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lcolladotor
/
derfinder
Annotation-agnostic differential expression analysis of RNA-seq data via expressed regions-level or single base-level approaches
http://lcolladotor.github.io/derfinder
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[Help required] setting cutoff
#46
Dalhte
opened
11 months ago
0
BiocParallel errors when running regionMat()
#45
rosshandler
opened
1 year ago
1
Coverage matrix for regions
#44
Prakrithi-P
opened
1 year ago
1
v1.27.3 -- use mcols() instead of values()
#43
hpages
closed
3 years ago
1
typo README
#42
c1au6i0
closed
3 years ago
3
Need help with makeModels() testvar error
#41
fruce-ki
closed
5 years ago
7
Question about the need for species and chromosome style
#40
fruce-ki
closed
7 years ago
2
namespace issues re: `tibble`?
#39
andrewejaffe
closed
7 years ago
1
filterData not providing feedback
#38
fomightez
closed
7 years ago
3
doesn't load on R 3.3
#37
andrewejaffe
closed
7 years ago
3
`targetSize` and `totalMapped` should be required inputs for `regionMatrix`
#36
andrewejaffe
closed
8 years ago
0
Please see issue
#35
LiNk-NY
closed
8 years ago
1
Add a way to set advanced options
#34
lcolladotor
closed
8 years ago
1
How Fstats are generated in analyzeChr()
#33
MonicaVara
closed
9 years ago
1
Problem with fullCoverage function
#32
PietaSchofield
closed
9 years ago
3
create a UCSC Track Hub from derfinder results
#31
andrewejaffe
closed
7 years ago
3
Can latest `derfinder` reproduce original (2013) analysis?
#30
brianhigh
closed
9 years ago
1
Speed up p-value calculation
#29
lcolladotor
closed
9 years ago
4
Width of devtools::session_info()
#28
lcolladotor
closed
9 years ago
1
Improve doc: filterData() after fullCoverage()
#27
lcolladotor
closed
9 years ago
0
filterData(cutoff = 0) fails in v0.0.69
#26
lcolladotor
closed
10 years ago
0
Missing derfinderPlot dependency
#25
lcolladotor
closed
10 years ago
1
Memory improvements to all parallel functions, new methods for F-stats calculation, recommended fullCoverage() and improved regionMatrix()
#24
lcolladotor
closed
10 years ago
0
Fully integrate GenomeInfoDb
#23
lcolladotor
closed
10 years ago
0
switch imports from GenomicRanges to GenomeInfoDb
#22
ttriche
closed
10 years ago
5
plotCluster() broken with ggbio 1.12.0
#21
lcolladotor
closed
10 years ago
0
Adopt GenomeInfoDb
#20
lcolladotor
closed
10 years ago
0
Warnings when using coverageToExon()
#19
lcolladotor
closed
10 years ago
0
add bigwig support?
#18
andrewejaffe
closed
10 years ago
1
Rcpp drop
#17
lcolladotor
closed
10 years ago
0
handle strand-specific alignments?
#16
alyssafrazee
closed
10 years ago
2
getRegionCoverage() improved by ajaffe
#15
lcolladotor
closed
10 years ago
0
fix NAMESPACE to work with current bioc-devel pkgs
#14
ttriche
closed
10 years ago
0
extra installation steps required
#13
alyssafrazee
closed
10 years ago
3
Changed to requiring ggbio 1.8.8 because the current 1.10.10 has a minor...
#12
lcolladotor
closed
10 years ago
1
Minor message tweak
#11
lcolladotor
closed
10 years ago
0
error in calculatePvalues() when fstats.output appears to be a list
#10
lcolladotor
closed
10 years ago
1
error in calculatePvalues() when fstats.output is NULL
#9
lcolladotor
closed
10 years ago
1
Bumped to version 0.0.42. A series of performance enhancements were made to reduce the memory load (albeit a very minor time increase).
#8
lcolladotor
closed
10 years ago
0
plotCluster() example fails due to a ggbio::autoplot() error
#7
lcolladotor
closed
10 years ago
1
Develpment updates
#6
lcolladotor
closed
10 years ago
0
import bumphunter, foldChange => log2FoldChange
#5
mikelove
closed
10 years ago
1
rename "foldChange" => "log2FoldChange" for the column in the output regions
#4
mikelove
closed
10 years ago
2
bumphunter as import
#3
mikelove
closed
10 years ago
4
Fixed bug in rccpFstats.cpp to make ss calculation correct on line 28
#2
jtleek
closed
11 years ago
0
plotCluster() not working on R 3.0.2
#1
lcolladotor
closed
10 years ago
2