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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 window iterator under Bio.Util module

github.com/BioJulia/Bio.jl - ac365eb1e81a708e399cca54e16d38f2f651942e authored almost 9 years ago by Kevin Murray <[email protected]>
Inline window iterator functions

github.com/BioJulia/Bio.jl - 114273d48915f9cdcb42e76c6d6581f4566a7909 authored almost 9 years ago by Kevin Murray <[email protected]>
Edited test to take into account if on a windows system when opening the null stream.

github.com/BioJulia/Bio.jl - e735be7513916f680abda7eb9c1bdeec444be641 authored almost 9 years ago by Ward9250 <[email protected]>
Merge pull request #5 from bicycle1885/ambig-aa

add a protein sequence

github.com/BioJulia/BioFmtSpecimens - 8a5c698f9fa6fae0027da5f4c145d7fafb3c337f authored almost 9 years ago by Kenta Sato (佐藤 建太) <[email protected]>
add RIKEN2015

github.com/BioJulia/talks - d90ab77ddb4b8b8c4496d4b22670414d2b0311c6 authored almost 9 years ago by Kenta Sato <[email protected]>
Update README.md

github.com/BioJulia/Bio.jl - 4212e76f3c61593f0e6aa281c44b7d9e22ca0939 authored almost 9 years ago by Ben J. Ward <[email protected]>
Update README.md

github.com/BioJulia/Bio.jl - ab251cd0d6605606e5525efdfdec13e5275865f9 authored almost 9 years ago by Ben J. Ward <[email protected]>
Update README.md

github.com/BioJulia/Bio.jl - 5c0897bae505a50e8be2226d7df385f39bf116c5 authored almost 9 years ago by Ben J. Ward <[email protected]>
Merge pull request #125 from Ward9250/master

Added Appveyor

github.com/BioJulia/Bio.jl - 93f353eea8c1c1e9286355fbcee95a831beb21af authored almost 9 years ago by Ben J. Ward <[email protected]>
Added Appveyor

github.com/BioJulia/Bio.jl - f1cb03a9275f6393257a7b9444131ab0a677b844 authored almost 9 years ago by Ward9250 <[email protected]>
Update README.md

github.com/BioJulia/Libz.jl - 27332bc5823f44fac730d78feb44945386e1825a authored almost 9 years ago by Ben J. Ward <[email protected]>
Merge pull request #6 from tkelman/master

Add appveyor, run travis on 0.4

github.com/BioJulia/Libz.jl - c2bc051ea539f6ed867f598b041f34f11e4b4fad authored almost 9 years ago by Ben J. Ward <[email protected]>
Added EBDM2015 slide-deck

github.com/BioJulia/talks - e2601f1b8dab803e413b5827e9c3289b50293270 authored almost 9 years ago by Ben Ward (TGAC) <[email protected]>
Merge pull request #120 from BioJulia/char-like

define arithmetic on nucleotides and amino acids

github.com/BioJulia/Bio.jl - f6e2568f0c9a47dbc7e59a6aeab7baa7d2644e24 authored almost 9 years ago by Kenta Sato (佐藤 建太) <[email protected]>
define arithmetic on nucleotides and amino acids

github.com/BioJulia/Bio.jl - dc3b669ba04fbfe5592b394612c2f54726d9d5f5 authored almost 9 years ago by Kenta Sato <[email protected]>
fix the docstring of mismatches

github.com/BioJulia/Bio.jl - 7d801284e71525a8443952f9338047d1f6eb9f95 authored almost 9 years ago by Kenta Sato <[email protected]>
define arithmetic for Kmer

github.com/BioJulia/Bio.jl - 4c3a5c379c3e5f96ddefe40b2f229686b6834c76 authored almost 9 years ago by Kenta Sato <[email protected]>
Changed Fonts

github.com/BioJulia/assets - 5b82ef4d91d359153cea52dfb6fd65883e22f083 authored almost 9 years ago by Ben Ward (TGAC) <[email protected]>
Changed Sinhala font css

github.com/BioJulia/assets - 33bda6c215608d5fae606694df8e270fdd61794c authored almost 9 years ago by Ben Ward (TGAC) <[email protected]>
Merge pull request #123 from BioJulia/kmer

Kmer Overhaul

github.com/BioJulia/Bio.jl - 443340ebc9f948fb72898ed52a73eb810250b90e authored almost 9 years ago by Kenta Sato (佐藤 建太) <[email protected]>
add hash(kmer)

github.com/BioJulia/Bio.jl - d6e7a04c4cb69751f9d3aab87cc52b213d1d2285 authored almost 9 years ago by Kenta Sato <[email protected]>
Kmer: the first nucleotide is at the MSBs

github.com/BioJulia/Bio.jl - c42424d999ca227be9a14730c8113cf57f0f6e6a authored almost 9 years ago by Kenta Sato <[email protected]>
Added new branding files as svg.

github.com/BioJulia/assets - 61763da0ff60775234f8aee90863632843cd7134 authored almost 9 years ago by Ward9250 <[email protected]>
Revamped BioJulia logos and branding to have the word 'bio' in the exact same font as that of the julia logo.

github.com/BioJulia/assets - 204a5da1e5eb51c2fc5af1bff1be08c67fa1f257 authored almost 9 years ago by Ward9250 <[email protected]>
Added a few slidewinder compat slides.

github.com/BioJulia/assets - 11c2e7ead8c45eb907b2ba9bef67185d93265e1b authored almost 9 years ago by Ben Ward (TGAC) <[email protected]>
Merge branch 'master' of github.com:BioJulia/assets

github.com/BioJulia/assets - cbe4e33ce10ccdf1e938422f5f686c81a66e36fc authored almost 9 years ago by Ben Ward (TGAC) <[email protected]>
Added new converted sinhalamn font files.

github.com/BioJulia/assets - 5a6d8f9ff54a27a0a78950dcff4070510812a75b authored almost 9 years ago by Ben Ward (TGAC) <[email protected]>
Add non-square biojulia logo

github.com/BioJulia/assets - 8f6b136b03e9fad866a8d1a293021f5c57b45f67 authored almost 9 years ago by Richard Smith-Unna <[email protected]>
Initial commit

github.com/BioJulia/biojulia.github.io - f0c0208c18e9385dfb642da0161ff0f2ce432299 authored almost 9 years ago by Richard Smith-Unna <[email protected]>
drop the support of v0.4-

github.com/BioJulia/FMIndexes.jl - 69aab79d52840d8ce1c396dd90985d3eb6bca5ae authored almost 9 years ago by Kenta Sato <[email protected]>
fix __precompile__()

github.com/BioJulia/FMIndexes.jl - 97788fd027ef5049af52b47637f08d950ff5aecb authored almost 9 years ago by Kenta Sato <[email protected]>
removed archive file

github.com/BioJulia/mkdocs-biojulia - e73af0ccf537fff749fe50065872fb0cf156505a authored almost 9 years ago by Chris Simpkins <[email protected]>
updated site build to v0.9.3 release

github.com/BioJulia/mkdocs-biojulia - bdb05928468a2248aa6df6a781a3258c075e3220 authored almost 9 years ago by Chris Simpkins <[email protected]>
new site build

github.com/BioJulia/mkdocs-biojulia - f1e5aac2b146069b740a5026282913f53df98596 authored almost 9 years ago by Chris Simpkins <[email protected]>
bumped Hack font version

github.com/BioJulia/mkdocs-biojulia - 5f5fa67accea45c2594d8ef9bc3c9dda98680a57 authored almost 9 years ago by Chris Simpkins <[email protected]>
removed version string from CSS file

github.com/BioJulia/mkdocs-biojulia - bb2a75cc5ee8f4fbcf63c919adb481e2169feece authored almost 9 years ago by Chris Simpkins <[email protected]>
Merge pull request #3 from jeffpeiyt/master

add support for >2 level navigation

github.com/BioJulia/mkdocs-biojulia - a68cc81f3043568dc7557eab2f6c5f018f6b41c8 authored almost 9 years ago by Chris Simpkins <[email protected]>
add support for >2 level navigation

fix firefox; add support for >2 level navigation

fix firefox; add support for >2 level navigation

github.com/BioJulia/mkdocs-biojulia - fc998ee71ff99a2e473737f47e80df314418774c authored almost 9 years ago by Jeff Pei <[email protected]>
Added true-type Julia fonts, called SinhalaMN - ships with OSX, so we can use it.

github.com/BioJulia/assets - d18bfd9147377cbd1fb1945ceff91b8189a1fec5 authored almost 9 years ago by Ward9250 <[email protected]>
support arbitrary byte-convertible sequences

github.com/BioJulia/FMIndexes.jl - 677e20e7c66b7bf3a189e85cae0d2eb4dff01c5f authored almost 9 years ago by Kenta Sato <[email protected]>
Merge pull request #119 from BioJulia/intvl-constr

Modify Interval constructors.

github.com/BioJulia/Bio.jl - 41bb5e6d5ab98c66bd15caea4a96db78d2469744 authored almost 9 years ago by Kenta Sato (佐藤 建太) <[email protected]>
add seqname accessor for interval type

github.com/BioJulia/Bio.jl - 4d04145ad234b3ce65f576ea4740f71bbac05f41 authored almost 9 years ago by Kenta Sato <[email protected]>
Add logo

github.com/BioJulia/Bio.jl - c0126d3a478c1d43965b70437f56ce0116f299a6 authored almost 9 years ago by Richard Smith-Unna <[email protected]>
Merge pull request #8 from julian-gehring/patch-1

Fix minor typos in readme

github.com/BioJulia/Libz.jl - babd4f46ea8756bd83f28d36211b5b7048383a04 authored almost 9 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Fix minor typos in readme

github.com/BioJulia/Libz.jl - 9eb39131e93756e04f5bac4c54f345acbdfb7aa5 authored almost 9 years ago by Julian Gehring <[email protected]>
show approximate data size

github.com/BioJulia/FMIndexes.jl - c419ea6ec56f7e6cc758adbf9364317eb9453d9c authored almost 9 years ago by Kenta Sato <[email protected]>
more inbounds

github.com/BioJulia/FMIndexes.jl - c775e3dc822f0e54be37a7fbf2138030128142d8 authored almost 9 years ago by Kenta Sato <[email protected]>
add strand accessor

github.com/BioJulia/Bio.jl - b9f35afb258fb3f1bbb55a93a8966ab98ced9521 authored almost 9 years ago by Kenta Sato <[email protected]>
make Interval constructors accept a strand char

github.com/BioJulia/Bio.jl - be8b5fcf6e0c83e12ab033a7cda707afe02b3a09 authored almost 9 years ago by Kenta Sato <[email protected]>
Merge pull request #113 from BioJulia/fix-alignment

fix firstref and lastref

github.com/BioJulia/Bio.jl - d3f2fbf2ec45528522d31d4459609ad43d9ef38c authored almost 9 years ago by Daniel C. Jones <[email protected]>
Merge pull request #115 from BioJulia/more-aa

Add more amino acids

github.com/BioJulia/Bio.jl - 963f853a719cef011359a858405e5c4da43f50a8 authored almost 9 years ago by Kenta Sato (佐藤 建太) <[email protected]>
use accrank1 of SucVector

github.com/BioJulia/WaveletMatrices.jl - 6005630e16cefb365d6530d062c8abfe6ef0b4db authored almost 9 years ago by Kenta Sato <[email protected]>
add accrank1

github.com/BioJulia/IndexableBitVectors.jl - 1b8e310f5ba436370321603c9a3180e24f6d8447 authored almost 9 years ago by Kenta Sato <[email protected]>
fix the order of amino acids

as the order of common substitution matrices downloaded from NCBI

github.com/BioJulia/Bio.jl - b71e501d34f0f2c983569c4f771049f048b97800 authored almost 9 years ago by Kenta Sato <[email protected]>
Added contributing file

github.com/BioJulia/PopGen.jl_archive - 3e0aace0fc2607cbb820db6477f7f2451ca32c64 authored almost 9 years ago by Ward9250 <[email protected]>
Added contributing file

github.com/BioJulia/PopGen.jl - 3e0aace0fc2607cbb820db6477f7f2451ca32c64 authored almost 9 years ago by Ward9250 <[email protected]>
Initial commit

github.com/BioJulia/PopGen.jl - f745a6b1c0d8ebd7fbe7a2b595f36d666a14b3a1 authored almost 9 years ago by Ben J. Ward <[email protected]>
Initial commit

github.com/BioJulia/PopGen.jl_archive - f745a6b1c0d8ebd7fbe7a2b595f36d666a14b3a1 authored almost 9 years ago by Ben J. Ward <[email protected]>
check ambiguous protein specimens

github.com/BioJulia/Bio.jl - 55d66d05bb11ea896de97934bd53f2e2caa6873f authored almost 9 years ago by Kenta Sato <[email protected]>
add a protein sequence

that contains ambiguous amino acids

github.com/BioJulia/BioFmtSpecimens - c510b6c5186adcb15b8e466c14bc094938746259 authored almost 9 years ago by Kenta Sato <[email protected]>
add 'J' amino acid

Leucine or Isoleucine

github.com/BioJulia/Bio.jl - 199d311d0fcdbb8e2c2accd6dc0f4db2d96d3a4a authored almost 9 years ago by Kenta Sato <[email protected]>
add 'O' and 'U' amino acids

'O' stands for pyrrolysine, and 'U' stands for selenocysteine.

github.com/BioJulia/Bio.jl - 5bf305c968e932e13908ff050746c22ab54554da authored almost 9 years ago by Kenta Sato <[email protected]>
add 'B' and 'Z' amino acids

'B' stands for aspartic acid or asparagine, and 'Z' stands for glutamine
or glutamic acid.

github.com/BioJulia/Bio.jl - 57ab4c433031cb6dd3511a00bcc65b5c30950ea4 authored almost 9 years ago by Kenta Sato <[email protected]>
minor performance improvement of getindex

github.com/BioJulia/WaveletMatrices.jl - 791d8985226cc41285a66ace8c38d455b73f2d22 authored almost 9 years ago by Kenta Sato <[email protected]>
fix a deprecated type name

github.com/BioJulia/WaveletMatrices.jl - 947c8ff67bc572b9545f4565a1979be359b59fda authored almost 9 years ago by Kenta Sato <[email protected]>
add a method that narrows down an SA range by char

github.com/BioJulia/FMIndexes.jl - 03324aa434f93058b73d7577f6dcdd874e770ad1 authored almost 9 years ago by Kenta Sato <[email protected]>
fix firstref and lastref

github.com/BioJulia/Bio.jl - d90cc3a78c064f39512d86212088f787c1924f30 authored almost 9 years ago by Kenta Sato <[email protected]>
move anchor's test

github.com/BioJulia/Bio.jl - 93a83c11edcff057849ea84e41d5aa82ce308131 authored almost 9 years ago by Kenta Sato <[email protected]>
Merge pull request #112 from BioJulia/fix-anchor

fix printing of anchor

github.com/BioJulia/Bio.jl - 266691f7b0696938f6349cad12283b93e17b2c8d authored almost 9 years ago by Daniel C. Jones <[email protected]>
fix printing of anchor

github.com/BioJulia/Bio.jl - efa76502c719003ca6c9010dc0364527fbe047f8 authored almost 9 years ago by Kenta Sato <[email protected]>
Merge pull request #110 from BioJulia/align2

Align Redux

github.com/BioJulia/Bio.jl - 16c9b49295dd4814d4fd0de900d06a77b2a50cd3 authored almost 9 years ago by Daniel C. Jones <[email protected]>
Add appveyor, run travis on 0.4

github.com/BioJulia/Libz.jl - 52e3e8a2d76c5b12028235c928aae21e16bf49c4 authored about 9 years ago by Tony Kelman <[email protected]>
Minor improvements.

github.com/BioJulia/Bio.jl - 6ac33f91edc2f15557187434c719cba22607b002 authored about 9 years ago by Daniel Jones <[email protected]>
Add a little documentation.

github.com/BioJulia/Bio.jl - 7d9a6c617c675ed678b317900ef7f30540aea109 authored about 9 years ago by Daniel Jones <[email protected]>
Fix accidentally disabled tests.

github.com/BioJulia/Bio.jl - 0214bd7f50259a06440734f0c16f77b423085883 authored about 9 years ago by Daniel Jones <[email protected]>
updated download link

github.com/BioJulia/mkdocs-biojulia - 6f3cb1a7b91c36755d31d2476a082756b7a18b5b authored about 9 years ago by Chris Simpkins <[email protected]>
updated Hack web fonts to release v2.015

github.com/BioJulia/mkdocs-biojulia - 7d01c58e4a6d9366eac645e64e187e72e69e1055 authored about 9 years ago by Chris Simpkins <[email protected]>
Temporarily remove alignment position mapping.

github.com/BioJulia/Bio.jl - f43b9c2ea1adbf743e2b73d92fc1c1835a310281 authored about 9 years ago by Daniel Jones <[email protected]>
Cigar string conversion.

github.com/BioJulia/Bio.jl - aff32df910ee564e7ce972bbe9bdb3945536d376 authored about 9 years ago by Daniel Jones <[email protected]>
Some reworking and testing of anchor encoded alignments.

github.com/BioJulia/Bio.jl - 99cd68066163e427c97380ea5f8207543ce3438d authored about 9 years ago by Daniel Jones <[email protected]>
Remove gaps and cigar for now.

github.com/BioJulia/Bio.jl - 71d529dfa99342215d4ece7420a5ee70606d0948 authored about 9 years ago by Daniel Jones <[email protected]>
Require julia 0.3

github.com/BioJulia/Codecs.jl - dbc3b9327fd6e4c84a88a1d0c2c6fc43a6d66793 authored about 9 years ago by Daniel Jones <[email protected]>
reorder definitions

github.com/BioJulia/IndexableBitVectors.jl - 041aa77486488a0e11991d39f1dfe136819a45df authored about 9 years ago by Kenta Sato <[email protected]>
add rsearch/rsearch0/rsearch1

github.com/BioJulia/IndexableBitVectors.jl - 09139ad261c84fe9c22a77ef549da221ee3f11ce authored about 9 years ago by Kenta Sato <[email protected]>
add search/search0/search1

github.com/BioJulia/IndexableBitVectors.jl - 3889234ca0a01dc9446bf6c961114e9dccfa42e8 authored about 9 years ago by Kenta Sato <[email protected]>
Merge pull request #4 from BioJulia/compat-v0.4

fix deprecated types

github.com/BioJulia/Libz.jl - 88899be3898c5b7681a3828f4e95de29b0c840a9 authored about 9 years ago by Daniel C. Jones <[email protected]>
Merge pull request #108 from BioJulia/import-hash

import hash from Base

github.com/BioJulia/Bio.jl - 0697dc92bc8394d447a6ec3e99454f3d59b2d471 authored about 9 years ago by Kenta Sato (佐藤 建太) <[email protected]>
import hash from Base

github.com/BioJulia/Bio.jl - 4fd8964ecbe737f674161246333f7d3a7208e490 authored about 9 years ago by Kenta Sato <[email protected]>
Merge pull request #106 from BioJulia/ragel7

Regenerate parsers with ragel 7.

github.com/BioJulia/Bio.jl - 571c954ec4112960c1feeed0a1c9ad11116c5185 authored about 9 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Make declarations const.

github.com/BioJulia/ragel7 - ba684f9ecb0bcb5c318d640ee7e5f34cdd8ce767 authored about 9 years ago by Daniel Jones <[email protected]>
Regen parsers using const globals.

github.com/BioJulia/Bio.jl - 1838751912ea63248685ca1aef49f728641c64ba authored about 9 years ago by Daniel Jones <[email protected]>
fix deprecated types

github.com/BioJulia/Libz.jl - f6b6be4e31892331cdd7670e45bbda0533cad7b6 authored about 9 years ago by Kenta Sato <[email protected]>
Encode CIGAR as it is in BAM.

github.com/BioJulia/Bio.jl - 961538d8bbe0aae8eae091612e07250703acb01b authored about 9 years ago by Daniel Jones <[email protected]>
Fix style.

* Don't use camel case.
* Julia 0.4 deprecations.
* No longer need `@doc ... ->`

github.com/BioJulia/Bio.jl - a7089ab0233fb21f138e5d3ae156da62c847e3a3 authored about 9 years ago by Daniel Jones <[email protected]>
Initial draft of alignment representations.

github.com/BioJulia/Bio.jl - e4042fa36af26468ba80bd3f86b2ea06885356da authored about 9 years ago by Ward9250 <[email protected]>
Use julia-0.4 int type names.

github.com/BioJulia/ragel7 - ec1fe6f94eb72712ec0c2fdb80daf8832ad4a750 authored about 9 years ago by Daniel Jones <[email protected]>
Regenerate parsers with ragel 7.

github.com/BioJulia/Bio.jl - e4b14d5922811e4313412ddc5ff4687002cbedb7 authored about 9 years ago by Daniel Jones <[email protected]>
Fix switch statements in julia.

github.com/BioJulia/ragel7 - 234706159128b8a64088c4593df75ef29e5a8e7f authored about 9 years ago by Daniel Jones <[email protected]>
Fix fbreak codegen for IpGoto.

github.com/BioJulia/ragel7 - 46621503332b4e5ed320ebf9cb6243e8f96c1571 authored about 9 years ago by Daniel Jones <[email protected]>
Use begin/end instead of curly brackets in julia.

github.com/BioJulia/ragel7 - 3d07e66094115e70a79e86428c673685daf46224 authored about 9 years ago by Daniel Jones <[email protected]>