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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

Precompile and info header

github.com/BioJulia/BioStructures.jl - 38828635bfbdd7509e5ff1811524b76b58ba5303 authored about 7 years ago by Joe Greener <[email protected]>
Fix Julia 0.6 deprecation warnings

github.com/BioJulia/BioStructures.jl - 4b35047cce997146764e3a57b357a288a2e6b1d3 authored about 7 years ago by Joe Greener <[email protected]>
Update imports and REQUIRE

github.com/BioJulia/BioStructures.jl - 90f191675b8bef9ab1c492a3a14bf7828e2fc45e authored about 7 years ago by Joe Greener <[email protected]>
Direct copy of files from Bio.jl master

github.com/BioJulia/BioStructures.jl - 8d7f9f769271895150c0971efac6102ee4cdc55e authored about 7 years ago by Joe Greener <[email protected]>
Remove codecov file

github.com/BioJulia/BioStructures.jl - dbe1215914d81c634a6f4c53b1e76cd2f096a6ed authored about 7 years ago by Joe Greener <[email protected]>
MIT license

github.com/BioJulia/BioStructures.jl - eeed1d776f5d2b27828a35b11e80e9464ab5304a authored about 7 years ago by Joe Greener <[email protected]>
BioStructures.jl generated files.

license: MIT
authors: Joe Greener
years: 2017
user: jgreener64

Julia V...

github.com/BioJulia/BioStructures.jl - 8164e33628958b552254042428e3b0ec6ebc1a6a authored about 7 years ago by Joe Greener <[email protected]>
initial empty commit

github.com/BioJulia/BioStructures.jl - 653fd0f9568fdd9d83afc477a32af2e2d950f693 authored about 7 years ago by Joe Greener <[email protected]>
Syntax change and News File addition.

Syntax change and News File addition.

github.com/BioJulia/BioSequences.jl - 097299644055033a9f2df174f23e170ee30a6de1 authored about 7 years ago by Ben J. Ward <[email protected]>
PDB download and database functions (#483)

github.com/BioJulia/Bio.jl - 1c89218ef1e3b5d351c279693310c5dce5521940 authored about 7 years ago by Joel S <[email protected]>
add position weight matrix search (#16)

github.com/BioJulia/BioSequences.jl - 501fce82de6e368b3aff84f8d8a1a0fbbd0eeba4 authored about 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
[WIP] Add unique sequence counting function (#22)

* Add unique sequence counting function

* Changed method to a generalised composition method....

github.com/BioJulia/BioSequences.jl - 45e5533d9f5305bc9016d5e9cd2cb20119667318 authored about 7 years ago by Ben J. Ward <[email protected]>
Merge pull request #3 from Ward9250/indexing

Inline the Base.getindex method

github.com/BioJulia/SubstitutionModels.jl - 1356f06ad69e353f0861001e95a6af3acf007d26 authored about 7 years ago by Justin Angevaare <[email protected]>
Merge pull request #4 from Ward9250/format-edits

Edits to CI infrastructure

github.com/BioJulia/SubstitutionModels.jl - 5e7f6cf02edd93b1cfb2868c3e34d21a105caedb authored about 7 years ago by Justin Angevaare <[email protected]>
Edits to CI infrastructure

github.com/BioJulia/SubstitutionModels.jl - 28e3914ff0355f68e698a2ebc349d30724daf63a authored about 7 years ago by Ben J. Ward <[email protected]>
inline getindex method

github.com/BioJulia/SubstitutionModels.jl - ab18db358d87c5a9449d507dce416f40b731a566 authored about 7 years ago by Ben J. Ward <[email protected]>
Merge pull request #2 from Ward9250/indexing

Eliminate the need for an indexing lookup table

github.com/BioJulia/SubstitutionModels.jl - b19fcc2c58446392942ff6f6c9456e6a83781d3e authored about 7 years ago by Justin Angevaare <[email protected]>
Eliminate the need for an indexing lookup table

github.com/BioJulia/SubstitutionModels.jl - 773cf6cb959d247f66f76fe38f5674faedfdae99 authored about 7 years ago by Ben J. Ward <[email protected]>
use Dict to store counts in Composition (#21)

This is a little bit slower than using Vector but it is able to store
counts of long k-mers wit...

github.com/BioJulia/BioSequences.jl - 33288b34b3ccb9992a930901fe646f7a98a6f807 authored about 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
dnds api (#10)

fix

fix

pairwise fix

fix

import fix

pairwise dnds

Edit some 0.5 sy...

github.com/BioJulia/GeneticVariation.jl - b1cf2f2f78941d774e205fd0e170829dff4d114d authored about 7 years ago by Ben J. Ward <[email protected]>
Decompose Bio.Align and Bio.Intervals (#482)

github.com/BioJulia/Bio.jl - e08f2a3cd0fb439586a58c198f8a7ebf83648962 authored about 7 years ago by Ben J. Ward <[email protected]>
Make minhash function for generic reader (#19)

* add fastq reader to minhash

* Use AbstractReader

github.com/BioJulia/BioSequences.jl - 08793354ba0950fe7c38d1d61dc4b687bd74fb93 authored about 7 years ago by Kevin Bonham <[email protected]>
add typemin and typemax for Kmer (#20)

github.com/BioJulia/BioSequences.jl - e419533daf8334c9b4e84cbf83095278229c3c91 authored about 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
use where clause for type parameters (#7)

github.com/BioJulia/BioAlignments.jl - 5592f3e0296e099e857c381056af63ad76701e9d authored about 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Drop julia 0.5 support (#31)

* Changed parametric method syntax

* Minor edit to runtests.jl

* New format for internal n...

github.com/BioJulia/IntervalTrees.jl - 044849d3b3776d3d7fcb73729d5adb5f3b616692 authored about 7 years ago by Ben J. Ward <[email protected]>
Attempt to set up documentation pages with documenter.jl

Add mkdocs.yml file

Further work on documentation

Further documentation work

add makelocal.jl...

github.com/BioJulia/SubstitutionModels.jl - 68bb8592a0df468142225bbe9438b878c8a3f5d1 authored about 7 years ago by Justin Angevaare <[email protected]>
Update docs (#6)

github.com/BioJulia/BioAlignments.jl - 1b0a99e1cc37452cd3447ccf515f7992fc7e95ec authored about 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Update .travis.yml

github.com/BioJulia/Contributing - d6aa088e6bec5747d379220032c1db1285b82b37 authored about 7 years ago by Ben J. Ward <[email protected]>
update doctests for Julia 0.6 (#18)

github.com/BioJulia/BioSequences.jl - c1eaf0fd27f2e142ee32d838f9a6d1fb9b113817 authored about 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Drop julia 0.5 syntax and support (#9)

* Drop julia 0.5 syntax and support

* fix a takebuf_array use

* depreceate more takebuf_ar...

github.com/BioJulia/GeneticVariation.jl - 3a7c88f04aad3ed9446731a241af22701309541c authored about 7 years ago by Ben J. Ward <[email protected]>
More precise issorted check.

github.com/BioJulia/IntervalTrees.jl - c5d5d303ad2679ad67c40a379433bb99599e1419 authored about 7 years ago by Daniel C. Jones <[email protected]>
define Q matrices directly for most substitution models

fix require

github.com/BioJulia/SubstitutionModels.jl - 5897b93674f95788ce2a877c067545c58678608f authored about 7 years ago by Justin Angevaare <[email protected]>
Add news about julia 0.5 support drop

github.com/BioJulia/biojulia.github.io - ae35961252e5f148bfdd018799047e81a12b5c44 authored about 7 years ago by Ben J. Ward <[email protected]>
Drop Julia 0.5 (#17)

* Julia 0.6 edits to files

* Update the CI configs

* Update syntax in alphabet.jl

* Rem...

github.com/BioJulia/BioSequences.jl - da650d5a5e8303f8b7540925ccd7f09e30653ad9 authored about 7 years ago by Ben J. Ward <[email protected]>
[Review] Drop Julia 0.5 (#17)

* Julia 0.6 edits to files

* Update the CI configs

* Update syntax in alphabet.jl

* Rem...

github.com/BioJulia/BioSequences.jl - 6e8a2f8697f73cb25e70bdc647d212dd4e84624f authored about 7 years ago by Ben J. Ward <[email protected]>
improve test coverage (#16)

* add more tests on amino acids

* add more tests on DNA/RNA

github.com/BioJulia/BioSymbols.jl - 9680751fabdb26ddc7a841c2115c149ec78e7617 authored about 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
add a description on (try)parse (#15)

github.com/BioJulia/BioSymbols.jl - 0540e11417a34e90bcdbba4b9b1a0fba7081956d authored about 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Add efficient P matrix method to TN93, add error checks to P()

github.com/BioJulia/SubstitutionModels.jl - 32a9beaa82380e09a4abbe690d3c28a0b7130ee7 authored about 7 years ago by Justin Angevaare <[email protected]>
Add efficient P matrix method to HKY85

github.com/BioJulia/SubstitutionModels.jl - 1a75106442437b66929845a5648247a5a2cac08d authored about 7 years ago by Justin Angevaare <[email protected]>
Add efficient P matrix method to F84, fix matrix orientations

github.com/BioJulia/SubstitutionModels.jl - b530ee4e0c01d1f6db686dc240bef75e4d9f522e authored about 7 years ago by Justin Angevaare <[email protected]>
Drop Julia 0.5 (#9)

* drop Compat.jl

* replace immutable with struct

* replace type with mutable struct

* f...

github.com/BioJulia/GenomicFeatures.jl - ce551969d9dabaf535cfd8edc4719c522ca16294 authored about 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Add faster P method for F81 models

github.com/BioJulia/SubstitutionModels.jl - 1b0027bf70492fcae629df83d30579a70e3d51cd authored about 7 years ago by Justin Angevaare <[email protected]>
Add more efficient P method to K80 models, add more tests

github.com/BioJulia/SubstitutionModels.jl - 40defc74a7841b9331f15dec08d70e1a964df60f authored about 7 years ago by Justin Angevaare <[email protected]>
Small readme changes

github.com/BioJulia/SubstitutionModels.jl - 3b8e63575c8b4e437c7a53660bfcc474037dcfc5 authored about 7 years ago by Justin Angevaare <[email protected]>
Prepare documentation for repo transfer to BioJulia

rename SubstitutionModels2 to SubstitutionModels throughout package

rename SubstitutionModels2 ...

github.com/BioJulia/SubstitutionModels.jl - f6f1fdfb2c7f29857ce275cad694e4d18889a76d authored about 7 years ago by Justin Angevaare <[email protected]>
Add show methods for all substitution models

github.com/BioJulia/SubstitutionModels.jl - ccc9b57e7836a942f5515c3ef7cc5d47fd84941a authored about 7 years ago by Justin Angevaare <[email protected]>
Faster P method for JC69 models

github.com/BioJulia/SubstitutionModels.jl - 71705a1c7093c256b7fd3879c62fbb08aa82e850 authored about 7 years ago by Justin Angevaare <[email protected]>
code cleanup

github.com/BioJulia/SubstitutionModels.jl - 6924e8dfacd1f882689917fc47fc95e062cb5378 authored about 7 years ago by Justin Angevaare <[email protected]>
Add GTR

github.com/BioJulia/SubstitutionModels.jl - b174ad2fce717d1bb0b4188d03f04aced2330543 authored about 7 years ago by Justin Angevaare <[email protected]>
Add TN93

github.com/BioJulia/SubstitutionModels.jl - 780cad211487c991950dcf5c0169bde4fdfb98fc authored about 7 years ago by Justin Angevaare <[email protected]>
Add HKY85, correct F84

github.com/BioJulia/SubstitutionModels.jl - b1119764249a7fe04153254beaaab73ac358cd81 authored about 7 years ago by Justin Angevaare <[email protected]>
Add F84 model

github.com/BioJulia/SubstitutionModels.jl - 7f576e1800b88602e5256f68c8d50a64174ffe1b authored about 7 years ago by Justin Angevaare <[email protected]>
Add f81 model, fix Q matrix calculation

github.com/BioJulia/SubstitutionModels.jl - eb7a3233108f83891368a612d9f05953a376ec33 authored about 7 years ago by Justin Angevaare <[email protected]>
Add K80 models

github.com/BioJulia/SubstitutionModels.jl - fa78a385acf604f5b2939fe59e84dab6def0a227 authored about 7 years ago by Justin Angevaare <[email protected]>
Fix most of 0.7 depwarns (#57)

github.com/BioJulia/Libz.jl - 308b1f353195a8966f7264f52af97c6f4c3f53ff authored about 7 years ago by Yichao Yu <[email protected]>
Basic functionality for JC69 models

Basic functionality for JC69 models

github.com/BioJulia/SubstitutionModels.jl - 490292460311306c399c2e130328114476dbcb04 authored about 7 years ago by Justin Angevaare <[email protected]>
SubstitutionModels2.jl generated files.

license: MIT
authors: Justin Angevaare
years: 2017
user: jangevaare

Ju...

github.com/BioJulia/SubstitutionModels.jl - ad20d515e7ff1b023005cad3f98c4bdedb81da9c authored over 7 years ago by Justin Angevaare <[email protected]>
initial empty commit

github.com/BioJulia/SubstitutionModels.jl - ff47a7d67cd090db9b845993f11b4bec92fd0f0c authored over 7 years ago by Justin Angevaare <[email protected]>
Minor optimization of loop unrolling (#22)

* increment position before break

* remove the upper limit of loop unrolling

github.com/BioJulia/Automa.jl - 8ee444caa71d14b8555f34e912d79800eacd2477 authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
[RTR]: Update get_fmt_specimens method (#6)

* Update get_fmt_specimens method

* Added git fetch origin and removed clone --depth 1

github.com/BioJulia/BioCore.jl - 72d64744643ba817ef79e07418d8b9afe5620f67 authored over 7 years ago by Ben J. Ward <[email protected]>
Drop support of Julia 0.5 (#3)

* require Julia ≥0.6

* drop Compat.jl

* update old-fashioned innter constructors

* upda...

github.com/BioJulia/BioAlignments.jl - afc14ad80c0b062f231ebc94c656a13f4f313029 authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
make index types immutable (#6)

github.com/BioJulia/GenomicFeatures.jl - 3d55c41cacc6cd9221535c34545946c5aa22f81a authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
support tabix (#5)

* support tabix for GFF3

* fix a typo

* merge GFF3 tests

* make the overlap iterator ge...

github.com/BioJulia/GenomicFeatures.jl - 5381331535866cbbac1c9a50b736513bdcf80f4e authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
generate amino acid parser with Automa.jl (#13)

github.com/BioJulia/BioSymbols.jl - 900875371caa194c650d6cc1d2db0af2fe37038e authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
add block compressed BED and GFF3 files (#22)

* add GFF3/TAIR10.part.gff.bgz

* add BED/ws245Genes.WBGene.bed.bgz

github.com/BioJulia/BioFmtSpecimens - 222f58c8ef3e3480f26515d99d3784b8cfcca046 authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Update CI URLs to point to new caching infrastructure (#10)

github.com/BioJulia/BGZFStreams.jl - e50cc55a73aa32833cc66e4d4e19d1e07efd3d49 authored over 7 years ago by Elliot Saba <[email protected]>
update code generator functions for Automa 0.3 (#4)

* update code generator functions for Automa 0.3

* add kwargs

github.com/BioJulia/BioCore.jl - ceb7c992ba1022011af637075a6bbf830afb9974 authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
fix codegen performance degradation (#21)

github.com/BioJulia/Automa.jl - a57c2fe19ff62bfe4954ce7bd9b0bd1b2765be22 authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Update .travis.yml (#56)

github.com/BioJulia/Libz.jl - a3c9ca5db6a19e4ba38ef9ccb7e26564766f6a3f authored over 7 years ago by femtotrader <[email protected]>
Merge pull request #36 from tkelman/patch-1

adjust tag message about version bounds

github.com/BioJulia/attobot - 872001e60e4c77fc9bc0f36431b7a999fd0d2b1a authored over 7 years ago by Simon Byrne <[email protected]>
adjust tag message about version bounds

"up to date" could be confusingly interpreted as "latest versions"
which isn't usually appropriate

github.com/BioJulia/attobot - d2ef9e6f5362ee4d2c8bed511cad056ffba1bd1a authored over 7 years ago by Tony Kelman <[email protected]>
recommend users to use CodecZlib.jl

github.com/BioJulia/Libz.jl - a1ef6bd0d4e0cdb1c5c5c1004af0da6abfa6b769 authored over 7 years ago by Kenta Sato <[email protected]>
Loop unrolling (#16)

github.com/BioJulia/Automa.jl - a2a321bc30d08b615ced78f0e0eaba6ff5db4272 authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
make code generation deterministic (fix #19) (#20)

* make code generation deterministic (fix #19)

* remove debug code

* update numbers.png

...

github.com/BioJulia/Automa.jl - fd2e974cb6d2c287a1cea651bed02338c27026cd authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
add CodeGenContext (#18)

* add CodeGenContext

* add more tests on SizedMemory

* replace tests with new interfaces
...

github.com/BioJulia/Automa.jl - 7e6e88f2fbea30066280b949b7412712eaf18601 authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Added biobridger release news

github.com/BioJulia/biojulia.github.io - d3409597b15c102642404c520490ebab30ccb7c6 authored over 7 years ago by Ben J. Ward <[email protected]>
Restructure docs (#12)

* use material

* fix index.md

* decompose docs

* references

* rename index page

*...

github.com/BioJulia/BioSymbols.jl - d57f19253b7c5bc9e3f3f9152d26905fbf218161 authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
in

github.com/BioJulia/BioBridgeR.jl - 3886fe8b12efbc00e6ec39a1dc2b7e3565030585 authored over 7 years ago by Ben J. Ward <[email protected]>
Simplify methods and increase perf (#4)

* Simplified rcopy(::Type{Array{DNAbin, 2}}, rs::Ptr{RawSxp})

* Added rcopy for Array{DNA, 2}...

github.com/BioJulia/BioBridgeR.jl - 3c77845bc09ca09d3ede476d123fc3d99d3a7b03 authored over 7 years ago by Ben J. Ward <[email protected]>
change log level

github.com/BioJulia/attobot - 1ce47a940f3a8ee5080ef8232e45bb9bc9b4f167 authored over 7 years ago by Simon Byrne <[email protected]>
Use IterTools instead of Iterators (#13)

github.com/BioJulia/BioSequences.jl - f7f4d882f1c8475a06b264fc4a10bf8f14d16c7a authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Fix potential protect-unprotect stack imbalance (#3)

* Fix potential protect-unprotect stack imbalance

* Change to new parametric method syntax fix

github.com/BioJulia/BioBridgeR.jl - ffc35dba755e880b40b38510df30c171f5f80521 authored over 7 years ago by Ben J. Ward <[email protected]>
Edit documentation

github.com/BioJulia/BioBridgeR.jl - 2d6d45b9d57a5f8abd699b10e62a16b63c3990a7 authored over 7 years ago by Ben J. Ward <[email protected]>
Merge remote-tracking branch 'origin/master'

github.com/BioJulia/BioBridgeR.jl - 4e6fc456d2d3cf91f0cdf822ed3161146c8c28a2 authored over 7 years ago by Ben J. Ward <[email protected]>
Added documentation files

github.com/BioJulia/BioBridgeR.jl - 0971bd79c8f2bfe00918586895454f7b8649e8b0 authored over 7 years ago by Ben J. Ward <[email protected]>
Updated readme

github.com/BioJulia/BioBridgeR.jl - a0b89fbed765205b73ccc774da041b9277a023fd authored over 7 years ago by Ben J. Ward <[email protected]>
Updated readme

github.com/BioJulia/BioBridgeR.jl - d4bc3b260bc3fe799e3cf7d695dad56ae54726fa authored over 7 years ago by Ben J. Ward <[email protected]>
Setup appveyor (#2)

* Added R download to appveyor

* edit appveyor

* edit appveyor

edit appveyor

edit appv...

github.com/BioJulia/BioBridgeR.jl - b6e26e4542fd08b82bf4718753da5a5c896b61cd authored over 7 years ago by Ben J. Ward <[email protected]>
Setup Travis (#1)

* edit travis

* travis edit

* travis edit

* edit travis

github.com/BioJulia/BioBridgeR.jl - e0310bcb27418dba526562899ec25f136cdcf852 authored over 7 years ago by Ben J. Ward <[email protected]>
Edited travis.yml

github.com/BioJulia/BioBridgeR.jl - 6cfa6e97455ae096dc581949ca449abefc811a80 authored over 7 years ago by Ben J. Ward <[email protected]>
Many fixes, and added R-julia transfer of DNAbin class

github.com/BioJulia/BioBridgeR.jl - b1bacc45c757f721dea4f219e7199bb33552592a authored over 7 years ago by Ben J. Ward <[email protected]>
Method generalisations (#10)

* Generalised UInt8 -> NucleicAcid conversion

Nessecery for the current design of BioBridgeR'...

github.com/BioJulia/BioSymbols.jl - c614cffa8c20ac54584aa34822d771b3fa5ad3dc authored over 7 years ago by Ben J. Ward <[email protected]>
fix docstrings (#11)

github.com/BioJulia/BioSymbols.jl - 9443faf071a10e44b223b1c631c947d17d8c53bc authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Added many methods and tests

github.com/BioJulia/BioBridgeR.jl - d308832bc30c7609a976ac8eb87ad4793d5f674d authored over 7 years ago by Ben J. Ward <[email protected]>
Added isambiguous and iscompatible

github.com/BioJulia/BioBridgeR.jl - 127adbf501878fe7300262e71b50187ae37d17af authored over 7 years ago by Ben J. Ward <[email protected]>
Added tests for conversion from characters

github.com/BioJulia/BioBridgeR.jl - e13bf1bf1973dc6b13e75cef7448ae21953ecb56 authored over 7 years ago by Ben J. Ward <[email protected]>
DNAbin symbol type

Defined a DNAbin symbol type which can be converted to and from BioSymbols.DNA symbol types, and...

github.com/BioJulia/BioBridgeR.jl - 709148bb59e495e3b4a4ac5ecb7c9c0e06d1c1e8 authored over 7 years ago by Ben J. Ward <[email protected]>
Update packages page

github.com/BioJulia/biojulia.github.io - cd88642cef1955c49279ad9dda6d34135dead28f authored over 7 years ago by Ben J. Ward <[email protected]>
BioAlignments.jl news update

github.com/BioJulia/biojulia.github.io - a0e96de65ba925261e394fb6840906c0732943d3 authored over 7 years ago by Ben J. Ward <[email protected]>
README update

github.com/BioJulia/BioSequences.jl - 37ee404877a53c7948f808624ea5dc9c113cbd74 authored over 7 years ago by Ben J. Ward <[email protected]>