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github.com/BioJulia/Bio.jl
[DEPRECATED] Bioinformatics and Computational Biology Infrastructure for Julia
https://github.com/BioJulia/Bio.jl
71bf51ffe4cb34cc22cf8859acfe3c06d6efea7f authored over 9 years ago by Daniel Jones <[email protected]>
9f1b8688d5dd7851ae61bc98e6457a459aec0bcc authored over 9 years ago by Daniel Jones <[email protected]>
90a49ad0e6090b554d714bf6accdb0e396fb4509 authored over 9 years ago by Daniel Jones <[email protected]>
b2b5b859a4bbdebe8724e91310475fe1b828b84b authored over 9 years ago by Daniel Jones <[email protected]>
1bfc3ba8b260a0d6bb41328b46842dd3e4fc6fef authored over 9 years ago by Daniel Jones <[email protected]>
2e6e53c89ab5e6470e586641de8b200ad7c6a23e authored over 9 years ago by Daniel Jones <[email protected]>
e296a4e0a06e4e49d7762a16bdcd8c93050b725e authored over 9 years ago by Daniel Jones <[email protected]>
31c4fab289bdde4492ff78b1f00bc18ddbff4faf authored over 9 years ago by Daniel Jones <[email protected]>
2a16921500e174dbbbafe4521cf32e2a0ddc528e authored over 9 years ago by Daniel Jones <[email protected]>
6b7187961521e102f7eea706622724d8027d99eb authored over 9 years ago by Daniel Jones <[email protected]>
7c898acf77a66c41d05de9704ac897389071ee85 authored over 9 years ago by Daniel Jones <[email protected]>
58992ae0c4754fdac7f34fd2577ed8c547041256 authored over 9 years ago by Daniel Jones <[email protected]>
4775527e81ff08f6620fde9e1ac0b355fe3cc0ba authored over 9 years ago by Daniel Jones <[email protected]>
bd68454b94d6a739c427ee12481fe50c3e46c20f authored over 9 years ago by Daniel Jones <[email protected]>
cfde0aa9dadf1bd7775b0eb99a852b2fb04ab169 authored over 9 years ago by Daniel Jones <[email protected]>
b20c3cb5df30e0294ea7ab7391279706dc824ed5 authored over 9 years ago by Daniel Jones <[email protected]>
Added waffle.io badges to the Bio.jl README.md
0d8e8cf880034cf3f11254bd7e2993012466e4e3 authored over 9 years ago by Ben J. Ward <[email protected]>Minor typo correction
1cafc05577421cb704997f8a48f5b9e3c6d84ea5 authored over 9 years ago by Daniel C. Jones <[email protected]>48e7a2f15e0dff14dc7c10230efb7fd19e07d6bc authored over 9 years ago by Nicolas Palopoli <[email protected]>
a2b68b8f958ebe3e8777a33497cfc3a5914ac978 authored over 9 years ago by Ben J. Ward <[email protected]>
a2e7e041f4519026c730c62faf925b8972dc4c15 authored over 9 years ago by Daniel Jones <[email protected]>
Writing of FASTQ sequences
e020e9e7249a8d6dfbcc7d16dbcddc38d8c13c3e authored over 9 years ago by Daniel C. Jones <[email protected]>c8641592f84c9d655e0d506d4149860a4ead2246 authored over 9 years ago by Kevin Murray <[email protected]>
8d160daded64c0bb4d7a5caa3ec1c4ef57c86d39 authored over 9 years ago by Kevin Murray <[email protected]>
3fe723245997691e1464376e50e5bc70d998e3c4 authored over 9 years ago by Kevin Murray <[email protected]>
This adds two functions for encoding quality score vectors as
PHRED-encoded strings (in-place an...
Now with added documentation :)
808ccee4d7d78458177b1ea4da571dd93f42b2a2 authored over 9 years ago by Kevin Murray <[email protected]>27538cb4d5dee551f4e778716dadb36edb0cd93c authored over 9 years ago by Kevin Murray <[email protected]>
7a2239e750f56c61d2f5ab10ae6e00574415e9a5 authored over 9 years ago by Kevin Murray <[email protected]>
5da8196dc7103c34decc95e3455a5b3c3a221dad authored over 9 years ago by Kevin Murray <[email protected]>
fc4dddc7c3c0ad450cdc75aecdeee23030c5e50c authored over 9 years ago by Kevin Murray <[email protected]>
d531283abaa4ad8ebc8c71bf63f2f84e359d41cb authored over 9 years ago by Daniel Jones <[email protected]>
Remove newlines
01f0ac70511ee2ee608ee91e0974452f838b396a authored over 9 years ago by Daniel C. Jones <[email protected]>define hash function for Alphabet to compile safely
6232a96e73c717d0a36dc234f48b66b2b8fed199 authored over 9 years ago by Daniel C. Jones <[email protected]>12733e0ada82b165db9d38f025fc5b355071b778 authored over 9 years ago by Kenta Sato <[email protected]>
2a5f586492517e96adead198097b116d087a0893 authored over 9 years ago by Kenta Sato <[email protected]>
706f703c2787fb311586f5ce222c911054650e94 authored over 9 years ago by Kenta Sato <[email protected]>
As promised - it's Saturday and there have been no objections. Remove 0.3 from travis
827f3ea2b98e0778a53a450ab8065c41b4aa65d9 authored over 9 years ago by Ben J. Ward <[email protected]>d62e9779cb4d33e3172c1f0e0a02008e06f39ad9 authored over 9 years ago by Ben J. Ward <[email protected]>
db74d95d7f37aae6996486a7de379ff3247f95e1 authored over 9 years ago by Ben J. Ward <[email protected]>
8823fab1c6e37f32c91084ec74a81ccdac22b653 authored over 9 years ago by Ben J. Ward <[email protected]>
New FactCheck syntax (=> / -->)
08f666366a8d3a575c77231a1b708401fcfec511 authored over 9 years ago by Paulo Roberto de Oliveira Castro <[email protected]>c1ae737bf7a40fda580bcfdd67713f48639b7b67 authored over 9 years ago by Paulo Roberto de Oliveira Castro <[email protected]>
import operators from Base explicitly
0bd1bb3a37e3b747d8e160f3225c0feac2988ab3 authored over 9 years ago by Paulo Roberto de Oliveira Castro <[email protected]>fa64378d29ad57e40589b3628ac86c7ee9494985 authored over 9 years ago by prcastro <[email protected]>
3560e10b3d27e811560419667fc5afbce1efc1bc authored over 9 years ago by Kenta Sato <[email protected]>
b58280f9d332fdf76f8ce3acb2abf76fc932338d authored over 9 years ago by Daniel Jones <[email protected]>
b9f79549851478455340632844416b3d3fc9724a authored over 9 years ago by Daniel Jones <[email protected]>
speed up the getindex method with inlining
0c282a35f9bddc12023a564c32b64a1c88038ef0 authored over 9 years ago by Daniel C. Jones <[email protected]>Typo fix by prcastro
3d9d75bd60ce909b1476161a2ccaff38b5e91e7b authored over 9 years ago by Ben J. Ward <[email protected]>Fix type leading to a travis failure
5b4c97ea00b29f3b5ff3119812bc625dedb2e46b authored over 9 years ago by Paulo Roberto de Oliveira Castro <[email protected]>77c93e75d1a4afa4af0a982141d3e78d3b3671df authored over 9 years ago by Kenta Sato <[email protected]>
WIP: Optimization/Bugfix Omnibus
c630a52eb0c5d3cfe121bf9dd66d618b2ae79d22 authored over 9 years ago by Daniel C. Jones <[email protected]>a337e2a71550913dfaf7d41cd3f68143bb74fd4d authored over 9 years ago by Daniel Jones <[email protected]>
8f9ec0c512a5021a29034e4f067a3d13e8709844 authored over 9 years ago by Daniel Jones <[email protected]>
936b2fcbe5b7c80bd1714deda9994e479c240c0d authored over 9 years ago by Daniel Jones <[email protected]>
850bc8410506cb588836504b10dc66393c1f82fa authored over 9 years ago by Daniel Jones <[email protected]>
61cd409e04b354d51f6ef12106f2e5800daa8e22 authored over 9 years ago by Daniel Jones <[email protected]>
3a204d669251a3043523d9a0096bf54deffbacf3 authored over 9 years ago by Daniel Jones <[email protected]>
6d10edb82994e99016cd461fbbd9a63237b6fb93 authored over 9 years ago by Daniel Jones <[email protected]>
fd4f5b3cbef857d09dc6d0839ef6a851bcbf6e0b authored over 9 years ago by Daniel Jones <[email protected]>
81e7c7a40af2ae0e6a513026a54912302658a8ed authored over 9 years ago by Daniel Jones <[email protected]>
956bf6be19920054ac86ca796495cdfd84e1dc39 authored over 9 years ago by Daniel Jones <[email protected]>
Ambiguous codons will be translated to X.
72aefebcd30625bee1a0f137536ae3ac80fdae70 authored over 9 years ago by Daniel Jones <[email protected]>72deb46f0a7181f14b69ca3b5f170fd835ad07da authored over 9 years ago by Daniel Jones <[email protected]>
f39323547684daba81b7550c70b3329e4941e9be authored over 9 years ago by Daniel Jones <[email protected]>
2e50b530e1bd9c7dfa2c8f52c0f0980686e21a71 authored over 9 years ago by Daniel Jones <[email protected]>
9d2d8608eba8b3ecf2702f5119e9ad5a41f9c318 authored over 9 years ago by Daniel Jones <[email protected]>
20183971c8451faf60b66af3571d12ea194682ce authored over 9 years ago by Daniel Jones <[email protected]>
586f3a3d2c8123a986f7db3cbae423287d21d5b0 authored over 9 years ago by Daniel Jones <[email protected]>
7beb054a43458ddd42fe18c0137891996c31c946 authored over 9 years ago by Daniel Jones <[email protected]>
4178e46fdaa242db4c2c69b669f2354d51ad12e6 authored over 9 years ago by Diego Javier Zea <[email protected]>
New doc syntax
196df9fee5c01885a55af2c429ff7fba05fa13d5 authored over 9 years ago by Daniel C. Jones <[email protected]>8a80e683b35a4d774e283309e89f990d675ae8a5 authored over 9 years ago by brk00 <[email protected]>
4b8f6331f1a0967c7b3efc65a3c01efe902eeb51 authored over 9 years ago by Paulo R. O. Castro <[email protected]>
da7e4237b9329567e864f861309d32d544c34957 authored over 9 years ago by Ben J. Ward <[email protected]>
Updated CONTRIBUTING.md - include Julia v number.
2ae3aab1f383a36579edc12820e9fe0984783264 authored over 9 years ago by Ben J. Ward <[email protected]>652181b1388e06dec0c9e9e52d23d2a84af8b400 authored over 9 years ago by Ben J. Ward <[email protected]>
[RFC] Interval Coverage
032d367bb8cd014fabf68d1ce706537f0df8dce1 authored over 9 years ago by Daniel C. Jones <[email protected]>52801b6b7d51fe7947b20167345aa2d4908ef422 authored over 9 years ago by Daniel Jones <[email protected]>
WIP: BED Parser
49c6c04671512a4d00f4068453b4aaaf3e189536 authored over 9 years ago by Daniel C. Jones <[email protected]>3e629f8b8dd8f024e78a5d7ee28f0eea3211bf91 authored over 9 years ago by Daniel Jones <[email protected]>
43691af4ee2635eb9150494ccb542429482a0024 authored over 9 years ago by Daniel Jones <[email protected]>
7aa0055bbd82653567e97bf97dbc7990cc007242 authored over 9 years ago by Daniel Jones <[email protected]>
11294459735921aeee020ddf2c96c0ca09c29904 authored over 9 years ago by Daniel Jones <[email protected]>
75039eabef68341c3578743fdb4beaafb73d46ff authored over 9 years ago by Daniel Jones <[email protected]>
a0876d04f1cb6234d5a5f4a50397df149ef1a029 authored over 9 years ago by Daniel Jones <[email protected]>
1053743ab72f615e4d2b1e01fcc0d8ac7f253e9e authored over 9 years ago by Daniel Jones <[email protected]>
6575c136e7b4cb7fb13edf69b1daf11677d10c98 authored over 9 years ago by Daniel Jones <[email protected]>
819e7e79ad2760b11cb8f257af29f94890b7124e authored over 9 years ago by Daniel Jones <[email protected]>
a99d9539d5eb1ab309ef40dfe0567b569ef148c7 authored over 9 years ago by Daniel Jones <[email protected]>
6d4d4d37962c6ba2fd71230821a02a6033fc4a88 authored over 9 years ago by Richard Smith-Unna <[email protected]>
df3156546c3e801c6de704f5c5de87bb2e707582 authored over 9 years ago by Richard Smith-Unna <[email protected]>
Intervals
f9842867514851524878f232d86b54a6d76288a9 authored over 9 years ago by Paulo Roberto de Oliveira Castro <[email protected]>8c0e96195918931cb2dfaaef90254c9497b07516 authored over 9 years ago by Daniel Jones <[email protected]>
cc33622f4eca8b6f3aa7f2afcfa550bb7f6f706d authored over 9 years ago by Daniel Jones <[email protected]>
3f70d7d700d6a0e25fb70216f0f60c86eae260d3 authored over 9 years ago by Daniel Jones <[email protected]>
de4e7c5ad4a92a145013925605508b6f8467dfe0 authored over 9 years ago by Daniel Jones <[email protected]>
3cc5f7d65e3c5540adaa5e619b1ab642cf4dea13 authored over 9 years ago by Daniel Jones <[email protected]>
79fe55212077b4b7ba37d302e308dfda2aa94871 authored over 9 years ago by Daniel Jones <[email protected]>