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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

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]>
Fix test command

github.com/BioJulia/Bio.jl - 6d4d4d37962c6ba2fd71230821a02a6033fc4a88 authored over 9 years ago by Richard Smith-Unna <[email protected]>
Moar typos

github.com/BioJulia/Bio.jl - df3156546c3e801c6de704f5c5de87bb2e707582 authored over 9 years ago by Richard Smith-Unna <[email protected]>
Initial proof of concept.

github.com/BioJulia/GenomeBrowsers.jl - 0d9a5ce948484c5da1adcd319940210cf879df09 authored over 9 years ago by Daniel Jones <[email protected]>
Merge pull request #32 from dcjones/intervals

Intervals

github.com/BioJulia/Bio.jl - f9842867514851524878f232d86b54a6d76288a9 authored over 9 years ago by Paulo Roberto de Oliveira Castro <[email protected]>
Added pretty printing for IntervalTree. Split show for Interval and IntervalMap into print and show.

github.com/BioJulia/IntervalTrees.jl - a9a8d91c65ba4cd9c5fac27bf8634a90c2d241ed authored over 9 years ago by Peter M. Haverty <[email protected]>
Added show methods for Interval and IntervalValue. I think these will be helpful for new users.

github.com/BioJulia/IntervalTrees.jl - ad3c6a1e3e22912cbdcf01c63f12cfc59154a71f authored over 9 years ago by Peter M. Haverty <[email protected]>
I thought it would be nice to have a getter method for the value in IntervalValue. I added this and tests for the Interval and IntervalValue getters.

github.com/BioJulia/IntervalTrees.jl - 9fe322dd8cef6ed9550592140555861ad675aba2 authored over 9 years ago by Peter M. Haverty <[email protected]>
Fix style inconsistencies and uneeded type parameters.

github.com/BioJulia/Bio.jl - 8c0e96195918931cb2dfaaef90254c9497b07516 authored over 9 years ago by Daniel Jones <[email protected]>
Document a couple things. Explicitly import Base methods.

github.com/BioJulia/Bio.jl - cc33622f4eca8b6f3aa7f2afcfa550bb7f6f706d authored over 9 years ago by Daniel Jones <[email protected]>
Rearrange and add tests.

github.com/BioJulia/Bio.jl - 3f70d7d700d6a0e25fb70216f0f60c86eae260d3 authored over 9 years ago by Daniel Jones <[email protected]>
More tests.

github.com/BioJulia/Bio.jl - de4e7c5ad4a92a145013925605508b6f8467dfe0 authored over 9 years ago by Daniel Jones <[email protected]>
Add Distributions to test/REQUIRE.

github.com/BioJulia/Bio.jl - 3cc5f7d65e3c5540adaa5e619b1ab642cf4dea13 authored over 9 years ago by Daniel Jones <[email protected]>
Add some missing imports.

github.com/BioJulia/IntervalTrees.jl - af6ff52706d70273abc3345352cd5828fac68c45 authored over 9 years ago by Daniel Jones <[email protected]>
Julia 0.4 compatibility

github.com/BioJulia/Bio.jl - 44fffdc612259a505a2594f0cc5aedc05362cf02 authored over 9 years ago by Daniel Jones <[email protected]>
Split intervals.jl into several files. Organize tests.

github.com/BioJulia/Bio.jl - 79fe55212077b4b7ba37d302e308dfda2aa94871 authored over 9 years ago by Daniel Jones <[email protected]>
More natural ordering for seqnames in IntervalCollection.

github.com/BioJulia/Bio.jl - 12f9adc4040f7294ba5693b55cf73c1eef30e81b authored over 9 years ago by Daniel Jones <[email protected]>
Rewrite IntervalCollection using new IntervalTrees.

github.com/BioJulia/Bio.jl - 70c61a49c8a485e8e1dada5f56755330557f035b authored over 9 years ago by Daniel Jones <[email protected]>
Add missing file.

github.com/BioJulia/Bio.jl - e3654ee22aeaf2423426b0a4f004cf9e27e13ac4 authored over 9 years ago by Daniel Jones <[email protected]>
Limit ⋮ usage for showing IntervalCollections

Show the `⋮` for an IntervalCollection only if the number of entries exceeds the number of entri...

github.com/BioJulia/Bio.jl - 83a73004ed98c7ba271b10005361eb7e68ea30a6 authored over 9 years ago by Julian Gehring <[email protected]>
Some tests and fixes.

github.com/BioJulia/Bio.jl - 96f0b8f0aa2f261913a9759fe0089fe45d514292 authored over 9 years ago by Daniel Jones <[email protected]>
Intersection for interval streams.

github.com/BioJulia/Bio.jl - 06eff246a63d9e9c996c52e6046d58eb98033753 authored over 9 years ago by Daniel Jones <[email protected]>
First pass at intersect for IntervalCollections.

github.com/BioJulia/Bio.jl - 3d2fbbe6c0a6f2cf047d9135d85d25c92dbe6fa6 authored over 9 years ago by Daniel Jones <[email protected]>
Show empty IntervalCollection

Fixes the `show` method for an empty `IntervalCollection`. Before,
IntervalCollection{Int}...

github.com/BioJulia/Bio.jl - 951df41e15822a9a43bb791051ee7953d0bb4940 authored over 9 years ago by Julian Gehring <[email protected]>
Rename IntervalSet → IntervalCollection

github.com/BioJulia/Bio.jl - ab7bfba0c3d3e3c28581092f3079a0480bd600e9 authored over 9 years ago by Daniel Jones <[email protected]>
Initial work on genomic intervals.

github.com/BioJulia/Bio.jl - ecc3bc4af7685446ccf1e590491a7f6d35e21e68 authored over 9 years ago by Daniel Jones <[email protected]>
Merge pull request #40 from dcjones/io

RFC: Parsing infrastructure, FASTA and FASTQ parsers

github.com/BioJulia/Bio.jl - 618bad333b6bbdefe0af2cf2a6e1c907bb52a773 authored over 9 years ago by Daniel C. Jones <[email protected]>
Fix first letter of descriptions missing in FASTA and FASTQ.

github.com/BioJulia/Bio.jl - 8cce44dae8d61e246a8284a1e795681ab191715b authored over 9 years ago by Daniel Jones <[email protected]>
Julia 0.4 compatibility

github.com/BioJulia/Bio.jl - f0c206912e427949d885fa3e5287e9b370f8a4a0 authored over 9 years ago by Daniel Jones <[email protected]>
Regenerate parsers with updated ragel: no unecessary begin/end blocks.

github.com/BioJulia/Bio.jl - eba27c2322500c6e5b25523e8bce1faa3bc2bc28 authored over 9 years ago by Daniel Jones <[email protected]>
Fix a bug that can occur when parsing large files.

github.com/BioJulia/Bio.jl - 1ca85ec98d2a5bde4b43b650b6c730852759a203 authored over 9 years ago by Daniel Jones <[email protected]>
Optimizations to FASTQ parsing.

github.com/BioJulia/Bio.jl - a1a843648e40851ea9933f3d35f7bfc9914a04bb authored over 9 years ago by Daniel Jones <[email protected]>
Explicitly import some Base methods.

github.com/BioJulia/Bio.jl - 057bf0500c355957c5472794daaf06a13c40e482 authored over 9 years ago by Daniel Jones <[email protected]>
Minor simplifications to FASTA and FASTQ parsers.

github.com/BioJulia/Bio.jl - e91f58bd12eebc5d2c41a7b1adad65b6a9a4db6f authored over 9 years ago by Daniel Jones <[email protected]>
Minor FASTA/FASTQ optimizations.

github.com/BioJulia/Bio.jl - b6987934dc85c1f0efc97713d06594f903e3c0a0 authored over 9 years ago by Daniel Jones <[email protected]>
Split SeqRecord types out of seq.jl.

github.com/BioJulia/Bio.jl - 12489c19b22137cb502d544743575c5ab2ebf68b authored over 9 years ago by Daniel Jones <[email protected]>
NucleotideSequence optimizations.

github.com/BioJulia/Bio.jl - 0304e9ed14fb034375b7f678a66a311eebba373d authored over 9 years ago by Daniel Jones <[email protected]>
Add warning messages to the top of generated files.

github.com/BioJulia/Bio.jl - 9b46dedc6b130d8989697f203b8b7b5781be7634 authored over 9 years ago by Daniel Jones <[email protected]>
Organize parsing tests.

github.com/BioJulia/Bio.jl - d1cc1517f482635c2569cd5f798212631e200f3d authored over 9 years ago by Daniel Jones <[email protected]>
Require Switch. Don't require FactCheck, that's in test/REQUIRE.

github.com/BioJulia/Bio.jl - 8e41f82040be45d410f8d982ed321940ab38306e authored over 9 years ago by Daniel Jones <[email protected]>
Use direct unbuffered file io.

github.com/BioJulia/Bio.jl - 79f0f64a050f90ce38c8df5124efc34c60c0bf8b authored over 9 years ago by Daniel Jones <[email protected]>
Some performance improvements to sequence parsing.

github.com/BioJulia/Bio.jl - 1ada64d040cfaadfdf05f8134d29c76b814b4e98 authored over 9 years ago by Daniel Jones <[email protected]>
Parsing infrastructure and parsers for FASTA and FASTQ.

github.com/BioJulia/Bio.jl - 40eadd2e0b13359738da70525573a52c2dc5163e authored over 9 years ago by Daniel Jones <[email protected]>
Test parsing memory mapped files.

github.com/BioJulia/Bio.jl - 9513eab13a6d88ca2e7c9e5c7486ac710e7f1549 authored over 9 years ago by Daniel Jones <[email protected]>
Automate fetching of BioFmtSpecimens for tests.

github.com/BioJulia/Bio.jl - e9a8df1533707716a7f960a8839c153aafc4fd81 authored over 9 years ago by Daniel Jones <[email protected]>
Fix tests on Julia 0.4

github.com/BioJulia/Bio.jl - 71a5e1247a080cd713a441abd81753df109ca3f8 authored over 9 years ago by Daniel Jones <[email protected]>
Merge pull request #49 from dcjones/contributing

Add a basic CONTRIBUTING.md

github.com/BioJulia/Bio.jl - 937679bd0f016f30ef1f6e58b62f9a52dc12214b authored over 9 years ago by Daniel C. Jones <[email protected]>
Merge pull request #47 from brk00/master

[Seq] More documentation

github.com/BioJulia/Bio.jl - e638be60cc98efdea1c45a9bf074af1f3313700e authored over 9 years ago by Daniel C. Jones <[email protected]>
Merge pull request #2 from Blahah/patch-1

Typo

github.com/BioJulia/Bio.jl - 2a9d866d3d42ddaa3165ef624eee06585c123be7 authored over 9 years ago by Daniel C. Jones <[email protected]>
Typo

github.com/BioJulia/Bio.jl - 75246be7b72915bb71599b949ef72961d62a0441 authored over 9 years ago by Richard Smith-Unna <[email protected]>
Link to julia ommunity standards.

github.com/BioJulia/Bio.jl - 81addc8559a02f1afb5ca1bf6a274ac361eec458 authored over 9 years ago by Daniel Jones <[email protected]>
Spelling, typos.

github.com/BioJulia/Bio.jl - 62a9bfb0cb64110e34cb6965222513e46e91709d authored over 9 years ago by Daniel Jones <[email protected]>
Fix typo.

github.com/BioJulia/Bio.jl - a06cf7a47e48644c71484003732d393bf696e5b9 authored over 9 years ago by Daniel Jones <[email protected]>
Don't indent module contents.

github.com/BioJulia/Bio.jl - b462454c1eadf0894f194ddf4f39ad780256aefa authored over 9 years ago by Daniel Jones <[email protected]>
Don't bother with begin/end blocks everywhere.

github.com/BioJulia/ragel - 3c1ebe8fcb41ed67110d841d6f3f293dafdf764e authored over 9 years ago by Daniel Jones <[email protected]>
Mark one BED specimen as invalid.

github.com/BioJulia/BioFmtSpecimens - d8cb29531338f441c14b4f3e8b122888e07337b4 authored over 9 years ago by Daniel Jones <[email protected]>
Some BED specimens from kent.

github.com/BioJulia/BioFmtSpecimens - 0dc6d35dc6aac0f098013d79753f4d03124104c9 authored over 9 years ago by Daniel Jones <[email protected]>
Corrected mismatches docs

github.com/BioJulia/Bio.jl - a620102e61794e41422c4cce7bd5eca0078031aa authored over 9 years ago by brk00 <[email protected]>
Clean up CONTRIBUTING a little.

github.com/BioJulia/Bio.jl - d92c360d3b6856fece457d61f91263513f3fb56f authored over 9 years ago by Daniel Jones <[email protected]>
Add a basic CONTRIBUTING.md

github.com/BioJulia/Bio.jl - f3b4c0fbaf313cd28f06030583982e5f2f5be0e8 authored over 9 years ago by Daniel Jones <[email protected]>
More docs and @assert into EachKmer constructor

github.com/BioJulia/Bio.jl - 0450833e4c579ea89ffedbade7164796fd86bd95 authored over 9 years ago by Paulo R. O. Castro <[email protected]>
More docs

github.com/BioJulia/Bio.jl - 824c00e16ce7a952842ab16d6010510c35f618c6 authored over 9 years ago by Paulo R. O. Castro <[email protected]>
Import complement from Base

github.com/BioJulia/Bio.jl - a088a9816ad85f2ccce0290eb494bdec348eb7e4 authored over 9 years ago by brk00 <[email protected]>
Missing quotes

github.com/BioJulia/Bio.jl - 5f81de7363962fdc0f46709c2cd59aff7318bd00 authored over 9 years ago by Paulo R. O. Castro <[email protected]>
Missing arrow

github.com/BioJulia/Bio.jl - 18be68aa92e8f313a98b5e3e32c650549aa5e080 authored over 9 years ago by Paulo R. O. Castro <[email protected]>
Undocument bitstype

github.com/BioJulia/Bio.jl - f3654c3dac95cc80aad28bc9d17afbb4450e1b52 authored over 9 years ago by Paulo R. O. Castro <[email protected]>
Seq: more documentation

github.com/BioJulia/Bio.jl - 8443e480f12e995e408979b2cff3c93b90eefa00 authored over 9 years ago by Paulo R. O. Castro <[email protected]>
Seq: more documentation

github.com/BioJulia/Bio.jl - c4c6038d3ee747968716d92dd41c4770e63f99cf authored over 9 years ago by Paulo R. O. Castro <[email protected]>
Require Docile.

github.com/BioJulia/IntervalTrees.jl - b435fae4685945d087c90147c9ac9ed10358f6e4 authored over 9 years ago by Daniel Jones <[email protected]>
Julia 0.4 compat.

github.com/BioJulia/IntervalTrees.jl - c77c7dbf226aac44e734afd1ef8ad90d02bd8196 authored over 9 years ago by Daniel Jones <[email protected]>
Explicitly import

github.com/BioJulia/Bio.jl - 7c03ef1a4d84d33d03948f177f23a43bb72ac24c authored over 9 years ago by Daniel Jones <[email protected]>
Simplify some code. Fix spelling.

github.com/BioJulia/Bio.jl - ec71c316e6d87b6da8877a71d7910f6469803455 authored over 9 years ago by Daniel Jones <[email protected]>
Add concat '*' and repeat '^' operators for sequences.

github.com/BioJulia/Bio.jl - b180363afa3d12a6995a5756f4c91088fcd9fbbb authored over 9 years ago by Daniel Jones <[email protected]>
Concatenation for sequence types.

github.com/BioJulia/Bio.jl - 7005f4ae54d6e737929d570f3786c25a4e872e15 authored over 9 years ago by Daniel Jones <[email protected]>
Merge pull request #16 from KristofferC/master

Updated test and deprecs

github.com/BioJulia/Codecs.jl - a8b6a8469e1d969966404ae8d771fbf573c39716 authored over 9 years ago by Daniel C. Jones <[email protected]>
Updated test and deprecs

github.com/BioJulia/Codecs.jl - d6ffd89d9400043bfe8a4e673ba8cfe260483a5b authored over 9 years ago by Kristoffer Carlsson <[email protected]>
Merge pull request #43 from bicycle1885/parse-aa

add parse method for amino acids

github.com/BioJulia/Bio.jl - 59bc8abcb44c76a695536c30ad9eb5376b2e4b5d authored over 9 years ago by Daniel C. Jones <[email protected]>
import parse function from Base

github.com/BioJulia/Bio.jl - 33f63754d16f17da9b9e7e04614f3dda2c3764a7 authored over 9 years ago by Kenta Sato <[email protected]>
remove exception types of tests

github.com/BioJulia/Bio.jl - 2ae1f53ba8e8752b3b8a81eaba355e1eedf335cc authored over 9 years ago by Kenta Sato <[email protected]>
add tests for the amino acid parser

github.com/BioJulia/Bio.jl - 83113a60579cdfa9471e06e986ba3bb8f5f2a06d authored over 9 years ago by Kenta Sato <[email protected]>
add parse method for amino acid

github.com/BioJulia/Bio.jl - fcf0b1abbde82efa235e4aafb5f6abf361519918 authored over 9 years ago by Kenta Sato <[email protected]>
Merge pull request #41 from bicycle1885/clipboard

add the 'clipboard' methods for sequence types

github.com/BioJulia/Bio.jl - ccf244bbd66fe4edb4795158a1b21d802690f728 authored over 9 years ago by Richard Smith-Unna <[email protected]>
add the 'clipboard' methods for sequence types

github.com/BioJulia/Bio.jl - 2f6f633936ec55cd1d01595361bf23540f25d96c authored over 9 years ago by Kenta Sato <[email protected]>
fit sequence printing to the window size

github.com/BioJulia/Bio.jl - 993712a901d7654aa11115d4d9e8d819756084b4 authored over 9 years ago by Kenta Sato <[email protected]>
Merge pull request #1 from Ward9250/patch-1

Update 2015-07-BOSC.md

github.com/BioJulia/abstracts - 201587c8362c3fefa37ced12a19e0a95ae06f0f7 authored over 9 years ago by Richard Smith-Unna <[email protected]>
Update 2015-07-BOSC.md

github.com/BioJulia/abstracts - 1079b32b5b8a0591ae72d0fc96b66ed2fbf27713 authored over 9 years ago by Ben J. Ward <[email protected]>
First draft of abstract for BOSC lightning talk

This is a first stab at a BOSC abstract. I think the structure is OK, but it spends too long on ...

github.com/BioJulia/abstracts - 66d329dd8f60b86a22a7e0ccee766345c230135b authored over 9 years ago by Richard Smith-Unna <[email protected]>
Merge pull request #35 from bicycle1885/compl

make unsafe_complement! return a transformed sequence

github.com/BioJulia/Bio.jl - 1bcb6d8655508ee35c1f20b8de9b61544cbcd647 authored over 9 years ago by Daniel C. Jones <[email protected]>
make unsafe_complement! return a transformed sequence

which is a standard behavior of destructive functions
(cf. Base.push!, Base.append!, etc.)

github.com/BioJulia/Bio.jl - 8bbadb5d6d07c859f3c8527fcb6c56f7ecb6561b authored over 9 years ago by Kenta Sato <[email protected]>
Merge pull request #34 from brk00/seq_tests

[Seq] More tests, less bugs

github.com/BioJulia/Bio.jl - 609c0c4fd787b519eada86d7e73d2a67a3b8198f authored over 9 years ago by Daniel C. Jones <[email protected]>
Merge pull request #1 from dcjones/seq_tests

Julia 0.4 compatibility.

github.com/BioJulia/Bio.jl - 5ce0e1d2b8ac3ff8a9fbb5945df5d89bd9aa3627 authored over 9 years ago by Paulo Roberto de Oliveira Castro <[email protected]>
Julia 0.4 compatibility.

github.com/BioJulia/Bio.jl - 682706bccdd7ab02dd811b7eae99e697f57d8337 authored over 9 years ago by Daniel Jones <[email protected]>
Initial commit

github.com/BioJulia/abstracts - 4cec1da9e9fe6c5457756a614110246a8411b2ef authored over 9 years ago by Richard Smith-Unna <[email protected]>
Intersection fix and optimization.

github.com/BioJulia/IntervalTrees.jl - 96dd6770c66b6cc695a0bf3a25f83baefd9e2098 authored over 9 years ago by Daniel Jones <[email protected]>
Overhaul

I realized there were some significant performance bottlenecks with the approach
I was taking in...

github.com/BioJulia/IntervalTrees.jl - 7df0251c97a0151b052300f393d7785420f86f57 authored over 9 years ago by Daniel Jones <[email protected]>
Even more tests

github.com/BioJulia/Bio.jl - 75d8614e6868c83c35824d7f10ff1c652e50fcbf authored over 9 years ago by brk00 <[email protected]>
More tests for Kmers

github.com/BioJulia/Bio.jl - 4b31ee548d77fb17f757fbf962c51e6023abe7f2 authored over 9 years ago by brk00 <[email protected]>
Fix intersection iterator order.

github.com/BioJulia/IntervalTrees.jl - 6441cff69f250085998b13ece35b25914301737f authored over 9 years ago by Daniel Jones <[email protected]>
More tests and export isless

github.com/BioJulia/Bio.jl - 217bb73642faf5667b37571c732ebde8f341dcaf authored over 9 years ago by brk00 <[email protected]>
More tests for Kmer from/to NucleotideSequence conversions

github.com/BioJulia/Bio.jl - 2da5c24e33b065a179df81b448b93a423b06408f authored over 9 years ago by brk00 <[email protected]>