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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

fix some syntax for Julia 0.6 (#4)

github.com/BioJulia/IndexableBitVectors.jl - ed6ea6782881068e4d1a861b1b31b9f3e11e1288 authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Merge branch 'release-0.5'

github.com/BioJulia/BioSequences.jl - 53f86d0e49cd5fbc52607367b89b05f9619cb2ea authored over 7 years ago by Ben J. Ward <[email protected]>
fix importing in Bio.Var (#465)

github.com/BioJulia/Bio.jl - 6ec0fb21c992388190ff0bc5b84f04e41789b863 authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
remove unused exported names (#466)

github.com/BioJulia/Bio.jl - 31bc1ccc334b77d16649f17ba31f496b51550cf4 authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
fix constructor syntax (#26)

* fix constructor syntax for Julia 0.6

* run TravisCI on Julia 0.6

github.com/BioJulia/IntervalTrees.jl - 3a668a1e5dece1ee5f9c9125f5a84c2ac42b3e7f authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
use dirname(@__FILE__) instead of Pkg.dir in one more location

missed this one

github.com/BioJulia/BioSequences.jl - 9707e3b3545184ba9303f5da1fc991a3ed4996f5 authored over 7 years ago by Tony Kelman <[email protected]>
check gap existence before making a kmer

github.com/BioJulia/BioSequences.jl - 175b615ab992f584167b896525b0688e0e21ab56 authored over 7 years ago by Kenta Sato <[email protected]>
use dirname(@__FILE__) instead of Pkg.dir (#2)

* use dirname(@__FILE__) instead of Pkg.dir

this allows the package to be installed and loade...

github.com/BioJulia/BioSequences.jl - 8bcf4a068bb42417a279387ae7ad172db2c7aebe authored over 7 years ago by Tony Kelman <[email protected]>
Added examples to the branching guide.

github.com/BioJulia/Contributing - a3520cd0207f8ba0f497657259c4df9c655e813c authored over 7 years ago by Ben J. Ward <[email protected]>
Added a contributing page to the docs

github.com/BioJulia/BioSequences.jl - b9196104fc119486b15b9c9ea865f84c0e144885 authored over 7 years ago by Ben J. Ward <[email protected]>
added kmer types and aliases. (#2)

(part 1 of many)

github.com/BioJulia/Kmers.jl - e4eecdd0b4aae9153975737ec862b91c666b397c authored over 7 years ago by Ben J. Ward <[email protected]>
edited mkdocs file

github.com/BioJulia/BioSequences.jl - 1e3828cd42f316ac54bd74ae85fe1439df659e7b authored over 7 years ago by Ben J. Ward <[email protected]>
added twobit manpage

github.com/BioJulia/BioSequences.jl - 77a28391a7d939863613c7d4621359713b870e79 authored over 7 years ago by Ben J. Ward <[email protected]>
Added docstring to source

github.com/BioJulia/BioSequences.jl - cd1d70f51a0990ce2f35bfface4f021a831d2267 authored over 7 years ago by Ben J. Ward <[email protected]>
Added FASTQ documentation

github.com/BioJulia/BioSequences.jl - 8f2f4320a69816c947861222e1130af45f0fb37b authored over 7 years ago by Ben J. Ward <[email protected]>
Added doc lines to source

github.com/BioJulia/BioSequences.jl - d5446d9811b95c441428aaf25311aea5fbcf3a3e authored over 7 years ago by Ben J. Ward <[email protected]>
Added FASTA to documentation

github.com/BioJulia/BioSequences.jl - 411a518e9b285e4b468bad97db7f51705e949233 authored over 7 years ago by Ben J. Ward <[email protected]>
Documentation changes

github.com/BioJulia/BioSequences.jl - 9b824e15ca25f8bc626397e27065581955264f05 authored over 7 years ago by Ben J. Ward <[email protected]>
make check and getbyte more generic

github.com/BioJulia/Automa.jl - 3783273b83ec5ed7c16676ef8036df4bc1c59bf5 authored over 7 years ago by Kenta Sato <[email protected]>
fix .travis.yml

github.com/BioJulia/Automa.jl - 4a2eb54a279703122f2bf2e09fa77cf1e0504e98 authored over 7 years ago by Kenta Sato <[email protected]>
Added doc src files

github.com/BioJulia/BioSequences.jl - cdb56cb8ac6be65e62f9b246c13a44fa409f524c authored over 7 years ago by Ben J. Ward <[email protected]>
added appveyor.yml

github.com/BioJulia/BioSequences.jl - cb038f3ccbb7e391d8abe7c30a47cbe1e5dae918 authored over 7 years ago by Ben J. Ward <[email protected]>
Moved quality string tests to FASTQ tests.

github.com/BioJulia/BioSequences.jl - 5d48462cf8a2da70348ccbb951d2c46398719f16 authored over 7 years ago by Ben J. Ward <[email protected]>
Added WriteRecord to 2bit

github.com/BioJulia/BioSequences.jl - fe4f567479e266d7ad4a311a64a76d132e08d9d1 authored over 7 years ago by Ben J. Ward <[email protected]>
test fixups

github.com/BioJulia/BioSequences.jl - 4f56b4c73b81540f36c28803f07001d9bf9189a5 authored over 7 years ago by Ben J. Ward <[email protected]>
Added quality string tests

github.com/BioJulia/BioSequences.jl - e823f4b728283e3fefbccf4569f5401157c4a73f authored over 7 years ago by Ben J. Ward <[email protected]>
Added organised IO tests

github.com/BioJulia/BioSequences.jl - 8d8a94d52aa91898a604b89df36470b79d834957 authored over 7 years ago by Ben J. Ward <[email protected]>
Added demultiplexer tests

github.com/BioJulia/BioSequences.jl - 2f032813b7afce035728694016e4686c74e58746 authored over 7 years ago by Ben J. Ward <[email protected]>
Added translation tests

github.com/BioJulia/BioSequences.jl - 939701eb65bb0c4f4e49dd1bc4c7b485d5de6a0d authored over 7 years ago by Ben J. Ward <[email protected]>
Added organised search tests

github.com/BioJulia/BioSequences.jl - 0bc0e7ac41675dc33d97c57e2847102f3679f0ba authored over 7 years ago by Ben J. Ward <[email protected]>
Added organised kmer tests

github.com/BioJulia/BioSequences.jl - e506bf128df540a9afa1cd557ba04dcb012af8dc authored over 7 years ago by Ben J. Ward <[email protected]>
Update README.md

github.com/BioJulia/BioCore.jl - e32ef1e0bf5ad3a915b89345530c872b17070978 authored over 7 years ago by Ben J. Ward <[email protected]>
Added organised reference sequence tests

github.com/BioJulia/BioSequences.jl - ae031196b6e0b0a167f1d15bb8225165b89ded50 authored over 7 years ago by Ben J. Ward <[email protected]>
Added organised BioSequence tests

github.com/BioJulia/BioSequences.jl - 840bbe262ad73ee8a860f58e71654a93a3e3308d authored over 7 years ago by Ben J. Ward <[email protected]>
Added tests for the basic operations - copy, length, access, equality etc.

github.com/BioJulia/BioSequences.jl - 381a634f0d5a3a2798859068d2c0024afa21fd64 authored over 7 years ago by Ben J. Ward <[email protected]>
Added construction and conversion tests

github.com/BioJulia/BioSequences.jl - ecf3942c8fb8a3091b3b7dbd51f37fba6458ec01 authored over 7 years ago by Ben J. Ward <[email protected]>
Added tests for symbols

github.com/BioJulia/BioSequences.jl - 747ded980c5811f6ced57c9ca48ff92eda71a49f authored over 7 years ago by Ben J. Ward <[email protected]>
Added bitparallel site counting

github.com/BioJulia/BioSequences.jl - 6e77ca6fe9e5161208809d96ad81ad6f27974950 authored over 7 years ago by Ben J. Ward <[email protected]>
Site counting framework completion (#436)

github.com/BioJulia/Bio.jl - 9aa60c5b557154f99d99e94076747295970dc12e authored over 7 years ago by Ben J. Ward <[email protected]>
Updated fasta module to imprt BioCore, not Bio

github.com/BioJulia/BioSequences.jl - 4461a442791fed4c190a12a5e9828d413354206d authored over 7 years ago by Ben J. Ward <[email protected]>
Updated readme

github.com/BioJulia/BioCore.jl - 826fb0a8c7bf0743bdf1e6679be985a3615109d4 authored over 7 years ago by Ben J. Ward <[email protected]>
Updated Readme.md

github.com/BioJulia/BioSymbols.jl - 08368ecd3edd25b353b8f389bdf4e7838b06f37b authored over 7 years ago by Ben J. Ward <[email protected]>
Added contributing and License files to docs

github.com/BioJulia/BioCore.jl - 894a8509b8d4d44aa1f204ae8566ebebf1da0b0c authored over 7 years ago by Ben J. Ward <[email protected]>
Configured Documenter.jl

github.com/BioJulia/BioCore.jl - 1b0a7133b0d1e57bc845b1b8813df677f28f683f authored over 7 years ago by Ben J. Ward <[email protected]>
travis.yml edit

github.com/BioJulia/BioCore.jl - e942134e13fa80e51e796fc71c1404fdbf3af19d authored over 7 years ago by Ben J. Ward <[email protected]>
Auto stash before merge of "master" and "origin/master"

github.com/BioJulia/BioCore.jl - 90b111f47d82839b029578a40bd28561c1553d44 authored over 7 years ago by Ben J. Ward <[email protected]>
Basic project setup (#1)

* Added declare and exceptions

* File updates

* Readme update

* Readme update

* Read...

github.com/BioJulia/BioCore.jl - 6cb429a127001fe50d1ede5e92848fda44f5bdb0 authored over 7 years ago by Ben J. Ward <[email protected]>
Added a branching model section

github.com/BioJulia/Contributing - 721f7329b30e650ab2face1d0dd0d76eabd26acc authored over 7 years ago by Ben J. Ward <[email protected]>
Updated layout of contributing guide

github.com/BioJulia/Contributing - 43ded0bc498bf688b27fac46be4e7025ce7b648b authored over 7 years ago by Ben J. Ward <[email protected]>
Edit to gitignore.

github.com/BioJulia/BioCore.jl - 45d574af6110b5f954c109ce37f74dbb39009621 authored over 7 years ago by Ben J. Ward <[email protected]>
Removed old seqrecord type

github.com/BioJulia/BioSequences.jl - 08faf4e95c285426932fa17be0a823f09ec81c98 authored over 7 years ago by Ben J. Ward <[email protected]>
Added parser modules, and bioseq folder

github.com/BioJulia/BioSequences.jl - 8a4a8b2c22f05f06b33bfa0fb6447cd5046aa3ef authored over 7 years ago by Ben J. Ward <[email protected]>
Added files minhash.jl, nmask.jl, refseq.jl, and files in src/search/

github.com/BioJulia/BioSequences.jl - 8c259cc2494efda316854826a569d9134dc64aa3 authored over 7 years ago by Ben J. Ward <[email protected]>
Added demultiplexer.jl and geneticcode.jl

github.com/BioJulia/BioSequences.jl - 6a46b713a06325b80b45e2a7404af89ea5144078 authored over 7 years ago by Ben J. Ward <[email protected]>
Added composition, eachkmer, and kmer.jl

github.com/BioJulia/BioSequences.jl - c0f4c082a2e56eaaed0e7b32abe134f0c0a45d96 authored over 7 years ago by Ben J. Ward <[email protected]>
Added alphabet, bitindex, and sequence.jl

github.com/BioJulia/BioSequences.jl - c6adf4094f5816a007259769e7c058a8d340532d authored over 7 years ago by Ben J. Ward <[email protected]>
Update CI URLs to point to new caching infrastructure

github.com/BioJulia/Automa.jl - e5d5539ebfb136898c71e8e33f4da9c7073526b6 authored over 7 years ago by Elliot Saba <[email protected]>
implement a faster and simpler eachkmer (#462)

github.com/BioJulia/Bio.jl - 4828b442293a3a704c6ebeaeb1b9be74292f9f4a authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Added REQUIRE and BioSequences.jl module file.

github.com/BioJulia/BioSequences.jl - 739ebde2df62480ac0f1b05cfb1c361b50f91514 authored over 7 years ago by Ben J. Ward <[email protected]>
Initial commit

github.com/BioJulia/BioSequences.jl - 7d3f0ff19516c8dc1f80091268b5714f8aa8ba28 authored over 7 years ago by Ben J. Ward <[email protected]>
Merge pull request #25 from staticfloat/updated_ci_url

Update CI URLs to point to new caching infrastructure

github.com/BioJulia/Codecs.jl - 43ef5f72dd6d575ca986764d6f8e0baec3adba40 authored over 7 years ago by Randy Zwitch <[email protected]>
Merge pull request #26 from yuyichao/yyc/align

Fix wrong use of reinterpret in tests

github.com/BioJulia/Codecs.jl - 32d10c5f02a661bfb79d653bdd8e2281397f20f7 authored over 7 years ago by Randy Zwitch <[email protected]>
add isprimary for SAM.Record and BAM.Record (#461)

github.com/BioJulia/Bio.jl - 70ea67e1c73008d24baf05ab6c115813b0c18f85 authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Fix wrong use of reinterpret in tests

github.com/BioJulia/Codecs.jl - e061fa0a31a39acda7fc9df0cb45ac32e44b809f authored over 7 years ago by Yichao Yu <[email protected]>
update README

github.com/BioJulia/attobot - 426fe8e5ec0aa86fae49b4632b4852f690ce0963 authored over 7 years ago by Simon Byrne <[email protected]>
get email from repo commits

github.com/BioJulia/attobot - 18aec45191cd836f9f74eeba32b5489419167537 authored over 7 years ago by Simon Byrne <[email protected]>
Update CI URLs to point to new caching infrastructure (#9)

github.com/BioJulia/BioSymbols.jl - 035316a637365709bbae1207524d1ca37f538b4e authored over 7 years ago by Elliot Saba <[email protected]>
Update CI URLs to point to new caching infrastructure (#53)

github.com/BioJulia/Libz.jl - 2dfd99ea1ef01303e3678b7795e9e8fcb061701b authored over 7 years ago by Elliot Saba <[email protected]>
Update CI URLs to point to new caching infrastructure (#460)

github.com/BioJulia/Bio.jl - a7264bd4fdaa0fab088c3f8498301856fec25730 authored over 7 years ago by Elliot Saba <[email protected]>
Update CI URLs to point to new caching infrastructure

github.com/BioJulia/Codecs.jl - 6fae5f6b76d73b301d2a7000195c11aa81bc2168 authored over 7 years ago by Elliot Saba <[email protected]>
Use improper mutating state iterator.

This is 2-4x faster that the proper immutable state iterator.

github.com/BioJulia/IntervalTrees.jl - d1be51670041c776070f447cc0fa8530cc360d6d authored over 7 years ago by Daniel C. Jones <[email protected]>
Faster nextintersection! function

github.com/BioJulia/IntervalTrees.jl - 18c293c006b1908249e61f6285b154e99b9035a8 authored over 7 years ago by Daniel C. Jones <[email protected]>
A slightly more informed cost estimation.

github.com/BioJulia/IntervalTrees.jl - e1f1f2c2bb5cdca4b1370166c03f016351a9c0e4 authored over 7 years ago by Daniel C. Jones <[email protected]>
Don't use isless to compare entries in leaf nodes.

This can be unecessarily slow for intervals that compare on other fields.

github.com/BioJulia/IntervalTrees.jl - 6c4adc331db8067df87d82a31d439b0532235f03 authored over 7 years ago by Daniel C. Jones <[email protected]>
Use a plain array rather than Slice to store leaf entries.

github.com/BioJulia/IntervalTrees.jl - ec934b3c01352866686908c79c5fbd49f62da480 authored over 7 years ago by Daniel C. Jones <[email protected]>
Store leaf node keys redundantly in contiguous memory. Clean up successive intersection.

github.com/BioJulia/IntervalTrees.jl - a14d8b70d8ea37df4446fb410e9c551d6439f1b1 authored over 7 years ago by Daniel C. Jones <[email protected]>
Merge pull request #32 from MikeInnes/patch-1

Remove checkboxes

github.com/BioJulia/attobot - 7c9f6be35df28bedca592265c3a5ecf61b648ccd authored over 7 years ago by Simon Byrne <[email protected]>
Update lambda_function.py

github.com/BioJulia/attobot - a9a778584cb38065ab38433cd4a4035a30e14a9a authored over 7 years ago by Mike J Innes <[email protected]>
note use of email address

github.com/BioJulia/attobot - 703dc46606e17a6484eb5bde214c2c4534267515 authored over 7 years ago by Simon Byrne <[email protected]>
use releaser as commit author (#18).

github.com/BioJulia/attobot - 14dd4216de8d13d92d14812626821e7833ce39e9 authored over 7 years ago by Simon Byrne <[email protected]>
Merge pull request #31 from MikeInnes/reqs

Add help for package authors

github.com/BioJulia/attobot - 3b771bf2a906f7154bfeabcad8845a5d52717d6e authored over 7 years ago by Simon Byrne <[email protected]>
don't use auth on travis

github.com/BioJulia/attobot - d3e2ea9917e09cb1bdad848d41a2a3cf1882f077 authored over 7 years ago by Simon Byrne <[email protected]>
add requirements

github.com/BioJulia/attobot - 03d1c81ba5fc78bdcf19b0808d0863702ac2a708 authored over 7 years ago by Mike J Innes <[email protected]>
add BigWig.values (#458)

github.com/BioJulia/Bio.jl - 76fe760db80e8e2349b52763180cf1f63ae87006 authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
add Interval(seqname, range) constructor (#459)

github.com/BioJulia/Bio.jl - 4640f0a60c6ae8420bf705bac1dc99ead8efa151 authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
add BigWig and BigBed modules (#452)

github.com/BioJulia/Bio.jl - bf974cd9cd073aa34caa4927305ac89bf4e8913d authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Promotion for DNA/RNA sequences (#457)

* Added promote_rules for DNAAlphabet and RNAAlphabet

* Added promotion rule for DNA and RNA ...

github.com/BioJulia/Bio.jl - 40e412169807569625b320c6cb2315464c542775 authored over 7 years ago by Ben J. Ward <[email protected]>
add BBI (bigWig and bigBed) files (#21)

github.com/BioJulia/BioFmtSpecimens - 3140ef6110bb309703ffde564ce705eeb80607d4 authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
fix eachoverlap of BAM (#455)

github.com/BioJulia/Bio.jl - d8c6f47eead3ce16bd17a8d50d063bd679f55a7c authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Kmers.jl regenerated files.

license: MIT
authors: Ben J. Ward, Kevin Murray
years: 2017
user: kdmur...

github.com/BioJulia/Kmers.jl - c8e2a7c8f538ac56f7a6ec609d1993e7f833fd17 authored over 7 years ago by Kevin Murray <[email protected]>
Typos, and table corrections

github.com/BioJulia/Contributing - c4cb0047cd879b0a4ca93867a1efd712783447a6 authored over 7 years ago by Ben J. Ward <[email protected]>
Added organisation info, and incident response.

github.com/BioJulia/Contributing - ac7d01306b243bd81763a6c4df2c848702654621 authored over 7 years ago by Ben J. Ward <[email protected]>
always use auth

github.com/BioJulia/attobot - e589e9c99b00239818c28794df17167f92095e8f authored over 7 years ago by Simon Byrne <[email protected]>
add return statement

github.com/BioJulia/attobot - 5589d59ae62ed31d2b9311ae5ea0a452fcf8248d authored over 7 years ago by Simon Byrne <[email protected]>
Normalize REQUIRE line endings

github.com/BioJulia/attobot - d0495c7d3774649011431cfd78cd45e9287b26bb authored over 7 years ago by Simon Byrne <[email protected]>
Update README.md

github.com/BioJulia/Kmers.jl - c70d5687bef136c49b93bef1c07e71f6045fcc38 authored over 7 years ago by Ben J. Ward <[email protected]>
Document GFF->IntervalCollection (#454)

I had to read the tests & source to work out how to do it, so probably could use
a note in the ...

github.com/BioJulia/Bio.jl - 25df82669140f174da9892c10cb0bddf4171a841 authored over 7 years ago by Kevin Murray <[email protected]>
Edited pages tree

github.com/BioJulia/Contributing - 5fe666f1915d384baaefb6db9cc42c542d937587 authored over 7 years ago by Ben J. Ward <[email protected]>
Update code style page.

github.com/BioJulia/Contributing - 2802eadd604525edacdbce611b0ac89a196681e5 authored over 7 years ago by Ben J. Ward <[email protected]>
Fix UndefVarError in IntervalCollection(GFFReader) (#453)

* Fix UndefVarError in IntervalCollection(GFFReader)

And add a test

* Import Interval and ...

github.com/BioJulia/Bio.jl - 8718c4bcb30dc8843fedd2a7546ea66064f7057b authored over 7 years ago by Kevin Murray <[email protected]>