af8a47856d0eca24144bf0753 authored over 7 years ago by Ben J. Ward <[email protected]>
Added Nucleotides graphics assets

github.com/BioJulia/assets - 9c1e6ea8b7626418fa22d4b2bd7af05850c028cd authored over 7 years ago by Ben Ward <[email protected]>
Initial commit

github.com/BioJulia/BioCore.jl - 238b17f548a47e5b3b6e84bff8f208fc1e4fb952 authored over 7 years ago by Ben J. Ward <[email protected]>
Include guidance on ternary operator

github.com/BioJulia/Contributing - 210c7f222dc13364a947b41120e3cb49ba0830f5 authored over 7 years ago by Ben J. Ward <[email protected]>
rename a file (#422)

github.com/BioJulia/Bio.jl - c7fa5d6b67da2da6b8386e18874e56002b566151 authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Deleted src/seq/bioseq.jl (#421)

github.com/BioJulia/Bio.jl - 4f64c5e12e4c427bafd43ff94adf6a50f78f0fd3 authored over 7 years ago by Ben J. Ward <[email protected]>
Added index and front page to manual (#419)

github.com/BioJulia/Bio.jl - bf3a89378c69ce059b2f33062c945728a35c26bf authored over 7 years ago by Ben J. Ward <[email protected]>
rewrite FASTA (#413)

github.com/BioJulia/Bio.jl - ce2c2fbd95d112d1ff87f16d5bd1c16b5dee2969 authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
use Base.isless to order sequence names by default (#417)

github.com/BioJulia/Bio.jl - 291d80d6e690592f927e71b640cb966faa5864de authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
home.md renamed to index.md (#416)

github.com/BioJulia/Bio.jl - c697e327493035086abadab4b0fa9b4b9573df9d authored over 7 years ago by Ben J. Ward <[email protected]>
corrected demultiplexer.jl to demultiplexer.md (#414)

github.com/BioJulia/Bio.jl - bd9c128f4ec2dc41d34844716dd81163b8cf103b authored over 7 years ago by Ben J. Ward <[email protected]>
Reorganize BioSequence code (#410)

* Started reorganizing biosequence code to be better navigated by humans

* edited bioseq.jl f...

github.com/BioJulia/Bio.jl - 84eee5b20238688f7eebb2eed3730d223394ca53 authored over 7 years ago by Ben J. Ward <[email protected]>
optimize transition order

github.com/BioJulia/Automa.jl - 7522765e2ec346232c1a51db902c337301f4cf3e authored over 7 years ago by Kenta Sato <[email protected]>
sort labels

github.com/BioJulia/Automa.jl - 534eaf1064d6782d6bb7e8db76f7cbddb90b9157 authored over 7 years ago by Kenta Sato <[email protected]>
refill buffer only when needed (#412)

github.com/BioJulia/Bio.jl - 2a1d3cda6fbbdf1edc219a6c66e718eb9f3e416b authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
escape only when a GFF3 record is in a target list (#411)

github.com/BioJulia/Bio.jl - 0c9ac69769d88f7961f95b03699ecaba55d8d0b2 authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
rewrite GFF3 (#409)

github.com/BioJulia/Bio.jl - e1e016827d24c5d93781377a65dd5a960553fbc9 authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
julia => Julia

github.com/BioJulia/Bio.jl - 4d2e8cac5ed29f604d17a5f91ec5966f18b6e640 authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Mutation Counting & Distance API redux (#383)

* Refreshed the mutation counting API to include more site types.
Refreshes the naive methods o...

github.com/BioJulia/Bio.jl - 3ed91d20d140b2385aa5673bbf949700eb62fec8 authored over 7 years ago by Ben J. Ward <[email protected]>
revise SAM accessors (#408)

github.com/BioJulia/Bio.jl - 0b5ba3a9f3be02d8835bd90c97332f2c9cffb538 authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
revise VCF accessors (#407)

This makes VCFRecord accessor functions check whether the field is missing or not. If it is miss...

github.com/BioJulia/Bio.jl - f503844d32f2244c1fdac3e4d401b0262d2ca7d1 authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
add constructors for SAM (#406)

github.com/BioJulia/Bio.jl - a53bcaae4ed4c40cc06571ab01eee566e71febdb authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
add more methods for VCFHeader like SAMHeader (#404)

github.com/BioJulia/Bio.jl - 57e03a3800becc126d13ddf4409e1c5bc3d7a378 authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
update README and NEWS (#403)

github.com/BioJulia/Bio.jl - 1f01bed3d0464caa32cc8c9abed47d5eb4527c75 authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
support VCF and BCF file formats (#378)

github.com/BioJulia/Bio.jl - 609d47e80c6a543be8e4b533d352d918630cccf6 authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
add BCF files (#19)

github.com/BioJulia/BioFmtSpecimens - a197e8c493d1bed72652298086d080f2fdea8f16 authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>