GoekeLab proActiv issues

GoekeLab / proActiv

Estimation of Promoter Activity from RNA-Seq data

https://goekelab.github.io/proActiv/

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unable to create promotor annotation for a non-model organism

#53 ShenTTT closed 2 weeks ago
7
Does getAlternativePromoters function work properly?

#52 Tianle-Li closed 5 months ago
0
Couldn't find a BSgenome data package that matches genome assembly: oryCun2.0

#51 houruiyan closed 9 months ago
2
core dumped

#50 houruiyan closed 9 months ago
1
What is the mean of names(genomeStyles()) ?

#49 houruiyan closed 9 months ago
2
Error in `[[<-`(`*tmp*`, name, value = new("SimpleIntegerList", elementType = "integer",

#48 mmpust closed 8 months ago
4
plotPromoters function not available in latest version

#47 notthathime opened 1 year ago
1
A little question about internal promoter^_^

#46 CuteGold0407 opened 1 year ago
0
Error in EstimateSizeFactorsForMatrix: at least one zero

#45 notthathime opened 1 year ago
1
calculatePromoterReadCounts were not running

#44 GuangyaoL opened 1 year ago
1
Identification of cancer-associated promoters

#43 alejandrogzi opened 1 year ago
0
could not find function "getAlternativePromoters"

#42 wenmm closed 1 year ago
1
Some question about getAlternativePromoters()

#41 ninjaxfy closed 2 years ago
2
used for 10x data

#40 houruiyan closed 2 years ago
2
cannot find extdata/testdata/bam

#39 houruiyan closed 2 years ago
2
Getting active/inactive and major/minor promoters when no condition is specified

#38 elenichri opened 2 years ago
1
fix a typo in doc

#37 lu000016 closed 2 years ago
0
some question about the paper

#35 ninjaxfy closed 2 years ago
1
DEXSeq hangs

#34 elenichri opened 2 years ago
0
estimating promoter activity from given bam files

#33 ninjaxfy closed 2 years ago
4
Docker image for proActiv

#32 NaotoKubota closed 3 years ago
2
Not summarized values across conditions

#31 elenichri closed 3 years ago
3
invalid class "DESeqDataSet" object error

#30 elenichri closed 3 years ago
6
map to txId by promoterId

#27 yuukiiwa closed 3 years ago
1
getAlternativePromoters (Bioconductor version dont have it)

#26 ashokpatowary closed 2 years ago
1
preparePromoterAnnotation for different species

#25 gabee-chan closed 3 years ago
5
update installation guide to Bioconductor

#24 jonathangoeke closed 3 years ago
0
getTranscriptRanges() function limits species this can be applied to

#23 G-Thomson closed 3 years ago
2
No major promoter when internal promoters are strong

#22 lukauskas opened 3 years ago
2
Example of how to generate junction file from fastq

#21 lukauskas opened 3 years ago
1
Updates to trim package size for Bioconductor submission

#20 jleechung closed 4 years ago
0
proActiv release 0.99.0

#19 jleechung closed 4 years ago
0
Vignette and READ.ME

#18 jleechung closed 4 years ago
0
proActiv throws error with xz-compressed Tophat2 junction file

#17 jleechung opened 4 years ago
0
Include Unit Tests

#16 jleechung closed 4 years ago
0
Modify Variable Names

#15 jleechung closed 4 years ago
0
Change variable names

#14 jleechung closed 4 years ago
0
Reduction of Promoter Annotation Size

#13 jleechung closed 4 years ago
0
Promoter Annotation Optimization

#12 jleechung closed 4 years ago
0
create a vignette with an example analysis script

#11 jleechung closed 4 years ago
1
optimize preparation of promoter annotation object

#10 jleechung closed 4 years ago
1
update to LICENSE (MIT) and README

#9 jonathangoeke closed 4 years ago
0
Implement parallelization, BAM usage and wrapper

#8 jleechung closed 4 years ago
1
updated .gitignore

#7 jonathangoeke closed 4 years ago
0
create proActiv wrapper to return summarizedExperiment with promoter ranges

#6 jonathangoeke closed 4 years ago
1
updated README with simplified code

#5 jonathangoeke closed 4 years ago
0
Included links to additional data

#4 jonathangoeke closed 4 years ago
0
estimate promoter activity from bam file

#3 jonathangoeke opened 4 years ago
2
how to prepare promoterAnnotationData?

#2 xflicsu closed 4 years ago
1
update to documentation

#1 GoekeLab closed 5 years ago
0