mshah

Is it possible to incorporate externally generated figures?

2

Hi, Is there a way to incorporate externally generated figures while composing layouts with this package? Thanks, Minita

Hi, This is a great tool. I work on multiple projects at a time and was wondering if there is a way to categorize or group commands in some way?...

Hi, In the single-end epiread format one of the fields in the output is "5) position of the cytosine in the first CpG (0-based)". Is it somehow possible to get...

Number of samples for custom PON

1

Hi, How many samples do you typically recommend one should use to create a custom PON? I'm trying to create one for GRCh38 with mean cvg around 30x/sample. Thanks, Minita

Issues running svict

3

Hi, I'm trying to run this on a regular bwa mem bam file. I noticed 2 issues: 1. svict expects "SO:coordinate" as the third column but in the bam that...

Oncoprint - color top, center and bottom third of rectange

2

> Please provide example datasets and the code you use. It will help me to understand your problem and help you! Hi, I am trying to generate an oncoprint like...

Final segmentation from alternate ichorCNA solutions

1

Hi, For samples where I think one of the alternate ichor solutions makes more sense, is it possible to re-generate or extract final segmentation for those solutions? Basically, is there...