proActiv

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plotPromoters function not available in latest version

1

Hi! Thank you very much for your great work! I am encountering a problem with the version 1.8.0 as the plotPromoters function is somehow not available. But in the version...

notthathime

Error in EstimateSizeFactorsForMatrix: at least one zero

1

Thank you very much for sharing your amazing work. I encountered a problem after running Result function. It showed as below: Calculating junction counts Calculating normalized read counts... converting counts...

notthathime

Hi, Thank you for sharing your work! I had a problem while reading your work. In the published paper, you said "_**We excluded internal promoters from our analysis with the...

CuteGold0407

calculatePromoterReadCounts were not running

1

hi~ proActiv::calculatePromoterReadCounts(files=files, promoterAnnotation = promoterAnnotion.genecode.dm6.subset,fileType="star") we counted promoters count by using this function and found that ···Error: 'calculatePromoterReadCounts' is not an exported object from 'namespace:proActiv' ···

GuangyaoL

Hi @jleechung, I am trying to reproduce part of the proActiv paper by combining different cancer/normal RNA-seq datasets. To identify cancer or pan-cancer associated promoters a batch effect removal is...

alejandrogzi

Getting active/inactive and major/minor promoters when no condition is specified

1

Hello, I am trying to find active and inactive promoters and also major and minor promoters across a brain cancer dataset. I only need to retrieve the promoters for this...

elenichri

Hello, I am using proActiv v1.0.0, because I run it on a server where R 4.0.0 is installed. I cannot install a newer version of R (I don't have the...

elenichri

estimate promoter activity from bam file

2

Implement an option to estimate promoter activity from bam files (currently proActiv requires the junction files from TopHat2 or STAR)

jonathangoeke

No major promoter when internal promoters are strong

2

Hi again, While investigating the `proActiv` results for my sample dataset I came across the fact that many genes do not have a "Major" promoter, yet they tend to have...

lukauskas

Example of how to generate junction file from fastq

1

I realise this is a bit beyond scope for `proActiv` but it would be helpful to have an example on how to generate a valid junction file from raw reads...

lukauskas