genomation

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Hi, I am trying to use generation and in particular the ScoreMatrix/ScoreMatrixList function to retrieve signal per base over windows in Granges object with targets BedGraph files. I know, and...

fgualdr

Site upstream of transcription start site annotated as intronic

2

Hi, I tried annotating a few sites with annotateWithGeneParts and I'm getting an intron annotation even though the site is upstream of transcription start site. Here's an example: BED12 entry...

pkothiyal

I'm wondering if there is a way to link the meta data to the annotation result for non-gene part annotation. For example, if you do the following, you can get...

shawpa

[Feature request] Keep all windows in the scoreMatrix

2

Currently ScoreMatrix does not keep all windows in the output. It removes all `windows` which overlap exactly 0 features in `target`. This causes two research problems: - it gives an...

balwierz

ScoreMatrix incorrectly removes valid windows

2

Example code: ``` gr3

balwierz

Example code: ``` gr1

balwierz

readTranscriptFeatures with GTF

6

`readTranscriptFeatures()` reads a BED file. Gene features are commonly stored as a GTF file. Is there a way to import a GTF file in the proper format for `annotateWithGeneParts()`? There...

igordot

invalid class “ScoreMatrix” object

1

**## When I run the code as below, I got an error. Could you help me deal with the bugs? Thanks a lot.** data(cage) data(promoters) scores1=ScoreMatrix(target=cage,windows=promoters,strand.aware=TRUE, weight.col="tpm") library(GenomicRanges) covs =...

LiyanJi-code

Hi, I am trying to use genomation and methylKit to analyze some RRBS data. I identified the identified the significantly differentially methylated cytosines (q-value threshold of 0.01 and a minimum...

abcosta

Hi, I'm currently using your package to visualize the RRBS data, following an example from [here](https://zvfak.blogspot.com/2015/03/using-genomation-to-analyze-methylation.html). Although some of the original links doesn't work now. I managed to manual download...

alexyfyf