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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

Store residue/atom lists for faster collections; some docs

github.com/BioJulia/Bio.jl - 9d122d82c6c9da65f9a7624735ac6272651a7094 authored over 8 years ago by Joe Greener <[email protected]>
added .gitignore file to repository

github.com/BioJulia/mkdocs-biojulia - 687619ef6b1399f603987739b92487e74915678e authored over 8 years ago by Chris Simpkins <[email protected]>
added __init__.py file for PyPI release

github.com/BioJulia/mkdocs-biojulia - 8461f57ac64b3382169f7fa14590fe3313231718 authored over 8 years ago by Chris Simpkins <[email protected]>
updates for PyPI release

github.com/BioJulia/mkdocs-biojulia - abdfc426fc63ecff01a7f05ed04558ff8637fab2 authored over 8 years ago by Chris Simpkins <[email protected]>
formatomlist; many bug fixes

github.com/BioJulia/Bio.jl - ac2593019cd1dd24f33a088b287abae132c8832d authored over 8 years ago by Joe Greener <[email protected]>
Merge from master; change test structure

github.com/BioJulia/Bio.jl - 80a77b5556776f2baba49b854898f4a0cf43c549 authored over 8 years ago by Joe Greener <[email protected]>
arg... fixing; some getter/setters; organise into res

github.com/BioJulia/Bio.jl - 50c7157940544ec91d296889a8da443842afa24b authored over 8 years ago by Joe Greener <[email protected]>
Merge pull request #130 from BioJulia/newtests

Replace FactCheck with BaseTestNext

github.com/BioJulia/Bio.jl - ebf7062e38c6fc9ca8c5426679dddaca205b59b1 authored over 8 years ago by Richard Smith-Unna <[email protected]>
parsing functions; ternary operators; organise

github.com/BioJulia/Bio.jl - 893c063e41e25397497dc93d6f53f5d3d04e2bcb authored over 8 years ago by Joe Greener <[email protected]>
addtomodel!; show; some model and spatial tests

github.com/BioJulia/Bio.jl - 8dd323d163750a490096f94ae3c0402172600f39 authored over 8 years ago by Joe Greener <[email protected]>
show; organise; spatial; test outline

github.com/BioJulia/Bio.jl - 9be74f000bebce4c5c99f929ec2b0d23d3676d11 authored over 8 years ago by Joe Greener <[email protected]>
more getters; organise and unfold

github.com/BioJulia/Bio.jl - 1ad8911d51889113f5f62788c81acafa1b901d99 authored over 8 years ago by Joe Greener <[email protected]>
type scheme; some getters, iterators and selectors

github.com/BioJulia/Bio.jl - e2b7fee2cbd6797247880b7e713bc8da24d6e22f authored over 8 years ago by Joe Greener <[email protected]>
replace FactCheck with BaseTestNext

github.com/BioJulia/IndexableBitVectors.jl - 8326b18c248b460cebacb091325fd7eac78f8248 authored over 8 years ago by Kenta Sato <[email protected]>
remove messages for debug

github.com/BioJulia/Bio.jl - a68bb886d47962b72feda48e008e0c660d5d46ed authored over 8 years ago by Kenta Sato <[email protected]>
fix equality syntax in tests

This patch replaces prefix equality operators with infix ones, which is more
natural in new test...

github.com/BioJulia/Bio.jl - 8b0ec34c282f372d2e0468f70268407d2aa13e6f authored over 8 years ago by Kenta Sato <[email protected]>
Fix broken inflate/deflate functions. Fixes #10

github.com/BioJulia/Libz.jl - c0be7d16db2fc7b6586e083c6fcebebcbf6c1242 authored over 8 years ago by Daniel Jones <[email protected]>
Bio file changes and empty files

github.com/BioJulia/Bio.jl - 36c5a876b880bcd166a41638a45e3c8a8ec274f1 authored over 8 years ago by Joe Greener <[email protected]>
fix .travis.yml

github.com/BioJulia/IntervalTrees.jl - f4884e0f9428035791584552f803abdc3b55dc68 authored over 8 years ago by Kenta Sato <[email protected]>
run Travis CI on v0.3

github.com/BioJulia/IntervalTrees.jl - 75b4af106015127b32759081de83212a8460220c authored over 8 years ago by Kenta Sato <[email protected]>
add Compat to REQUIRE

github.com/BioJulia/IntervalTrees.jl - aa9a66bc6e11df627ab417f3c87b980ccd57accb authored over 8 years ago by Kenta Sato <[email protected]>
Merge pull request #12 from tkelman/patch-1

remove - on julia version in REQUIRE

github.com/BioJulia/IntervalTrees.jl - f24b9ee99f2f6fb5558f43fe52677e49c41478a2 authored over 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
replace FactCheck with BaseTestNext

github.com/BioJulia/Bio.jl - d949e5e93d50fb9559c572be73a42ee902c6ea68 authored over 8 years ago by Kenta Sato <[email protected]>
drop FactCheck dependency

github.com/BioJulia/Bio.jl - 2d1789e73f85d944fdf088850c1853e6f1c50552 authored over 8 years ago by Kenta Sato <[email protected]>
allow to pass test targets as command-line arguments

The test/runtests.jl script can take command-line arguments to specify test
targets, which saves...

github.com/BioJulia/Bio.jl - fe2eaba11485d4837d1eac7be927560079c03f11 authored over 8 years ago by Kenta Sato <[email protected]>
require v0.4

github.com/BioJulia/Bio.jl - 0db18e889994bb690555f0ddf1fa86b50d9021b3 authored over 8 years ago by Kenta Sato <[email protected]>
Update README.md with examples per #12

github.com/BioJulia/Libz.jl - 3b3b1f3da5d725677e832d3122cc1164103e68ca authored over 8 years ago by Sam O'Connor <[email protected]>
Merge pull request #12 from samoconnor/patch-1

Convenience functions for dealing with .gz files

github.com/BioJulia/Libz.jl - ba42de7502d062ef15a57933a70959c1a7a3ef9b authored over 8 years ago by Ben J. Ward <[email protected]>
test cases for readgz, writegz, readgzstring

github.com/BioJulia/Libz.jl - 35f3ea2e1531dd246631e6274ba75f9563d2b4fc authored over 8 years ago by Sam O'Connor <[email protected]>
Fix example in README.md

github.com/BioJulia/Libz.jl - c59b56949c973a3da8b9a505ae0a17547ef4b4a1 authored over 8 years ago by Sam O'Connor <[email protected]>
Merge pull request #14 from yuyichao/dep-off_t

Remove deprecated FileOffset

github.com/BioJulia/Libz.jl - f3da0ac00014256efb32d130ca924dcc2704617f authored over 8 years ago by Richard Smith-Unna <[email protected]>
Remove deprecated FileOffset

github.com/BioJulia/Libz.jl - 7b4c31e41bfc2dd20685f210a6a9ea90c299fd3a authored over 8 years ago by Yichao Yu <[email protected]>
Merge pull request #111 from BioJulia/pairalign

Pairwise-alignment algorithms

github.com/BioJulia/Bio.jl - 013373f597520d807b46d79071e97ef8d66d61d8 authored over 8 years ago by Ben J. Ward <[email protected]>
export names

github.com/BioJulia/Bio.jl - 47c1ca4d7b12f74556c186ba81eafcbf171f5c84 authored over 8 years ago by Kenta Sato <[email protected]>
remove an unnecessary macro

github.com/BioJulia/Bio.jl - 50351d2bcb4a4a9fbb9ad11bcfceb572d525ac2c authored over 8 years ago by Kenta Sato <[email protected]>
many tweaks

github.com/BioJulia/Bio.jl - 5dba2f44dbc4953d010b9299d5d002d0ef30448f authored over 8 years ago by Kenta Sato <[email protected]>
add PairwiseAlignment type

github.com/BioJulia/Bio.jl - 6c10e70e43c0a632b0e75ad441dc845c30de5d05 authored over 8 years ago by Kenta Sato <[email protected]>
fix wording

github.com/BioJulia/Bio.jl - 857adb33cc562e16c90f3b1c067def9ef201516f authored over 8 years ago by Kenta Sato <[email protected]>
minor performance improvement of findanchor

github.com/BioJulia/Bio.jl - ff3c1ced19dc6a79fcc4a1b8433a1e6e66757355 authored over 8 years ago by Kenta Sato <[email protected]>
add position mapping between seq and ref

github.com/BioJulia/Bio.jl - efba0da6c62bf27888f8c157fbcc2299ef537da5 authored over 8 years ago by Kenta Sato <[email protected]>
performance optimization for banded Needleman-Wunsch

github.com/BioJulia/Bio.jl - 529558da0b400be904ddafdb0bb3d0a05985acc6 authored over 8 years ago by Kenta Sato <[email protected]>
add a docstring for pairalign

github.com/BioJulia/Bio.jl - 9f8a14d81c0217f8ae5909b6f10d5abf8236e7ee authored over 8 years ago by Kenta Sato <[email protected]>
redesign the substitution matrix

github.com/BioJulia/Bio.jl - a7e355d95e21999c9167e79377e7847e494a2e98 authored over 8 years ago by Kenta Sato <[email protected]>
fix the interfaces of CostModel like affine gap

github.com/BioJulia/Bio.jl - 3955ba3380cd51c5e7fb29a6a75231af5ad799b4 authored over 8 years ago by Kenta Sato <[email protected]>
clean up the interfaces of AffineGapScoreModel

github.com/BioJulia/Bio.jl - 7e93cd98187617d4d032c54e5d5c4a9a46bcc7d0 authored over 8 years ago by Kenta Sato <[email protected]>
add the overlap alignment

github.com/BioJulia/Bio.jl - 2e2a56929cde2b8a98916344e1ef73838bf77c2f authored over 8 years ago by Kenta Sato <[email protected]>
remove old files and refactoring

github.com/BioJulia/Bio.jl - 1ac2f7497eda08199f35e91bcae1993113268554 authored over 8 years ago by Kenta Sato <[email protected]>
fix global alignment algorithms

github.com/BioJulia/Bio.jl - 5bcdada084d496390eba543a8c21d2f993ac04b1 authored over 8 years ago by Kenta Sato <[email protected]>
add minimum and maximum for SubstitutionMatrix

github.com/BioJulia/Bio.jl - b102f70047c567eb03887c650f77628ef88e0156 authored over 8 years ago by Kenta Sato <[email protected]>
add pretty printer for substitution matrices

github.com/BioJulia/Bio.jl - 1c1b790c6ff0cac5c11bea8363741234d3e7612c authored over 8 years ago by Kenta Sato <[email protected]>
delete some macros

github.com/BioJulia/Bio.jl - 24e6b6bc0f3be6f48353f81ddf280d07000cd898 authored over 8 years ago by Kenta Sato <[email protected]>
break a long line

github.com/BioJulia/Bio.jl - 7831c445a6c52a80c789c3035f7214a9a198631a authored over 8 years ago by Kenta Sato <[email protected]>
rename a field

github.com/BioJulia/Bio.jl - 016773f9c5ec2220a93b460443ba98883015eaed authored over 8 years ago by Kenta Sato <[email protected]>
minor performance improvement of banded global alignment

github.com/BioJulia/Bio.jl - 9ad37dc94fad9161088c6032a86dfbddf3db828b authored over 8 years ago by Kenta Sato <[email protected]>
minor performance improvement of semi-global alignment

github.com/BioJulia/Bio.jl - f6abd51f620330266e74de9fce7d1a372eb638fa authored over 8 years ago by Kenta Sato <[email protected]>
minor performance improvement of local alignment

github.com/BioJulia/Bio.jl - 328b7ceff8da917c84d062cc6c88c702446794aa authored over 8 years ago by Kenta Sato <[email protected]>
add a few accessors for pairwise alignment

github.com/BioJulia/Bio.jl - a384582ed011a03a5349d3ae9cb0707e24e32ae3 authored over 8 years ago by Kenta Sato <[email protected]>
add some submat conversions

github.com/BioJulia/Bio.jl - 66f5280639dd12074a200926d09cd174fbe0c23e authored over 8 years ago by Kenta Sato <[email protected]>
fix AffineGapScoreModel constructors

github.com/BioJulia/Bio.jl - 64a94290836a489741aa90914bb82eafd38dcaa1 authored over 8 years ago by Kenta Sato <[email protected]>
add a few tests for the banded global

github.com/BioJulia/Bio.jl - 147b8f2783c7f65298fcd331a043b99c77c7831e authored over 8 years ago by Kenta Sato <[email protected]>
remove unnecessary `esc`s

github.com/BioJulia/Bio.jl - 0e1571acd84a4e4de985cbaa2d8511047cafb931 authored over 8 years ago by Kenta Sato <[email protected]>
add more substitution matrices

github.com/BioJulia/Bio.jl - 02596e323f9715db3e1372252ef0be9316ceb8e0 authored over 8 years ago by Kenta Sato <[email protected]>
fix Smith-Waterman

github.com/BioJulia/Bio.jl - d618f4d4617787a601adf35d2a6321d57e64dae5 authored over 8 years ago by Kenta Sato <[email protected]>
add some tests for pairwise alignment

github.com/BioJulia/Bio.jl - a2ea72d00c232f459dfba600834974276c53bb33 authored over 8 years ago by Kenta Sato <[email protected]>
add the hamming distance

github.com/BioJulia/Bio.jl - badc6a38abd32b95f336feb3bc441ed6f2701c79 authored over 8 years ago by Kenta Sato <[email protected]>
add the edit distance

github.com/BioJulia/Bio.jl - 841513a260906eb2d06a9a4e60fca4779255e8fa authored over 8 years ago by Kenta Sato <[email protected]>
add the semi-global alignment

github.com/BioJulia/Bio.jl - 0597906a39f4ec21a15966e81694e227dec64bd8 authored over 8 years ago by Kenta Sato <[email protected]>
add the local alignment

github.com/BioJulia/Bio.jl - dc0ef90e0bf454ead9681789858994cc561ef7d3 authored over 8 years ago by Kenta Sato <[email protected]>
add the banded global alignment

github.com/BioJulia/Bio.jl - d644806facafe4d4901ba7c79a7a2812a932205f authored over 8 years ago by Kenta Sato <[email protected]>
add the global alignment

github.com/BioJulia/Bio.jl - 3dc4f3fd78d4b10890f5b5691029394844a5aadc authored over 8 years ago by Kenta Sato <[email protected]>
clean up tests

github.com/BioJulia/Bio.jl - 6406b1f5c68fd14453d84c59abdba12d1ff60ca9 authored over 8 years ago by Kenta Sato <[email protected]>
fix traceback and test alignment

github.com/BioJulia/Bio.jl - 24473633de568bf5100304669cd431db2ca833a1 authored over 8 years ago by Kenta Sato <[email protected]>
minor performance improvement of global alignment

github.com/BioJulia/Bio.jl - 662f20d65b88dd36d8c915c47582455b390fd792 authored over 8 years ago by Kenta Sato <[email protected]>
add docstrings for pairwise alignment

github.com/BioJulia/Bio.jl - 97a50e0df063807f2141decea0c2c16df83cb24b authored over 8 years ago by Kenta Sato <[email protected]>
add count and count_<op> functions in place of nmatching etc.

github.com/BioJulia/Bio.jl - 782a23d2635c0c7097576d9c9cef1534ea08e923 authored over 8 years ago by Kenta Sato <[email protected]>
add nmatching/nmismatching/naligned methods

github.com/BioJulia/Bio.jl - 8b04ed7e196d15b762438a7931385e3b0c7dcf21 authored over 8 years ago by Kenta Sato <[email protected]>
removed horizontal rules

github.com/BioJulia/Bio.jl - 938916481606ea255b9ab7fe650578f3e5f33304 authored almost 9 years ago by Ben J. Ward <[email protected]>
changed size of headings

github.com/BioJulia/Bio.jl - dba73f3e211a8438bf2ccd4973c0a8dece7c6a52 authored almost 9 years ago by Ben J. Ward <[email protected]>
Added documentation badge

github.com/BioJulia/Bio.jl - 08f8de20e5e1c9cad9e837892a2901b48bc4b3df authored almost 9 years ago by Ben J. Ward <[email protected]>
Annotated badges

github.com/BioJulia/Bio.jl - c5d0dbbc6b7537b00b00fa96c74c15ff4c3895eb authored almost 9 years ago by Ben J. Ward <[email protected]>
update exports

github.com/BioJulia/Libz.jl - dfd00917058a18003123d4b9e9b3116ec21e1ad0 authored almost 9 years ago by Sam O'Connor <[email protected]>
revised names for consistency with base (e.g. writecsv, readcsv)

See also https://github.com/JuliaLang/julia/issues/14608

github.com/BioJulia/Libz.jl - e95bdf1b898f94dfad17fdca54700224f82e7b1a authored almost 9 years ago by Sam O'Connor <[email protected]>
Convenience functions for dealing with .gz files

Convenience functions to read/write directly from/to a named file.

I'm doing a cleanup of my ...

github.com/BioJulia/Libz.jl - afbbeef242e531a1223fc400af584f5aa15317bd authored almost 9 years ago by Sam O'Connor <[email protected]>
year bump

github.com/BioJulia/mkdocs-biojulia - bd8630cb6eef9e2ce86c1e98732139c003664b59 authored almost 9 years ago by Chris Simpkins <[email protected]>
Merge pull request #127 from BioJulia/Ward9250-appveyor-patch

Update appveyor.yml

github.com/BioJulia/Bio.jl - adec84502cc439af6db18fa5fa510c90ff63442a authored almost 9 years ago by Ben J. Ward <[email protected]>
Update appveyor.yml

Removing 32 bit support. Most computers are 64 bit now anyway.

github.com/BioJulia/Bio.jl - 4f83f6c5f1a8ce1ce53193f0f11addab6490390e authored almost 9 years ago by Ben J. Ward <[email protected]>
Merge pull request #116 from Ward9250/sliding-windows

Sliding windows - redux

github.com/BioJulia/Bio.jl - d8df29109f05eaa4565fe3fba17715e40b4adc6b authored almost 9 years ago by Ben J. Ward <[email protected]>
Made testintervals cross platform with DevNull

github.com/BioJulia/Bio.jl - da32c6e44fa20372111ce831cb7adcb29b3d6401 authored almost 9 years ago by Ward9250 <[email protected]>
Added typealias statement

github.com/BioJulia/Bio.jl - 569c3ac005fea1b6ec33466d281f70d1d6485e2b authored almost 9 years ago by Ward9250 <[email protected]>
src/util/Util.jl

github.com/BioJulia/Bio.jl - e7168e349e7a429f2eb7ba97b24a23da57a61af1 authored almost 9 years ago by Ward9250 <[email protected]>
Added corrections and suggestions by bicycle1885

github.com/BioJulia/Bio.jl - 5795d714346ebca408bc8e0a2823e1311d91126d authored almost 9 years ago by Ben Ward (TGAC) <[email protected]>
Edited constructor function.

github.com/BioJulia/Bio.jl - 80dd88dc8c1629716dbf0ebd408e53d18204bbe1 authored almost 9 years ago by Ward9250 <[email protected]>
Edited assertion in constructor and added string and sequences cases to some tests

github.com/BioJulia/Bio.jl - 0e03ce1228d939c460b1cdea28eb606b61ebd16c authored almost 9 years ago by Ward9250 <[email protected]>
Added string and sequences to tests

github.com/BioJulia/Bio.jl - 70cc854f46a4f98be830f36bb0c742fcc6c9123a authored almost 9 years ago by Ward9250 <[email protected]>
Added next method for strings.

github.com/BioJulia/Bio.jl - 008efac5075dfbaedc9b812cf52b9d78ef244179 authored almost 9 years ago by Ward9250 <[email protected]>
A revival and improvement on the previous sliding window PR.

github.com/BioJulia/Bio.jl - 817b1c2b2193ee13c13df98bc363234e39c96a52 authored almost 9 years ago by Ward9250 <[email protected]>
Inline window iterator functions

github.com/BioJulia/Bio.jl - 7068d2f682cbd6d0c9dfd4e46f0259563d2d097d authored almost 9 years ago by Kevin Murray <[email protected]>
Remove import Base in windows.jl, it's in Util.jl

Also minor refactoring for a more illustrative name

github.com/BioJulia/Bio.jl - 9cae6e944d7c060b269f7b96613b027cc3808b59 authored almost 9 years ago by Kevin Murray <[email protected]>
Add window iterator under Bio.Util module

github.com/BioJulia/Bio.jl - dcab992a811a29c014370406ccafa994b689ee9e authored almost 9 years ago by Kevin Murray <[email protected]>
Add window iterator under Bio.Util module

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