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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 iteratorsize check (#20)

github.com/BioJulia/IntervalTrees.jl - 22271b5132b086cf911252d5d619357dd90bc6c6 authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
remove Compat.jl depndency (#19)

github.com/BioJulia/IntervalTrees.jl - f97a29a64683fde4627b6fff142c7169ec077a96 authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Merge pull request #234 from bicycle1885/demultiplexer

add demultiplexer

github.com/BioJulia/Bio.jl - 55d750505e6c1a60124d46fea3381f06d98164f3 authored about 8 years ago by Kevin Murray <[email protected]>
Update index.md

github.com/BioJulia/Bio.jl - a4c7b4614e3c96622625a9e7f2f7c02acba2a164 authored about 8 years ago by Ben J. Ward <[email protected]>
Added Var to manual.

github.com/BioJulia/Bio.jl - b869cfce000c715e16432a82b226c0a034c6fbd8 authored about 8 years ago by Ben J. Ward <[email protected]>
run TravisCI on Julia 0.5 (#18)

github.com/BioJulia/IntervalTrees.jl - f4b0e3023f66213f68df210ba81f2cd2f7a43cbe authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Moved mutation counting to var module. (#258)

Moved mutation counting tests.

For now just using all of the Bio.Seq module

Added debug li...

github.com/BioJulia/Bio.jl - dfefd76053a4650cabfbdd152524e42fe215ef0f authored about 8 years ago by Ben J. Ward <[email protected]>
rename ispalindrome to ispalindromic (#262)

github.com/BioJulia/Bio.jl - 5c0c17ebd8eeee3dc7d0c4bacafe2b1550c12534 authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
remove deprecated names (#261)

github.com/BioJulia/Bio.jl - 088c8f9561be246885bf6743df364b53d6698f99 authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Add example to parsing of fastq sequences (#260)

github.com/BioJulia/Bio.jl - a583119ec5ad226535fd601400db50ba2c3d4963 authored about 8 years ago by Kevin Murray <[email protected]>
add random sequence generators (#251)

* add random sequence generators

* fixup! add random sequence generators

* fixup! fixup! a...

github.com/BioJulia/Bio.jl - 5c7125745dc2a382d495f73fc4404e293e818822 authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Add labelled square matrix parser (#253)

* Add labelled square matrix parser w/ docs & tests

* Fix file readers

* Add test of comme...

github.com/BioJulia/Bio.jl - ce1ebeb9d5ad84e871e9740c19ff6c432206bf96 authored about 8 years ago by Kevin Murray <[email protected]>
remove clipboard(seq) (#257)

github.com/BioJulia/Bio.jl - da5577bbcab276ff360b39e0cc4d406603c2aafe authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Merge pull request #13 from kdmurray91/lsm

Add labelled square matrix samples

github.com/BioJulia/BioFmtSpecimens - df98979c3878c780d616ac09ebb207ad234cc4ee authored about 8 years ago by Kevin Murray <[email protected]>
Add LSM index.yml

github.com/BioJulia/BioFmtSpecimens - 90389ebbdb7541c90ee85f30a55e9cb2ac6bdd25 authored about 8 years ago by Kevin Murray <[email protected]>
Add substitution matrices per comments on #13

github.com/BioJulia/BioFmtSpecimens - 18c36b6a278cce174411b0f636fc0a5cc7401a83 authored about 8 years ago by Kevin Murray <[email protected]>
fixup! fixup! fixup! fixup! fixup! fixup! fixup! fixup! add StaticTrie

github.com/BioJulia/Bio.jl - 9c6c62ef733a8446dc5fad0913b56d038cf15ce4 authored about 8 years ago by Kenta Sato <[email protected]>
fixup! fixup! fixup! fixup! fixup! fixup! fixup! fixup! fixup! add StaticTrie

github.com/BioJulia/Bio.jl - b665d3718e1c0a504748b0473065f58e4e4bc61f authored about 8 years ago by Kenta Sato <[email protected]>
fixup! fixup! fixup! fixup! fixup! fixup! fixup! add StaticTrie

github.com/BioJulia/Bio.jl - 4e726d4d8c37159707ba03390e2253304cbbfb9b authored about 8 years ago by Kenta Sato <[email protected]>
fixup! fixup! fixup! fixup! fixup! fixup! add StaticTrie

github.com/BioJulia/Bio.jl - 0c7c5adcd8f61c634a2cfc4b5f5be47c2ca73077 authored about 8 years ago by Kenta Sato <[email protected]>
fixup! fixup! fixup! fixup! fixup! add StaticTrie

github.com/BioJulia/Bio.jl - cedb3eaff2963a691a8f7519d72568b3ed488c77 authored about 8 years ago by Kenta Sato <[email protected]>
fixup! fixup! fixup! fixup! add StaticTrie

github.com/BioJulia/Bio.jl - 9d46aff5230844a68b7f1d477fe95bb9eb542b0c authored about 8 years ago by Kenta Sato <[email protected]>
fix some

github.com/BioJulia/Bio.jl - d50a3ac7fb66b52072f7ee44b1ca8cbc5b815099 authored about 8 years ago by Kenta Sato <[email protected]>
fixup! add StaticTrie

github.com/BioJulia/Bio.jl - ea2f7f293c110884e316e7029020982af9257811 authored about 8 years ago by Kenta Sato <[email protected]>
add StaticTrie

github.com/BioJulia/Bio.jl - 0ef6dae61a5c115f9c59854546e3ac46aa46e873 authored about 8 years ago by Kenta Sato <[email protected]>
use hasambiguity to check barcodes

github.com/BioJulia/Bio.jl - 16fb9974688e53786e50116c3471109308235eef authored about 8 years ago by Kenta Sato <[email protected]>
add demultiplexer

github.com/BioJulia/Bio.jl - e5e998077a1ff62f99192dc85415c9c14d8f453f authored about 8 years ago by Kenta Sato <[email protected]>
fixup! fixup! fixup! add StaticTrie

github.com/BioJulia/Bio.jl - b2f6833bfce527b698e959c946671b1b8b640e7b authored about 8 years ago by Kenta Sato <[email protected]>
add docs on demultiplexer

github.com/BioJulia/Bio.jl - fca3b45372acb3ee3d42ebfe5dd0a5eb0e76d36d authored about 8 years ago by Kenta Sato <[email protected]>
remove redundant order check

github.com/BioJulia/Bio.jl - e3c614b47ef9a8366040f323a9e747f4e23dbf70 authored about 8 years ago by Kenta Sato <[email protected]>
fixup! fixup! add StaticTrie

github.com/BioJulia/Bio.jl - 32eae53ccde622c09f42454eef73d8e1b0e49038 authored about 8 years ago by Kenta Sato <[email protected]>
simplify branches

github.com/BioJulia/Bio.jl - 5941803c6400812784a86546a5035a1eedbb1905 authored about 8 years ago by Kenta Sato <[email protected]>
rename mutated barcodes

github.com/BioJulia/Bio.jl - 686ca48f658b9cca44d9991933b7c6bfd162e437 authored about 8 years ago by Kenta Sato <[email protected]>
Added U for ambiguous nucleotides in Seq docs (#254)

github.com/BioJulia/Bio.jl - 2870dfc06abf87702a57408be3e25116de57e57a authored about 8 years ago by Kevin Bonham <[email protected]>
Use same matrices as in unit tests

github.com/BioJulia/BioFmtSpecimens - f5100ad207247561c528bf6250089e88bf7ea12c authored about 8 years ago by Kevin Murray <[email protected]>
Add labelled square matrix samples

github.com/BioJulia/BioFmtSpecimens - 4a70eda2aaccc14a04fa5baea01cd38360391e33 authored about 8 years ago by Kevin Murray <[email protected]>
open with a do block (#252)

so the file handle gets closed and the file can be cleaned up on Windows

github.com/BioJulia/Bio.jl - e0461b21a64aa80032ae0abb60eb50c66b7e2fc1 authored about 8 years ago by Tony Kelman <[email protected]>
Rewrite Composition (#247)

* fix composition

* make Composition <: Associative

* composition(eachkmer)

* deprecate...

github.com/BioJulia/Bio.jl - ea70abb72143687b6d4c5a7e1e1f82e5e4e63c3f authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
add close for FASTAParser and FASTQParser (#250)

github.com/BioJulia/Bio.jl - 9951522b5605d7a6b8d933ad1121f12544242b84 authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
fix a typo in intervals.md (#249)

github.com/BioJulia/Bio.jl - 21dcdf20dc9ff69bfc6e1c16c9bae59a53765270 authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
fix intervals.md (#248)

github.com/BioJulia/Bio.jl - d8386b0cada35ef9aa58021553b4fc829bb854a3 authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Io docs (#240)

* update IO docs

* fixup! update IO docs

* fixup! fixup! update IO docs

* fixup! fixup!...

github.com/BioJulia/Bio.jl - 2ab90d0992312c7028d8e1b97510935d1c9200fe authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
make unexported docstrings comments (#246)

github.com/BioJulia/Bio.jl - 80c0b47eea26707c7cbcfc2b560bc4c753dfc9d5 authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Merge pull request #23 from dcjones/update-CI

Update Travis, add Appveyor

github.com/BioJulia/Codecs.jl - e490f4042a53354b88c5ad88190173f1eab3101e authored about 8 years ago by Randy Zwitch <[email protected]>
Update README.md

github.com/BioJulia/Codecs.jl - e8d18c3693b971cf06b89be543e885957f70ef10 authored about 8 years ago by Randy Zwitch <[email protected]>
Update badges

github.com/BioJulia/Codecs.jl - 60f7d822f209eb80ae3a2c12e836fca3ab8c848f authored about 8 years ago by randyzwitch <[email protected]>
Update Travis, add Appveyor

Update Travis to test 0.3 - 0.5, add Windows tests as well. Will inform
next tagged version REQU...

github.com/BioJulia/Codecs.jl - c57a9f21a5851cbedf205a84f1e4bff4c0e5acb7 authored about 8 years ago by randyzwitch <[email protected]>
Merge pull request #20 from abhijithch/ac/depwarns

Fix deprecations

github.com/BioJulia/Codecs.jl - a1c0f5c39cf9fa063964c49e090d000a9c3c645b authored about 8 years ago by Randy Zwitch <[email protected]>
Appveyor badge in README.md displays master status only. Stops misleading red badges.

github.com/BioJulia/Bio.jl - c0ad84c4221eacb1b646220de1ecd1ad62647717 authored about 8 years ago by Ben J. Ward <[email protected]>
Fix fastq quality encoding inference (#243)

* FASTQ parser actually uses given `quality_encoding` argument.

`infer_quality_encoding()` wa...

github.com/BioJulia/Bio.jl - 046f166544ef4bcf312849ba4366e071b89742bd authored about 8 years ago by Kemal Eren <[email protected]>
Merge pull request #1 from tkelman/patch-1

use dirname(@__FILE__) rather than Pkg.dir

github.com/BioJulia/BGZFStreams.jl - 904e81a5d1cef8002abc6b421171123e9294118b authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
add testing against 0.5 to Travis

this is the RC now, will be releases once final is tagged

github.com/BioJulia/BGZFStreams.jl - c0be7b64bd043e8b91ff17a2a1bc8325d9781613 authored about 8 years ago by Tony Kelman <[email protected]>
use dirname(@__FILE__) rather than Pkg.dir

allows installing the package elsewhere

github.com/BioJulia/BGZFStreams.jl - 37642a4dbd7434a976e53dce758356a99c3cbd4e authored about 8 years ago by Tony Kelman <[email protected]>
extract BigBed types from .rl (#241)

github.com/BioJulia/Bio.jl - b8e991b164688b4b94e096458fa818b6a0f2523b authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
FASTA Index (#238)

github.com/BioJulia/Bio.jl - d1c60712c51190dce958df422abcbfbcd06285ab authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
set lower bound of Libz requirement

github.com/BioJulia/BGZFStreams.jl - fc5afdd080cc54d0e5f5cb3529a3c0de561e1357 authored about 8 years ago by Kenta Sato <[email protected]>
add tests on BGZFStream

github.com/BioJulia/BGZFStreams.jl - afb61d3c48207440204840f69ef4483368d899ac authored about 8 years ago by Kenta Sato <[email protected]>
add tests on VirtualOffset

github.com/BioJulia/BGZFStreams.jl - 0058bd2c36026d15efcd97a12db1276ffdb37b74 authored about 8 years ago by Kenta Sato <[email protected]>
activate code coverage

github.com/BioJulia/BGZFStreams.jl - d74548c627fcc67538cd7f2138e4158a409bdcc4 authored about 8 years ago by Kenta Sato <[email protected]>
fix .travis.yml

github.com/BioJulia/BGZFStreams.jl - 1edd90e9a4a1ca08566a130c04441f6126dc695f authored about 8 years ago by Kenta Sato <[email protected]>
fix link of Travis CI

github.com/BioJulia/BGZFStreams.jl - bca951fe6381c8e99935a7e2efd54b80ac938332 authored about 8 years ago by Kenta Sato <[email protected]>
Removed rouge println statement (#239)

github.com/BioJulia/Bio.jl - 9cc8990acd5547cbcebcf37998ffdb6d459ea543 authored about 8 years ago by Ben J. Ward <[email protected]>
follow the Libz change (#236)

github.com/BioJulia/Bio.jl - 458cbaf2a3c5322e82c3a5562916dd1276b8f323 authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
ispurine and ispyrimidine for nucleotides (#235)

* Implemented ispurine and ispyrimidine for nucleotides

* Fixed functions.

* Fixed from ca...

github.com/BioJulia/Bio.jl - 28b2d4d1aa2c44f20a902f4e5dadc2c66b54a2c3 authored about 8 years ago by Ben J. Ward <[email protected]>
rename checksum functions (#34)

github.com/BioJulia/Libz.jl - 2d78fd415dbb5c2731157701cd66c259ecbff4e6 authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Regular expression search (#233)

github.com/BioJulia/Bio.jl - 3ef85d968c51499419a20ca8cba0da122a012ee3 authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
define ref2seq and seq2ref for PairwiseAlignment (#232)

github.com/BioJulia/Bio.jl - a69fd5916c39dcc9d4b0da4cfca361eeaa581bd5 authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
support .2bit format (#155)

github.com/BioJulia/Bio.jl - 2606ab8e030b1ff9bb2e5de26e2bedfdf92cb11a authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Merge pull request #229 from BioJulia/Ward9250-patch-1

Export isambiguous from Seq module.

github.com/BioJulia/Bio.jl - e3b8ceb17b2286f88be7d89fb15da11ed614ac34 authored about 8 years ago by Ben J. Ward <[email protected]>
Added a line to docs listing isambiguous as a usable function for biological symbols

github.com/BioJulia/Bio.jl - 265c500928bb01804c5af7b46ed49267d105b4b4 authored about 8 years ago by Ben J. Ward <[email protected]>
Added tests

github.com/BioJulia/Bio.jl - f93a6d5b46438d0e2f61514d806d667668d65c78 authored about 8 years ago by Ben J. Ward <[email protected]>
Export isambiguous from Seq module.

Sometimes if a user is dealing with individual nucleotides, or iterating a seq nucleotide by nuc...

github.com/BioJulia/Bio.jl - 89c6666f047b4d6bbee53dc451b822b6bb4cf3aa authored about 8 years ago by Ben J. Ward <[email protected]>
add getindex for VirtualOffset

github.com/BioJulia/BGZFStreams.jl - 77b2ac4492f43d0c6755e2e968eaeea4973018d9 authored about 8 years ago by Kenta Sato <[email protected]>
fix some typo

github.com/BioJulia/BGZFStreams.jl - 07beac905367840f2661b526887fc0d21f3a116e authored about 8 years ago by Kenta Sato <[email protected]>
update README.md

github.com/BioJulia/BGZFStreams.jl - 7ec71f4e2e04026827f0103875f076f9672523cc authored about 8 years ago by Kenta Sato <[email protected]>
check zlib's return code

github.com/BioJulia/BGZFStreams.jl - bd79e831abd2d602a93005102644ee5d6a1cc463 authored about 8 years ago by Kenta Sato <[email protected]>
Merge pull request #184 from BioJulia/mol_dating

Added the Dating submodule to Phylo.

github.com/BioJulia/Bio.jl - cfaefd3a5b5417f18c3c020da767010d2ff60fdd authored about 8 years ago by Ben J. Ward <[email protected]>
implement filter and filter! for BioSequence (#227)

github.com/BioJulia/Bio.jl - 91e2c0c31ba4d4cdd73788ab618dde998f35079a authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Corrected error in coaltime SimpleEstimate method

github.com/BioJulia/Bio.jl - 20517fabdc4f53bcd1b672822f7d766fe1045016 authored about 8 years ago by Ben J. Ward <[email protected]>
implement map and map! for BioSequence (#226)

github.com/BioJulia/Bio.jl - 4583971480a204d08c1fe01f216fbe8588cdba29 authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Corrected tests for dating.jl and added another method

github.com/BioJulia/Bio.jl - f8ddf63be739b848d133bdf6a4632c4c142a09cf authored about 8 years ago by Ben J. Ward <[email protected]>
add ispalindrome, hasambiguity, and isrepetitive (#222)

github.com/BioJulia/Bio.jl - 90062946f82b34e547f8c5c3a6b21ca7a50cf751 authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
add .2bit files (#12)

github.com/BioJulia/BioFmtSpecimens - 9939328c852ae04ef6f1f917c9868399b0467859 authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Shuffle BioSequence and Kmer (#225)

* add rand(::Kmer) to generate random k-mers

* add shuffle and shuffle! for BioSequence

* ...

github.com/BioJulia/Bio.jl - f508aff4d9914c48d6ab1725b2384b78d4cc813f authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
add gc_content (#223)

* add gc_content

* fixup! add gc_content

github.com/BioJulia/Bio.jl - 47c692bf19aadf907eda43c18893b20c05d9277d authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
temporarily disable BLAST tests on Windows (#221)

github.com/BioJulia/Bio.jl - 9676ae681fe214f40dcd5adf9b5644d8780783aa authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
clean up mismatches and docs (#194)

github.com/BioJulia/Bio.jl - c198ba10c608f67add3a3cd6a6740fa404244387 authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Added simple estimation method, as well as HybridCheck estimation method.

github.com/BioJulia/Bio.jl - 6bd7c049b5157ef3676ec2d8fce7f73440f7c1fd authored about 8 years ago by Ben J. Ward <[email protected]>
Added tests for the coaltime function

github.com/BioJulia/Bio.jl - 83a6cf3fba1d5d062e95cafce2f784d9fa14051e authored about 8 years ago by Ben J. Ward <[email protected]>
Changed dependency to mkdocs-biojulia

github.com/BioJulia/Contributing - c372c043aeea1ddd0cf8ea633f3b8348adae3a70 authored over 8 years ago by Ben J. Ward <[email protected]>
Changed theme to the biojulia theme

github.com/BioJulia/Contributing - 60f61ee5fbc73676d8c972a10dfff23757f6e540 authored over 8 years ago by Ben J. Ward <[email protected]>
Added docstring and citation.

github.com/BioJulia/Bio.jl - 8804e463e8efaa45857c208cc081324caac28c55 authored over 8 years ago by Ben J. Ward <[email protected]>
Modified runtests.jl

github.com/BioJulia/Bio.jl - a3a188f7f9a756f82828fee53ff669402d765937 authored over 8 years ago by Ben J. Ward <[email protected]>
Added the Dating submodule to Phylo.

github.com/BioJulia/Bio.jl - 885576a746ccab9a2f8f693da47aa44d9daaeca3 authored over 8 years ago by Ben J. Ward <[email protected]>
Low-level APIs (#33)

* add src/lowlevel.jl

* remove _zlib

* move _crc32 and _adler32 to lowlevel.jl

* move a...

github.com/BioJulia/Libz.jl - ee012cef23d3bd6ace29a51426ae14fa2db40c4a authored over 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
replacee some ccalls with wrapper functions

github.com/BioJulia/BGZFStreams.jl - 7512cb023cab6bd58bbb127622b142a961ea87ec authored over 8 years ago by Kenta Sato <[email protected]>
remove Tabix (moved to a HTS-specific package)

github.com/BioJulia/BGZFStreams.jl - 88d88c46cc7496640e2e7f3a007468d172c16bf6 authored over 8 years ago by Kenta Sato <[email protected]>
add seekstart(::BGZFStream)

github.com/BioJulia/BGZFStreams.jl - e8e6413ce71a0a085444042a04747d20da38ade6 authored over 8 years ago by Kenta Sato <[email protected]>
add details on overlapchunks

github.com/BioJulia/BGZFStreams.jl - bf213d7e37d4adb62f40e7846b5d7c2e682f4b22 authored over 8 years ago by Kenta Sato <[email protected]>
add test files

github.com/BioJulia/BGZFStreams.jl - 66d10027bf45cab0aaf7946845691d0c11dd7b0c authored over 8 years ago by Kenta Sato <[email protected]>