GENOVA

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PESCAn Error: cannot allocate vector of size 150.9 Gb

4

Hi, @teunbrand I am so sorry to bother you again. When I use the PESCAn function, I always encounter the problem of cannot allocating vector of size. Even if I...

YuZhang337

Errors with chromosome_matrix() and load_contacts() function~

2

Hi, @teunbrand I am so sorry to bother you. For GENOVA, I'm not a veteran. I would prefer to use GENOVA because of the lightness and color palette. But just...

Miracle-Yao

hic file load error

2

when i using "balancing='KR'", i received the error: Reading data... Reading data... Error in juicer_in[, c(4, 1, 5, 2, 3)] : incorrect number of dimensions Calls: load_contacts -> loadJuicer ->...

Chuan0518

I following the code chunk example in PE-SCAn ，and i've got my own super-enhancer data, my code likes: TNBC_SE_OUT

usernicai

centromeres setting

1

My species is pig that not annotated with centromeres information. My code is : EDL

tan5251

calculating insulation score get inconsistant results

5

Hi, I am using GENOVA to calculate insulation score. the code is hic

jiangshan529

list of loops in hic_matrixplot

3

Dear all, I am using the function hic_matrixplot to compare two hic matrices. And I also want to add the loops info of two samples (called by hiccups) into the...

Guanchen-Li

ARA and pyramid plots issues

1

Hello, I am facing some issues when I try to use ARA and pyramid plot functions. ### For the ARA here is my script: **library(GENOVA) library(rhdf5) library(strawr) setwd('/gpfs/data/HernandoLab/home/bericp01/HiC/results/ARA') dir

BERICP01

HiCExplorer final mcool file load in GENOVA

1

I recently worked on cool files between GENOVA and HiCExplorer. I first converted the matrix file from hic-pro to cool file. Then we use HiCExplorer's hicNormalize and hicCorrectMatrix (--correctionMethod KR)....

usernicai

Memory footprint in Rstudio

6

When loading .hic files is finished, there is a ton of memory not cleaned up. My .hic file after loading is ~ 3-4 GB, but the memory footprint in my...

LucasMcNU