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jonathonthill
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MMAPPR2
Mutation Mapping Analysis Pipeline for Pooled RNA-Seq
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Does callSampleSpecificVariants eliminate variants that have low frequency in WT?
#54
kjohnsen
closed
6 years ago
1
Bamfile setter
#53
kjohnsen
closed
6 years ago
0
Output log file
#52
kjohnsen
closed
6 years ago
2
Replicate tests, file reading
#51
kjohnsen
closed
6 years ago
0
Remove showDebug
#50
kjohnsen
closed
6 years ago
0
Test output functionality
#49
kjohnsen
closed
6 years ago
0
Replace cat with message
#48
kjohnsen
closed
6 years ago
0
Eliminate need to install VEP by using web API
#47
kjohnsen
opened
6 years ago
0
Output gene name instead of ID from VEP
#46
kjohnsen
opened
6 years ago
0
Make Windows compatible
#45
kjohnsen
opened
6 years ago
0
Replace data.frame with data.table
#44
kjohnsen
opened
6 years ago
0
Auto-index BAM files
#43
kjohnsen
closed
6 years ago
1
Handle alignment and pre-processing purely within R
#42
kjohnsen
opened
6 years ago
0
Default parameter optimization
#41
kjohnsen
opened
6 years ago
0
Make secondary candidate list of loci with reduced expression
#40
kjohnsen
opened
6 years ago
0
Improve validity checking functions
#39
kjohnsen
opened
6 years ago
0
Implement AICc value plotting
#38
kjohnsen
opened
6 years ago
0
Update R version dependency to 3.5.0
#37
kjohnsen
closed
6 years ago
0
Make printing nice
#36
kjohnsen
closed
6 years ago
1
Update candidates.R
#35
kjohnsen
closed
6 years ago
0
Remove numcores
#34
kjohnsen
closed
6 years ago
0
Fix print method
#33
kjohnsen
closed
6 years ago
0
Vep integration
#32
kjohnsen
closed
6 years ago
0
Pass check in Travis
#31
kjohnsen
closed
6 years ago
0
WIP: Check fix
#30
kjohnsen
closed
6 years ago
1
Refactor BAM reading
#29
kjohnsen
opened
6 years ago
1
Parallelize candidate generation/VEP
#28
kjohnsen
opened
6 years ago
1
Implement coverage testing
#27
kjohnsen
opened
6 years ago
0
Analyze differential expression in peak area
#26
kjohnsen
closed
6 years ago
0
Create NEWS, 'inst' folder with CITATION
#25
kjohnsen
closed
6 years ago
0
Fix contact info in DESCRIPTION
#24
kjohnsen
closed
6 years ago
0
Refactor density plot into output function
#23
kjohnsen
closed
6 years ago
0
Revise function and variable names
#22
kjohnsen
closed
6 years ago
0
Pass BiocCheck in Travis CI
#21
kjohnsen
opened
6 years ago
1
Merge remote-tracking branch 'origin' into remove-loess-warnings
#20
kjohnsen
closed
6 years ago
0
Remove loess fit warnings in peakRefinement
#19
kjohnsen
closed
6 years ago
0
Seqname fix
#18
kjohnsen
closed
6 years ago
0
Tests for replicates in variant calling
#17
kjohnsen
closed
6 years ago
0
Tests for replicates in file reading
#16
kjohnsen
closed
6 years ago
0
Peak tests
#15
kjohnsen
closed
6 years ago
0
.peakRefinementChr raises warnings
#14
kjohnsen
closed
6 years ago
2
MmapprData object printing wrong
#13
kjohnsen
closed
6 years ago
0
Error if distance is empty
#12
kjohnsen
opened
6 years ago
1
Output tests
#11
kjohnsen
closed
6 years ago
0
VEP tests
#10
kjohnsen
closed
6 years ago
0
Peak function tests
#9
kjohnsen
closed
6 years ago
0
Write vignette
#8
kjohnsen
opened
6 years ago
0
Set up Travis CI
#7
kjohnsen
closed
6 years ago
1
Make MmapprParam printing more compact
#6
kjohnsen
opened
6 years ago
0
ggplot2 instead of base graphics
#5
kjohnsen
opened
6 years ago
0
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