TOBIAS

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BINDdetect vs plotHeatmap

3

Hi First of all, thanks a lot for such a nice and useful tool! I have two sets of ATAC-samples; control cells and cells over-expressing TF A. I have ChIP-seq...

mbergsland

BINDetect not giving out error when the motif file is "deformed"

2

Might be a continuation of issue #78. When I tried to run BINDetect using "pfm" motif file created by gimmemotifs, i get a problem where The pfm file looks something...

johannesnicolaus

batch effect

3

Hi, Im working on bulkATAC data. The experiment was run in two batches and when I made the PCA plot, the data is separated by batches indicating strong batch effect....

drosop

TOBIAS ATACorrect fails on some datasets, without any error message

4

Hello, I'm running TOBIAS on aggregated data from different single-cell ATAC-seq clusters. The ATACorrect step fails on a subset of clusters without any error message, but works on others. It...

liz-is

Different locus numbers across conditions and Strategies for Multi-Tissue TF Footprint Score Comparison

3

Hello, I appreciate your continued assistance, it has been very useful to me!! I am working on multiple conditional data， And I want to identify which TFs are important in...

Myrtle-bio

Clustergram --- "(Clusters below threshold are colored)"

8

Hi, 1. The phrase "below threshold" is a tiny bit confusing. So colored clusters are *not* significant? 2. Also, in the same figure "Differential binding score" there are some circles...

c2b2pss

Installation problem - solving environment

1

Hello, I've tried to install TOBIAS a few times, and each time, I get stuck on Solving environment for 24+ hours, and have been terminating it. Is this expected? Should...

sngholee

BINDetect warning and error

1

Thanks for providing this tool to the community. I have encountered the following error "AttributeError: FancyArrowPatch.set() got an unexpected keyword argument 'add_objects'" using BINDetect (TOBIAS 0.16.1 BINDetect). Some warning messages...

peryq

Hi, I have the following three questions for CreateNetwork:

1

Hi, I have the following three questions for CreateNetwork: 1. The two columns in the motif2gene_mapping.txt file are supposed to be the motif name \t gene name or the gene...

hyBio

bam and -peaks bed file in ATACorrect

3

Thank you for your great work! I would like to ask if the genomic region of the bam file needs to be exactly the same as the range of peak.bed?...

31474molly