deepTools

deepTools copied to clipboard

heatmap - name and position of gene of itnerest

1

Dear all, For my data set, I am interested how it looks over TSS throughout different chromosome, however once I got the result I noticed some regions really pop out...

mvukk

AttributeError: 'module' object has no attribute 'to_hex'（deeptools v2.3.2）

1

Dear all, Thank your team to code so great software that I cannot wait to learn when I first know it. However, there is a problem that I cannot resolve...

Golden-proteogenomics

This is related to issue [#1108](https://github.com/deeptools/deepTools/issues/1108#issue-1071108266). Running `bamCompare` with `--skipZeroOverZero` gives incorrect results. From left to right, the attached figure shows the following deepTools heatmaps: a ChIP-seq input control (RPGC-normalized...

joshscurll

different sizes of .fasta files inputs changes output

1

Hey, My name is Rotem from the Hebrew University, Israel. Im using bamcoverage and noticed in the [none.bw] output files that the reads are decimal numbers instead of integers, I...

rotemavr

Hi I am analyzing ATAC-seq data and want to visualize GC bias using the DeepTools function "computeGCBias". However, I always get a number of warnings and lastly an error. deepTools...

Simso86

Possible to calculate AUC and/or statistics for computeMatrix/plotProfile results?

2

I have some data from computeMatrix which I have drawn plots with plotProfile. Is there a way to compute the area under the curve of the line drawn by plotProfile...

bhanratt

**Welcome to deepTools GitHub repository! Please check the following regarding your pull request :** - [X] Does the PR contain new feature? - [ ] Does the PR contain bugfix?...

joshtburdick

keeping track of chr:start-end of bins when using multiBamSummary in bin mode

1

Hi everyone, I was wondering if there is a way to intercept/recreate the list of bins chr,stop,end to match the multiBamSummary output rows for annotation purposes. Thanks, Davide

castaway1990

Can I draw a whole-genome chromatin metaplot with Deeptools?

1

Hello! I want to know the method of drawing metaplot like this,the width of each box correlates with the chromosome length.  Thank you

TheAbsy

Hello, I think there may be an error in bamCoverage when using the --MNase option. It seems that four nucleotides are reported (one left to the center, the center, and...

feraltp