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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

README update

github.com/BioJulia/BioAlignments.jl - d06c829b229388c494de7c5ce4dea7b99635928b authored over 7 years ago by Ben J. Ward <[email protected]>
Merge branch 'release-0.1'

github.com/BioJulia/BioAlignments.jl - 4305fcbbd6e031406808239883d04887f4235401 authored over 7 years ago by Ben J. Ward <[email protected]>
Added Automa, BufferedSteams, and BGZFStreams, and Compat0.17 to require

github.com/BioJulia/BioAlignments.jl - b7f71910c25fbcdfcf18a78aebdadbc42586c4fb authored over 7 years ago by Ben J. Ward <[email protected]>
fix appveyor.yml (#2)

- Test on 64-bit.
- Add Julia 0.6.
- Allow failure on nightly.

github.com/BioJulia/BioAlignments.jl - 61fc3b4d965496065cbc07cf1a4ca2f620d10256 authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Update README and docs

github.com/BioJulia/BioAlignments.jl - 9d0806336965f4793bcbc9e1b34df6640046bb4c authored over 7 years ago by Ben J. Ward <[email protected]>
add read and write methods for VirtualOffset (#11)

* add read and write methods for VirtualOffset

* replace nightly with 0.6

github.com/BioJulia/BGZFStreams.jl - 92f21180d0be80d382b13c6069e9841795a19284 authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
add read and write methods for Strand (#4)

Since these are needed for multi-process parallelism.

github.com/BioJulia/GenomicFeatures.jl - a2e54222240a0b06d52074a216b0f09ce3d2ba68 authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
NG86 methods (#5)

* Added first draft of ng86 distance methods

* Finished draft of dnds NG86 method

* Added ...

github.com/BioJulia/GeneticVariation.jl - fbbdb08a6a284120119c7169913642f5401836c2 authored over 7 years ago by Ben J. Ward <[email protected]>
Added jekyll-feed

github.com/BioJulia/biojulia.github.io - 4053e355919f42c85f3435eb3fa24524cf496f60 authored over 7 years ago by Ben J. Ward <[email protected]>
Release post added

github.com/BioJulia/biojulia.github.io - 5f666cda49b32fb35f72f92fafff14025d620911 authored over 7 years ago by Ben J. Ward <[email protected]>
remove max(x) method

github.com/BioJulia/BioAlignments.jl - 286034f9f1bbce80bf225828174447840cf844ea authored over 7 years ago by Kenta Sato <[email protected]>
Merge pull request #3 from BioJulia/dcj/filter

Add optional filter functions to eachoverlap, and a findfirst function.

github.com/BioJulia/GenomicFeatures.jl - baecd090de80b241c981ec4e195708abf1ed3c2f authored over 7 years ago by Daniel C. Jones <[email protected]>
Fix a couple bugs in findfirst.

github.com/BioJulia/IntervalTrees.jl - 53619513f954781311f5cb2f22fdf72bd88dffb6 authored over 7 years ago by Daniel C. Jones <[email protected]>
Update IntervalTrees require. Make filter keyword arg in findfilter.

github.com/BioJulia/GenomicFeatures.jl - 8aacb699a1e7905157b0d77bdbfcfb23bdb9de9c authored over 7 years ago by Daniel C. Jones <[email protected]>
make eachoverlap accept an Interval-convertible object

github.com/BioJulia/BioAlignments.jl - c54bb87fd5f68020c10a6bf49c8ea8db211d660c authored over 7 years ago by Kenta Sato <[email protected]>
move HTS docs

github.com/BioJulia/BioAlignments.jl - 896cbd1570e87fd582fe8fca5fe177e9a776dd6b authored over 7 years ago by Kenta Sato <[email protected]>
Add the proportion distance (#4)

* Added abstract types

* Modified evodistances.jl

* Draft proportion distance method

* ...

github.com/BioJulia/GeneticVariation.jl - db632df094982cfd46082147364dadabc6190266 authored over 7 years ago by Ben J. Ward <[email protected]>
Complete Bio.Seq decomposition (#468)

* Complete Bio.Seq decomposition

* Removed sequence tests, as BioSequences.jl has its own tes...

github.com/BioJulia/Bio.jl - f127343ff10d91848ede63be1898c031196cc285 authored over 7 years ago by Ben J. Ward <[email protected]>
Merge branch 'release-0.1'

github.com/BioJulia/GeneticVariation.jl - f412345132d19a0e86a6412e2202ac6dc3513938 authored over 7 years ago by Ben J. Ward <[email protected]>
Use get_bio_fmt_specimens from BioCore.Testing.

github.com/BioJulia/GeneticVariation.jl - a6b5301ac5bf42c3f9208e9acbdc3216c72af9ac authored over 7 years ago by Ben J. Ward <[email protected]>
Add optional filter predicates to intersect, and a findfirst function (#28)

* Add findfirst function that takes an optional filter function.

* Add optional filter predic...

github.com/BioJulia/IntervalTrees.jl - 9bcb231b70bd961839c773f8fcdfc9213f020b4b authored over 7 years ago by Daniel C. Jones <[email protected]>
Add optional filter functions to eachoverlap, and a findfirst function.

github.com/BioJulia/GenomicFeatures.jl - 4c4e1e89865816fa5e7c617940a4338e498ccf4b authored over 7 years ago by Daniel C. Jones <[email protected]>
Overload BioSequences.diag_val

github.com/BioJulia/GeneticVariation.jl - 3abd0f3d0def2dc59261a98bdf81f16de4244a30 authored over 7 years ago by Ben J. Ward <[email protected]>
Added diag_val

github.com/BioJulia/BioSequences.jl - 3c02bfe7cf8999ce191adcc93f4a7aaf6beb88ce authored over 7 years ago by Ben J. Ward <[email protected]>
Changed REQUIREd Compat version

github.com/BioJulia/GeneticVariation.jl - 06c5638da0a43dfb80dea1d56e1368983d2ed902 authored over 7 years ago by Ben J. Ward <[email protected]>
MASH Distances (#3)

* Added MASH distances for MinHashes

* Added tests for MASH

* export tweak

* Added docu...

github.com/BioJulia/GeneticVariation.jl - 74c9d1aa01f5400f0d665c2fc926ed57eeca431b authored over 7 years ago by Ben J. Ward <[email protected]>
add __precompile__

github.com/BioJulia/BioAlignments.jl - a89656d6074fa684af30d7babbd51ea621c509b3 authored over 7 years ago by Kenta Sato <[email protected]>
separate docs on pairwise alignments

github.com/BioJulia/BioAlignments.jl - 8c2600694f28ef00ad2edf1ae535df83385124e9 authored over 7 years ago by Kenta Sato <[email protected]>
Minor import edit

github.com/BioJulia/GeneticVariation.jl - e647a86b28019e09a8fd58e6b183938dbb328acf authored over 7 years ago by Ben J. Ward <[email protected]>
Added CNAME file

github.com/BioJulia/biojulia.github.io - ba2c7a058ada8a135c7e4148778b6e6988f8a0bd authored over 7 years ago by Ben J. Ward <[email protected]>
Added news item about genomic features release.

github.com/BioJulia/biojulia.github.io - 8cc1c38e59f1642108973e8d44f331dc9919fff3 authored over 7 years ago by Ben J. Ward <[email protected]>
Added documentation files

github.com/BioJulia/GeneticVariation.jl - 77e975a3f0fd33e6bec1ef8dcb57badef303cd72 authored over 7 years ago by Ben J. Ward <[email protected]>
Author corrections and jumbotron background

github.com/BioJulia/biojulia.github.io - 4cc4e38f4e4b6cd34932165e799ed8259481732a authored over 7 years ago by Ben J. Ward <[email protected]>
Edited readme

github.com/BioJulia/GeneticVariation.jl - cf068cd2bb48ad36b320f74cd3f1e1b835871aa7 authored over 7 years ago by Ben J. Ward <[email protected]>
Site counting (#2)

* Added site counting methods

* testing

* conserved and mutated testing

* include site_...

github.com/BioJulia/GeneticVariation.jl - d7ceedd0e14099c902904885575833c7bebdfb29 authored over 7 years ago by Ben J. Ward <[email protected]>
Site counting hotfix

github.com/BioJulia/BioSequences.jl - 3904c46d6f513dae3cb13c533c46251e09adff5a authored over 7 years ago by Ben J. Ward <[email protected]>
added types and top category for packages

github.com/BioJulia/biojulia.github.io - 93f135a05e19869c98ab3167abf48240a235be27 authored over 7 years ago by Ben J. Ward <[email protected]>
Added author config file

github.com/BioJulia/biojulia.github.io - e1b7eb1270ddfa20bce0bb1f1e18c3f83e8a1270 authored over 7 years ago by Ben J. Ward <[email protected]>
add Usage section in the index page

github.com/BioJulia/BioAlignments.jl - 9af6d397f7c26680fa647096d10f00a0491b6276 authored over 7 years ago by Kenta Sato <[email protected]>
print info only when interactive mode

github.com/BioJulia/BioAlignments.jl - 4e505384f50ebeaf5fdc6d9b9aa6b96d760e7174 authored over 7 years ago by Kenta Sato <[email protected]>
news and members updates

github.com/BioJulia/biojulia.github.io - 460be6d3250c9855ac6d4b048b7fa836cb5b7f7a authored over 7 years ago by Ben J. Ward <[email protected]>
release 1.1.0 edits

github.com/BioJulia/BioCore.jl - 58c0db4e8c28aeb2b91e794c0ad2ba6951cb90a4 authored over 7 years ago by Ben J. Ward <[email protected]>
BioCore.Testing module (#3)

* BioCore.Testing module

* fixes to the testing helper module

github.com/BioJulia/BioCore.jl - 8599433bbeeaf3de6d4466128091869829333b25 authored over 7 years ago by Ben J. Ward <[email protected]>
Merge pull request #1 from Ward9250/master

First site draft

github.com/BioJulia/biojulia.github.io - bf45330915d4dd5838bf92f8dd7a264de5570950 authored over 7 years ago by Ben J. Ward <[email protected]>
First site draft

Added glyphicons to navbar buttons

Rearranged files

Added few changes

test post and layout ch...

github.com/BioJulia/biojulia.github.io - 007773723b5a519b00c4ffd1351624e82ca0f296 authored over 7 years ago by Ben J. Ward <[email protected]>
merge chunks more aggressively

github.com/BioJulia/GenomicFeatures.jl - 57944d338ffd333716a8b1c8605e83622e2eaa02 authored over 7 years ago by Kenta Sato <[email protected]>
make eachoverlap faster for BAM

github.com/BioJulia/BioAlignments.jl - 2154672e6a03456d87579e8c39135156b2929a4e authored over 7 years ago by Kenta Sato <[email protected]>
add docs

github.com/BioJulia/BioAlignments.jl - 23df00a855a6e4151526bc29371fbc5ac8875ef8 authored over 7 years ago by Kenta Sato <[email protected]>
support Julia v0.6 (#1)

* fix type keywords

* fix finish_traceback macro

* use take! instead of takebuf*

* fix ...

github.com/BioJulia/BioAlignments.jl - e4e2bdf6dd0925a9f3461cdda1f1960e9a37fc76 authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
fix docs link [ci skip]

github.com/BioJulia/BioAlignments.jl - fcfb4c90803ff02e6c705b2128ff3e9fd8ca6396 authored over 7 years ago by Kenta Sato <[email protected]>
move code from Bio.jl

github.com/BioJulia/BioAlignments.jl - 93d784bc57c653ba4e3873eb29aaf8c18f72c0a6 authored over 7 years ago by Kenta Sato <[email protected]>
use a specific commit when testing on specimens

github.com/BioJulia/GenomicFeatures.jl - 3619443128a09774fb6583f6d2ab651eb60245e3 authored over 7 years ago by Kenta Sato <[email protected]>
Added codecov badge

github.com/BioJulia/BioSequences.jl - 9dadb5e21848c39066af36b903abb636f8419ff2 authored over 7 years ago by Ben J. Ward <[email protected]>
BCF IO

* Added BCF code

* Added tests

* import GeneticVariation.VCF to BCF

* Bio -> BioCore

...

github.com/BioJulia/GeneticVariation.jl - d6fb3aa9cad3b2059b754b92b249e7f20ce4f395 authored over 7 years ago by Ben J. Ward <[email protected]>
VCF Submodule

github.com/BioJulia/GeneticVariation.jl - 62aae80022f064ac36a18eeb1f6c4ff84602ffea authored over 7 years ago by Ben J. Ward <[email protected]>
replace type aliases with constants

github.com/BioJulia/GenomicFeatures.jl - 0dd37f4ec87682fbf8982bd2c5c0571e052e9e18 authored over 7 years ago by Kenta Sato <[email protected]>
print compactly when showing an interval collection

github.com/BioJulia/GenomicFeatures.jl - a80a64791d540a2195e47d7c9ebc496cfa955f0c authored over 7 years ago by Kenta Sato <[email protected]>
fix the link to docs [ci skip]

github.com/BioJulia/GenomicFeatures.jl - 471e7f0700e4c1084d4798158eb05ecf158f8523 authored over 7 years ago by Kenta Sato <[email protected]>
add Indexes

github.com/BioJulia/GenomicFeatures.jl - 77bf7daab777f78b451b2cc7fccb4ca13cf4aaec authored over 7 years ago by Kenta Sato <[email protected]>
Update CI URLs to point to new caching infrastructure (#3)

github.com/BioJulia/Phylogenies.jl - ea2f44f2b1f1661de87e77de464df841fb5760bc authored over 7 years ago by Elliot Saba <[email protected]>
support Julia v0.6 (#1)

* use heappop!/heappush! in DataStructures.jl

* use primitive type

* replace typealias wit...

github.com/BioJulia/GenomicFeatures.jl - fa6e3293f0786c2a2bbd3dc63adb881ac7a53f0a authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
BioAlignments.jl generated files.

license: MIT
authors: Kenta Sato
years: 2017
user: bicycle1885

Julia V...

github.com/BioJulia/BioAlignments.jl - 4b15c879871d0eaede2c1408e0d353b89135c1a9 authored over 7 years ago by Kenta Sato <[email protected]>
initial empty commit

github.com/BioJulia/BioAlignments.jl - 6deb8bd9766a2d4e8eb359ee27ac9e846be16d31 authored over 7 years ago by Kenta Sato <[email protected]>
Initial commit

github.com/BioJulia/GeneticVariation.jl - 9d8f1e3cccd81f053104a64d6ab1bd3f8285092e authored over 7 years ago by Ben J. Ward <[email protected]>
add 0.6 to the TravisCI's list

And allow to fail on nightly.

github.com/BioJulia/BioCore.jl - 8eefa802b9be3cc8750bf5f8c4a1bdf8843f9e50 authored over 7 years ago by Kenta Sato <[email protected]>
import BioCore in tests

github.com/BioJulia/BioCore.jl - 55bea58c26ab6f7350a94e1d9216c8cc4544311b authored over 7 years ago by Kenta Sato <[email protected]>
fix deprecated type declaration syntax

github.com/BioJulia/BioCore.jl - bb259264a66e2b26af2fe3512e6cec495992bc2f authored over 7 years ago by Kenta Sato <[email protected]>
add more tests on GFF3

github.com/BioJulia/GenomicFeatures.jl - c3a3f9b616484a6d3be4323af92ccaf5c9533f09 authored over 7 years ago by Kenta Sato <[email protected]>
replace Bio with BioCore

github.com/BioJulia/GenomicFeatures.jl - c93c774795af2484b6ac334058f702000bedd88b authored over 7 years ago by Kenta Sato <[email protected]>
An eachkmer iterator fix (#8)

* eachkmer alterations

* use iscertain

* Added test for gap excluding.

* A simplificati...

github.com/BioJulia/BioSequences.jl - 992a8108e1025d9093790453aa9e8972b84878aa authored over 7 years ago by Ben J. Ward <[email protected]>
tidy up docs of IO and add examples

github.com/BioJulia/GenomicFeatures.jl - 40f2e3ea1cce127cf8a3bbbcc082827dc6c7fb45 authored over 7 years ago by Kenta Sato <[email protected]>
print info only when interactive mode

github.com/BioJulia/GenomicFeatures.jl - be1664806aeb68a9430afadec5e38e2c647e2f7a authored over 7 years ago by Kenta Sato <[email protected]>
update links in README.md

github.com/BioJulia/GenomicFeatures.jl - 4c4dc19da7022f7e867b28baecb3f39d4d5f4596 authored over 7 years ago by Kenta Sato <[email protected]>
update intervals.md

github.com/BioJulia/GenomicFeatures.jl - 06dd2b18c6356041475aebe70f0e1c497bae60c9 authored over 7 years ago by Kenta Sato <[email protected]>
move docs from Bio.jl

github.com/BioJulia/GenomicFeatures.jl - f33f1e87e57dd3b932ad32c3f1d819a8088bb924 authored over 7 years ago by Kenta Sato <[email protected]>
add __precompile__

github.com/BioJulia/GenomicFeatures.jl - a142969b91e5497a2d0fabd810b10f5093e214e2 authored over 7 years ago by Kenta Sato <[email protected]>
remove alphanum_isless

github.com/BioJulia/GenomicFeatures.jl - f155b94b9c7e1e6609643f487f52f0548788a268 authored over 7 years ago by Kenta Sato <[email protected]>
test BED printing

github.com/BioJulia/GenomicFeatures.jl - 76de472ea36d607a20aca0a4c3c571d8a32ca196 authored over 7 years ago by Kenta Sato <[email protected]>
remove coverall badge

github.com/BioJulia/GenomicFeatures.jl - 3d7025ebebb6e14ddeef7b4ab030c328de0c697e authored over 7 years ago by Kenta Sato <[email protected]>
make Interval immutable

github.com/BioJulia/GenomicFeatures.jl - 54dec0c8d829ad9df434c4ad57c3e688d1f30ff9 authored over 7 years ago by Kenta Sato <[email protected]>
move code from Bio.jl

github.com/BioJulia/GenomicFeatures.jl - 1ff45f3b345a854352409057e72332c6e1a75016 authored over 7 years ago by Kenta Sato <[email protected]>
GenomicFeatures.jl generated files.

license: MIT
authors: Kenta Sato
years: 2017
user: bicycle1885

Julia V...

github.com/BioJulia/GenomicFeatures.jl - ec10bd06c99671f80ab217fdcc904e6f6efb2575 authored over 7 years ago by Kenta Sato <[email protected]>
initial empty commit

github.com/BioJulia/GenomicFeatures.jl - 407dfe61b1cdafe57969208795b44293cee946d8 authored over 7 years ago by Kenta Sato <[email protected]>
print info only when interactive (#9)

github.com/BioJulia/BioSequences.jl - 729191ebbbe5f01282df1ab3deabb7beb4d399eb authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Added convenience method for removing gaps from a sequence. (#7)

* Added conveinience method for removing gaps from a sequence.

* test alterations

github.com/BioJulia/BioSequences.jl - 78b39b15393bea472ad3abc96376f2b54cc6417d authored over 7 years ago by Ben J. Ward <[email protected]>
escape a macro

github.com/BioJulia/BioSequences.jl - cae7eee6c9bb2756f7d0f8c18a182ebe3e13c4fa authored over 7 years ago by Kenta Sato <[email protected]>
fix inner constructors of parametric types

github.com/BioJulia/BioSequences.jl - a345ec8575bfebcff0d782b4a01899107770b5c4 authored over 7 years ago by Kenta Sato <[email protected]>
replace $ with \xor

github.com/BioJulia/BioSequences.jl - 076cb37430c75326637c8b8e3369f71b9eaf8492 authored over 7 years ago by Kenta Sato <[email protected]>
run appveyor on Julia 0.6 as well

github.com/BioJulia/BioSequences.jl - 5b228ea37609b55f7465242b86a73cd25a87818d authored over 7 years ago by Kenta Sato <[email protected]>
test on Julia 0.6 as well

github.com/BioJulia/BioSequences.jl - 0e3c236e8de1e7d5a14e1c85e3d9f2961aa96bd3 authored over 7 years ago by Kenta Sato <[email protected]>
replace repeated with fill

github.com/BioJulia/BioSequences.jl - dd1159ddbb0b0ae459974fc69a664c60ef1296a2 authored over 7 years ago by Kenta Sato <[email protected]>
replace takebuf_array

github.com/BioJulia/BioSequences.jl - a169a985c1d821b854d128621aa895332b571082 authored over 7 years ago by Kenta Sato <[email protected]>
use Vector{T} syntax

github.com/BioJulia/BioSequences.jl - 4b1a26dcd1fd774e6dd8438cbe71dd33d8f5066c authored over 7 years ago by Kenta Sato <[email protected]>
fix deprecated type declarations

github.com/BioJulia/BioSequences.jl - 0527308eea772278619994fbc1c008f5e04a5bc0 authored over 7 years ago by Kenta Sato <[email protected]>
fixup! fixup! fix inner constructors of parametric types

github.com/BioJulia/BioSequences.jl - 1d8c666519046ca964163e6196be9b4bccacffc8 authored over 7 years ago by Kenta Sato <[email protected]>
fixup! fix inner constructors of parametric types

github.com/BioJulia/BioSequences.jl - 4dc89f5f9e6314228338e0bb4db347ef0218ab30 authored over 7 years ago by Kenta Sato <[email protected]>
replace takebuf_string

github.com/BioJulia/BioSequences.jl - 67d34f823476e772f2fc2e8a7638e42591b03117 authored over 7 years ago by Kenta Sato <[email protected]>
drop dependency on PairwiseListMatices.jl

github.com/BioJulia/BioSequences.jl - 634cb3d65fc13cf38b5fc1d08710c2ccc032981c authored over 7 years ago by Kenta Sato <[email protected]>
require Compat 0.18

github.com/BioJulia/BioSequences.jl - 42ddf3880a20ca41df75edbe9d667b003c5db641 authored over 7 years ago by Kenta Sato <[email protected]>
loosen Compat requirement

github.com/BioJulia/IndexableBitVectors.jl - a119793a5b2302e38276c4506c0c2ccf9ecbadeb authored over 7 years ago by Kenta Sato <[email protected]>