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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 constructor for NucleotideSequence from Nucleotide vectors.

github.com/BioJulia/Bio.jl - fd4f5b3cbef857d09dc6d0839ef6a851bcbf6e0b authored about 9 years ago by Daniel Jones <[email protected]>
Let parsers read from shell commands.

github.com/BioJulia/Bio.jl - 956bf6be19920054ac86ca796495cdfd84e1dc39 authored about 9 years ago by Daniel Jones <[email protected]>
Add KmerCounts, analogous to NucleotideCounts.

github.com/BioJulia/Bio.jl - 81e7c7a40af2ae0e6a513026a54912302658a8ed authored about 9 years ago by Daniel Jones <[email protected]>
Add iterator over k-mer de bruijn graph neighbors.

github.com/BioJulia/Bio.jl - 72deb46f0a7181f14b69ca3b5f170fd835ad07da authored about 9 years ago by Daniel Jones <[email protected]>
Add an option to allow ambiguous codons in translate.

Ambiguous codons will be translated to X.

github.com/BioJulia/Bio.jl - 72aefebcd30625bee1a0f137536ae3ac80fdae70 authored about 9 years ago by Daniel Jones <[email protected]>
Fix potential buffer overflow in parsers.

github.com/BioJulia/Bio.jl - f39323547684daba81b7550c70b3329e4941e9be authored about 9 years ago by Daniel Jones <[email protected]>
Optimizations to eachkmer.

github.com/BioJulia/Bio.jl - 9d2d8608eba8b3ecf2702f5119e9ad5a41f9c318 authored about 9 years ago by Daniel Jones <[email protected]>
Even faster eachkmer.

github.com/BioJulia/Bio.jl - 2e50b530e1bd9c7dfa2c8f52c0f0980686e21a71 authored about 9 years ago by Daniel Jones <[email protected]>
Even faster sequence iteration.

github.com/BioJulia/Bio.jl - 20183971c8451faf60b66af3571d12ea194682ce authored about 9 years ago by Daniel Jones <[email protected]>
Faster iteration over nucleotides.

github.com/BioJulia/Bio.jl - 7beb054a43458ddd42fe18c0137891996c31c946 authored about 9 years ago by Daniel Jones <[email protected]>
Slightly faster sequence reverse.

github.com/BioJulia/Bio.jl - 586f3a3d2c8123a986f7db3cbae423287d21d5b0 authored about 9 years ago by Daniel Jones <[email protected]>
fix AminoAcidSeqRecord

github.com/BioJulia/Bio.jl - 4178e46fdaa242db4c2c69b669f2354d51ad12e6 authored about 9 years ago by Diego Javier Zea <[email protected]>
Merge pull request #61 from prcastro/new_doc_syntax

New doc syntax

github.com/BioJulia/Bio.jl - 196df9fee5c01885a55af2c429ff7fba05fa13d5 authored over 9 years ago by Daniel C. Jones <[email protected]>
Reqire Julia v0.4

github.com/BioJulia/Bio.jl - 8a80e683b35a4d774e283309e89f990d675ae8a5 authored over 9 years ago by brk00 <[email protected]>
New documentation syntax

github.com/BioJulia/Bio.jl - 4b8f6331f1a0967c7b3efc65a3c01efe902eeb51 authored over 9 years ago by Paulo R. O. Castro <[email protected]>
Updated CONTRIBUTING.md - include Julia v number.

github.com/BioJulia/Bio.jl - da7e4237b9329567e864f861309d32d544c34957 authored over 9 years ago by Ben J. Ward <[email protected]>
.travis.yml

github.com/BioJulia/Dat.jl - 6bf76db64ab9e5b69031e6bc4dbeb51a53889693 authored over 9 years ago by Ben J. Ward <[email protected]>
Initial commit

github.com/BioJulia/Dat.jl - 9432fe63b1e17b2e35861c3e3e7a34331e145744 authored over 9 years ago by Ben J. Ward <[email protected]>
Missing image.

github.com/BioJulia/talks - ff4a4e2860a5312fb6dc63ea75af65107285d564 authored over 9 years ago by Daniel Jones <[email protected]>
Add juliacon talk.

github.com/BioJulia/talks - acc53b3d48f6603d2187b85643fab4c530750098 authored over 9 years ago by Daniel Jones <[email protected]>
Merge pull request #58 from BioJulia/Ward9250-contributing-edit

Updated CONTRIBUTING.md - include Julia v number.

github.com/BioJulia/Bio.jl - 2ae3aab1f383a36579edc12820e9fe0984783264 authored over 9 years ago by Ben J. Ward <[email protected]>
Updated CONTRIBUTING.md - include Julia v number.

github.com/BioJulia/Bio.jl - 652181b1388e06dec0c9e9e52d23d2a84af8b400 authored over 9 years ago by Ben J. Ward <[email protected]>
Use BigWig for interval streams with numerical metadata.

github.com/BioJulia/GenomeBrowsers.jl - fe9cd7deb59be21d2e27677503fca29bc0831839 authored over 9 years ago by Daniel Jones <[email protected]>
use NTuple for bit vectors

github.com/BioJulia/WaveletMatrices.jl - 00aad35129123a10ee13aa779cf84c57fd498f4a authored over 9 years ago by Kenta Sato <[email protected]>
Fix under-specified type.

github.com/BioJulia/IntervalTrees.jl - 9b379b0c04ea03391b7ea853916f66810fb49de3 authored over 9 years ago by Daniel Jones <[email protected]>
add sizeof(WaveletMatrix)

github.com/BioJulia/WaveletMatrices.jl - cefd7825065aae977e31a76000dcb42f010d24f5 authored over 9 years ago by Kenta Sato <[email protected]>
add Vector{Uint64} test

github.com/BioJulia/WaveletMatrices.jl - fa72104abca3b669bca7d9e5125221148da61272 authored over 9 years ago by Kenta Sato <[email protected]>
Some intersection optimization.

github.com/BioJulia/IntervalTrees.jl - 272010572a12a22d3a9b6c8b271718153dd16138 authored over 9 years ago by Daniel Jones <[email protected]>
Relax type of bulk insertion constructor.

github.com/BioJulia/IntervalTrees.jl - d9399217b24a5b97e2bb98daef218cbb661d4fae authored over 9 years ago by Daniel Jones <[email protected]>
Fix cost estimation in intersect.

github.com/BioJulia/IntervalTrees.jl - bdd9ed1d9f3024f55c3930a763a765702a1725f4 authored over 9 years ago by Daniel Jones <[email protected]>
implement N-bit encoding

github.com/BioJulia/WaveletMatrices.jl - 8ee390d906797f217c59e567a7700d27b58c543c authored over 9 years ago by Kenta Sato <[email protected]>
add type tests (and fix a bug)

github.com/BioJulia/IndexableBitVectors.jl - dc7e9e803300ad56c86069ebe2878f3a0b1356c9 authored over 9 years ago by Kenta Sato <[email protected]>
fix subtyping

github.com/BioJulia/IndexableBitVectors.jl - 0f7e3a7efcbacfc1b20770d88e2a7ae7674a583c authored over 9 years ago by Kenta Sato <[email protected]>
rename a deprecated function in v0.4

github.com/BioJulia/IndexableBitVectors.jl - 8feabd8eef50b3359320a5bf9800b9ef2d909f55 authored over 9 years ago by Kenta Sato <[email protected]>
add some notes

github.com/BioJulia/IndexableBitVectors.jl - 370d52e31e8a1cc9264ee7ee48b6d83cf3571b36 authored over 9 years ago by Kenta Sato <[email protected]>
add benchmarks

github.com/BioJulia/IndexableBitVectors.jl - e584cdfe1d00b4493dad057548359aba7415a431 authored over 9 years ago by Kenta Sato <[email protected]>
add Switch.jl to REQUIRE

github.com/BioJulia/IndexableBitVectors.jl - a0cd656c2c2f28355aee278cebcf3d107f08d912 authored over 9 years ago by Kenta Sato <[email protected]>
clean up

github.com/BioJulia/IndexableBitVectors.jl - 57f989465ead94240ca01e6bea809f9691ee93de authored over 9 years ago by Kenta Sato <[email protected]>
rename SuccBitVector to CompactBitVector

github.com/BioJulia/IndexableBitVectors.jl - b648cc0d7c58d155d61c0e1c7adffc1e6ee39e6e authored over 9 years ago by Kenta Sato <[email protected]>
fix argument types

github.com/BioJulia/IndexableBitVectors.jl - 1b653f766ae0e355e8f6f5e57ae4618ba13a9d1e authored over 9 years ago by Kenta Sato <[email protected]>
extend SuccinctBitVector to 2^40 bits

github.com/BioJulia/IndexableBitVectors.jl - efa07b2de54f27fa8571ad295bd2f0bddc9e19a4 authored over 9 years ago by Kenta Sato <[email protected]>
move some functions

github.com/BioJulia/IndexableBitVectors.jl - 0b1f0359a21ee2bdd218ddf091f676b82ee159f9 authored over 9 years ago by Kenta Sato <[email protected]>
fix derived getindex

github.com/BioJulia/IndexableBitVectors.jl - fde8d402e0ae7ee3d2e8b80b9fa77d60942c0e38 authored over 9 years ago by Kenta Sato <[email protected]>
remove unused code

github.com/BioJulia/IndexableBitVectors.jl - cb2c598a0ce3ab6e6cffa11e2e264d0930d28185 authored over 9 years ago by Kenta Sato <[email protected]>
fix bench.jl

github.com/BioJulia/IndexableBitVectors.jl - d940fada50fa2e3552a05493619b2afd4f425d15 authored over 9 years ago by Kenta Sato <[email protected]>
move fallback functions to derived.jl

github.com/BioJulia/IndexableBitVectors.jl - e49d32b84651776b79ecc491b940b07fd6050704 authored over 9 years ago by Kenta Sato <[email protected]>
add a derived getindex method

github.com/BioJulia/IndexableBitVectors.jl - c3ece73abd00d4b9229f616f6500a93b6194d091 authored over 9 years ago by Kenta Sato <[email protected]>
rename package name

github.com/BioJulia/IndexableBitVectors.jl - d3146848ecca06b455d13debc41015125bb0faa7 authored over 9 years ago by Kenta Sato <[email protected]>
enlarge maximum size of RRRs

github.com/BioJulia/IndexableBitVectors.jl - bbf17d918e060491c60d44cb3812cd96df0c71e3 authored over 9 years ago by Kenta Sato <[email protected]>
small optimizations and renames

github.com/BioJulia/IndexableBitVectors.jl - ed02f865ca4b8951e0009f02a750d92a929f49c8 authored over 9 years ago by Kenta Sato <[email protected]>
v0.4 compatibility improvement

github.com/BioJulia/IndexableBitVectors.jl - 9697bb67370167f81162f4a59866de96b08c49af authored over 9 years ago by Kenta Sato <[email protected]>
remove magic numbers

github.com/BioJulia/IndexableBitVectors.jl - 9055b4136949f2f0f59adb1aff6e4f19d7c46017 authored over 9 years ago by Kenta Sato <[email protected]>
add some @inbounds

github.com/BioJulia/IndexableBitVectors.jl - b144af64025f9f93e21e00404c56f87000fe0050 authored over 9 years ago by Kenta Sato <[email protected]>
fix some

github.com/BioJulia/IndexableBitVectors.jl - 65f591de3d3354baf7e3b42fdcf669d43f5cdc9b authored over 9 years ago by Kenta Sato <[email protected]>
use the switch macro

github.com/BioJulia/IndexableBitVectors.jl - 12ff34d3b571c041b586beeafad0ec029ac670bc authored over 9 years ago by Kenta Sato <[email protected]>
unify RRRs' constructors

github.com/BioJulia/IndexableBitVectors.jl - d76166cf6d9586ced04cb273bd2d20047f1b368e authored over 9 years ago by Kenta Sato <[email protected]>
remove global constants

github.com/BioJulia/IndexableBitVectors.jl - 3016f524859dcdf7b7db2ad398aa9d0111fa2862 authored over 9 years ago by Kenta Sato <[email protected]>
implement RRRNP

github.com/BioJulia/IndexableBitVectors.jl - d34018fd8b3a712ffbea46ba96ee513f89fb273d authored over 9 years ago by Kenta Sato <[email protected]>
Merge pull request #53 from dcjones/coverage

[RFC] Interval Coverage

github.com/BioJulia/Bio.jl - 032d367bb8cd014fabf68d1ce706537f0df8dce1 authored over 9 years ago by Daniel C. Jones <[email protected]>
Function to compute coverage over IntervalStreams

github.com/BioJulia/Bio.jl - 52801b6b7d51fe7947b20167345aa2d4908ef422 authored over 9 years ago by Daniel Jones <[email protected]>
Merge pull request #50 from dcjones/intervals-io

WIP: BED Parser

github.com/BioJulia/Bio.jl - 49c6c04671512a4d00f4068453b4aaaf3e189536 authored over 9 years ago by Daniel C. Jones <[email protected]>
use a precomputed table to look up binomial values

github.com/BioJulia/IndexableBitVectors.jl - a58bbfed1daeeda86e21b3305cc1736b5518bf4d authored over 9 years ago by Kenta Sato <[email protected]>
implement sizeof (and compatibility improvement)

github.com/BioJulia/IndexableBitVectors.jl - db548b66692c81b8d27d81edc5d938a48f35ca2e authored over 9 years ago by Kenta Sato <[email protected]>
add some comments

github.com/BioJulia/IndexableBitVectors.jl - 6f77ab8137e175e392ef16d05a55ef3e08343f7d authored over 9 years ago by Kenta Sato <[email protected]>
improve type stability and performance

github.com/BioJulia/IndexableBitVectors.jl - 120d70fcd3f078307541d987b0298074cc228283 authored over 9 years ago by Kenta Sato <[email protected]>
extend some basic operations (+ some tests)

github.com/BioJulia/IndexableBitVectors.jl - e6c7e6116e06c6abd4bee8fd1ed1604bc254547b authored over 9 years ago by Kenta Sato <[email protected]>
add tests

github.com/BioJulia/IndexableBitVectors.jl - e836c4ccc16f630ba10067cfe741e938ed86a337 authored over 9 years ago by Kenta Sato <[email protected]>
getindex of RRR works

github.com/BioJulia/IndexableBitVectors.jl - 02824c84d212ddc16f60b90d9533f7cd213c9cde authored over 9 years ago by Kenta Sato <[email protected]>
add CSucVector

github.com/BioJulia/IndexableBitVectors.jl - f001323b64e8d912bfb2835ac113e54e1df50cde authored over 9 years ago by Kenta Sato <[email protected]>
add SucVector

github.com/BioJulia/IndexableBitVectors.jl - 8f4c670c620f1bf04782d9261c2af3420857260f authored over 9 years ago by Kenta Sato <[email protected]>
Respect io in show.

github.com/BioJulia/IntervalTrees.jl - 9f42d72b531a44e490b1b971f6bec5748e7c2d25 authored over 9 years ago by Daniel Jones <[email protected]>
Merge branch 'pull-request/a9a8d91c' of https://github.com/phaverty/IntervalTrees.jl into phaverty

github.com/BioJulia/IntervalTrees.jl - 1f96c7d8175c73a4c4e3b4fde15518ced0d4c447 authored over 9 years ago by Daniel Jones <[email protected]>
Merge branch 'pull-request/ad3c6a1e' of https://github.com/phaverty/IntervalTrees.jl into phaverty

github.com/BioJulia/IntervalTrees.jl - 80c2bf371046726bd92b0fad93d934c52c910d57 authored over 9 years ago by Daniel Jones <[email protected]>
Export value function.

github.com/BioJulia/IntervalTrees.jl - 7de07a9d09c19d24016f297c708fb82c551c212c authored over 9 years ago by Daniel Jones <[email protected]>
Update IntervalTrees diagram to reflect current design.

github.com/BioJulia/Bio.jl - 3e629f8b8dd8f024e78a5d7ee28f0eea3211bf91 authored over 9 years ago by Daniel Jones <[email protected]>
Missing imports.

github.com/BioJulia/Bio.jl - 43691af4ee2635eb9150494ccb542429482a0024 authored over 9 years ago by Daniel Jones <[email protected]>
Fix off-by-one on BED coordinates.

github.com/BioJulia/Bio.jl - 7aa0055bbd82653567e97bf97dbc7990cc007242 authored over 9 years ago by Daniel Jones <[email protected]>
More performance improvements to bed parsing and intersecting.

github.com/BioJulia/Bio.jl - 11294459735921aeee020ddf2c96c0ca09c29904 authored over 9 years ago by Daniel Jones <[email protected]>
Some performance improvements.

github.com/BioJulia/Bio.jl - 75039eabef68341c3578743fdb4beaafb73d46ff authored over 9 years ago by Daniel Jones <[email protected]>
Tests for IntervalStream intersection.

github.com/BioJulia/Bio.jl - a0876d04f1cb6234d5a5f4a50397df149ef1a029 authored over 9 years ago by Daniel Jones <[email protected]>
Allow '.' and '?' in BED strand field. Print STRAND_NA as '?'.

github.com/BioJulia/Bio.jl - 1053743ab72f615e4d2b1e01fcc0d8ac7f253e9e authored over 9 years ago by Daniel Jones <[email protected]>
Fix a parsing integers.

github.com/BioJulia/Bio.jl - a99d9539d5eb1ab309ef40dfe0567b569ef148c7 authored over 9 years ago by Daniel Jones <[email protected]>
Add tests for BED parser. Fix a couple bugs.

github.com/BioJulia/Bio.jl - 819e7e79ad2760b11cb8f257af29f94890b7124e authored over 9 years ago by Daniel Jones <[email protected]>
BED parser.

github.com/BioJulia/Bio.jl - 6575c136e7b4cb7fb13edf69b1daf11677d10c98 authored over 9 years ago by Daniel Jones <[email protected]>
digitseps

github.com/BioJulia/WaveletMatrices.jl - e2aca9f21c7a287f59fb58085d12382396412c9b authored over 9 years ago by Kenta Sato <[email protected]>
print text length and uppercase

github.com/BioJulia/WaveletMatrices.jl - 8da1669abcffeddbc78207bb654f62ee59759dc4 authored over 9 years ago by Kenta Sato <[email protected]>
fix readme

github.com/BioJulia/IndexableBitVectors.jl - 0ab28f3ec5bd78bcc4f11f3554f66e79e2814d96 authored over 9 years ago by Kenta Sato <[email protected]>
remove newlines

github.com/BioJulia/WaveletMatrices.jl - a845233c80c78e29ad243332e954971ddf2875b4 authored over 9 years ago by Kenta Sato <[email protected]>
fix a link

github.com/BioJulia/WaveletMatrices.jl - d2354923d9040eeb787ebaf241f4b09336589018 authored over 9 years ago by Kenta Sato <[email protected]>
add README and small fixes

github.com/BioJulia/WaveletMatrices.jl - 85805ebe1897521bb8bd7cafeeb06d01eff0d5c5 authored over 9 years ago by Kenta Sato <[email protected]>
add REQUIRE

github.com/BioJulia/IndexableBitVectors.jl - 3953fc944f44cb4423340a76c2b3ecd6084e6e25 authored over 9 years ago by Kenta Sato <[email protected]>
rename package name + README

github.com/BioJulia/IndexableBitVectors.jl - dc6e2dd3efc77d126898b5afea68f7bf65f7bc20 authored over 9 years ago by Kenta Sato <[email protected]>
add FM-index demo

github.com/BioJulia/WaveletMatrices.jl - 80540027131e396fc957deead2407804834680cd authored over 9 years ago by Kenta Sato <[email protected]>
store length

github.com/BioJulia/WaveletMatrices.jl - 363748caeb2635243bbcf7f487b9a4bf9319d8c3 authored over 9 years ago by Kenta Sato <[email protected]>
add constructor and rank

github.com/BioJulia/WaveletMatrices.jl - ada210299ed231ae787c705092bf5f2ca02e6779 authored over 9 years ago by Kenta Sato <[email protected]>
WaveletMatrices.jl generated files.

license: MIT
authors: Kenta Sato
years: 2015
user: bicycle1885

Julia V...

github.com/BioJulia/WaveletMatrices.jl - 1967a738abb8a47b5a7d9e6f121df98845f71fa4 authored over 9 years ago by Kenta Sato <[email protected]>
initial empty commit

github.com/BioJulia/WaveletMatrices.jl - 35b78451f47751c72a1ae44eb0295fd2aedf43a1 authored over 9 years ago by Kenta Sato <[email protected]>
add a simple succinct bit vector

github.com/BioJulia/IndexableBitVectors.jl - 2ea84b4398b3e51cb5649e21c4a4a4f04f53fdc9 authored over 9 years ago by Kenta Sato <[email protected]>
add a reference implementation

github.com/BioJulia/IndexableBitVectors.jl - 056b24f63dbc0d283055d15676e0e05adc044286 authored over 9 years ago by Kenta Sato <[email protected]>
IndexableDicts.jl generated files.

license: MIT
authors: Kenta Sato
years: 2015
user: bicycle1885

Julia V...

github.com/BioJulia/IndexableBitVectors.jl - 8c518edbc9593a7f9fb1fded1997bada3eb67739 authored over 9 years ago by Kenta Sato <[email protected]>