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YeoLab
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outrigger
Create a *de novo* alternative splicing database, validate splicing events, and quantify percent spliced-in (Psi) from RNA seq data
http://yeolab.github.io/outrigger/
BSD 3-Clause "New" or "Revised" License
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Add issue and pr templates
#54
willingc
closed
7 years ago
3
Add issue and pull request templates
#53
olgabot
closed
7 years ago
0
Release v0.2.9
#52
olgabot
closed
7 years ago
0
--resume has no effect for event creation
#51
olgabot
opened
7 years ago
0
Parallelize psi calculation
#50
olgabot
closed
7 years ago
0
Allow bam files as input
#49
olgabot
closed
7 years ago
0
Parallelize Psi calculation
#48
olgabot
closed
7 years ago
1
Incompatible chroms between fasta and annotation
#47
olgabot
opened
7 years ago
1
Release v0.2.8
#46
olgabot
closed
7 years ago
1
0.2.7 Release
#45
olgabot
closed
7 years ago
1
--output doesn't actually work with `outrigger index`
#44
olgabot
opened
7 years ago
0
Upload to bioconda
#43
olgabot
opened
7 years ago
2
WIP: Support ENSEMBL gtf files
#42
olgabot
closed
7 years ago
3
Parallelize event finding
#41
olgabot
closed
7 years ago
0
Amend event metadata
#40
olgabot
closed
7 years ago
0
Support ENSEMBL and other gtf files
#39
olgabot
opened
7 years ago
0
Running out of memory when finding events
#38
olgabot
closed
7 years ago
0
CONTRIBUTING.rst is outdated
#37
olgabot
opened
7 years ago
0
Unify util.progress() and util.done() interfaces
#36
olgabot
opened
7 years ago
0
WIP: Smart restart
#35
olgabot
closed
7 years ago
2
Add more indentation for sub-items of searching for new exons on chro…
#34
olgabot
closed
7 years ago
0
Errors in running outrigger index
#33
lcscs12345
opened
7 years ago
10
Test commandline
#32
olgabot
closed
7 years ago
0
Test command line programs
#31
olgabot
closed
7 years ago
1
Allow `bam` input and other formats of splice junction files
#30
olgabot
opened
7 years ago
0
Version info
#29
olgabot
closed
7 years ago
1
Add version tag
#28
olgabot
closed
7 years ago
0
Release v0.2.6
#27
olgabot
closed
8 years ago
0
Properly parallelize
#26
olgabot
closed
8 years ago
0
Use AppVeyor to test build on Windows
#25
olgabot
opened
8 years ago
0
Release v0.2.5
#24
olgabot
closed
8 years ago
0
Release v0.2.5
#23
olgabot
closed
8 years ago
0
pep8 fixes
#22
olgabot
closed
8 years ago
0
Subfolder installation bug
#21
olgabot
closed
8 years ago
0
Release v0.2.3
#20
olgabot
closed
8 years ago
1
linux installation bug?
#19
olgabot
closed
8 years ago
0
Clarify genomic or transcriptomic upstream/downstream
#18
olgabot
opened
8 years ago
0
Validate events
#17
olgabot
closed
8 years ago
1
add test data for other event types
#16
olgabot
closed
8 years ago
0
Add `region.bed` for whole event region, from start of first exon to end of last exon
#15
olgabot
opened
8 years ago
0
Add `intron.bed` for all splice types
#14
olgabot
closed
7 years ago
1
Fix tests!
#13
olgabot
closed
8 years ago
1
Add test+data for finding exons in unannotated genes
#12
olgabot
closed
8 years ago
1
Add option to specify maximum length of de novo exon
#11
olgabot
closed
8 years ago
0
Add `outrigger all` to perform index, validate, and psi with default parameters
#10
olgabot
opened
8 years ago
0
Add other event types
#9
olgabot
opened
8 years ago
0
Save events as gff files
#8
olgabot
opened
8 years ago
1
Parallelize novel exon finding
#7
olgabot
closed
8 years ago
1
Parallelize exon-junction adjacency finding
#6
olgabot
opened
8 years ago
0
Add `outrigger validate` command to validate exons and splicing events
#5
olgabot
closed
7 years ago
1
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