CaSpER

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Hi, @akdess Thanks for this great work. Recently, When I tested CaSpER, I didn't know how to draw a phylogenetic tree.   Whether to use the plotSCellCNVTree function to...

Mashuaiii

runCaSpER error

2

Hi, friend when I use this good software to analyse bulk RNAseq (PE reads), when I run the following step: ` final.objects

baoyl818

how to create geno.rna object in https://rpubs.com/akdes/673120

2

@akdess Hi , Can you tell me how to create geno.rna object in https://rpubs.com/akdes/673120. Best, minfang

BioAmelie

Using CaSpER with single bulk RNA-Seq sample

2

Hello, Thank you for amazing tool. I am new to CNV analysis using RNA-Seq. Is it possible to use CaSpER for a single bulk RNA-Seq sample such as a tumor...

hkarakurt8742

Is there a way to retrieve/calculate CNV score from CaSpER for bulk data? I have seen other tool calculating log2ratio of reads depth tumor vs normal. Thanks for the help

alkurowska

error of loh <- readBAFExtractOutput

8

Dear sir, I tried to create loh and got error below: > loh

deb0612

Hello Dr. Akdes, I would like to use CaSpER to a 10x scRNA-seq tumor dataset, and I know the group of normal cells. The bam file contains reads from all...

kzb193

HMM Segmentation Error "memory not mapped"

3

Hi, can you tell me what might have caused this segmentation fault? I do realize this may not have been a CaSpER issue, but I have no idea what caused...

chatterjee89

Non model species using casper

3

Hi, I would like to use casper to find CN from bulk RNA-seq data of mouse and chicken. I have followed successfully the instruction until the function "generateAnnotation". However since...

reuvenieli00

runCaSpER error

1

**Getting below error in runCaSpER function:** **object

SaritaPoonia