ccmeth

Thanks a lot for the hicInterIntraTAD function, and one question is whether the calculation of intra-TAD considered the diagonal contacts (self-interacting contacts). Thanks!

Bismark mapping issue

1

Hi Developers, Thanks a lot for providing such a useful tool. When I used the bismark code, I met with a very strange issue that did not appear before. I...

Unexpected combination of read and genome conversion: /

5

Hi, Thanks for providing such a useful tool for DNA methylation analysis. Recently, I used the bismark_methylation_extractor to extract methylation information from a sorted bam file (which was generated by...

CommandNotFoundError

2

Hi, Thanks for this useful tool and I met with a problem when I "bash test.sh | bash", and the error is "CommandNotFoundError: Your shell has not been properly configured...

Disruption after load files

8

Hi, developers, I met with an issue related to load_contacts. After I load hic matrix, the R studio became disrupted and I could do nothing, could not save the data....

Dear developers, Thanks for providing a powerful tool for us to deal with Hi-C data. Recently, I used hic_matrixplot to exhibit Hi-C contact matrices as well as H3K4me3/H3K9me3 signals, however,...

Concern related to function "intra_inter_TAD"

3

Hi, developers, Thanks a lot for providing such a powerful tool for us to analyze Hi-C data, recently I used results obtained from "intra_inter_TAD" to compare the TAD insulation variation...

list index out of range!

5

Hi developers, Thanks a lot for developing a very useful tool for loop analysis. However, I met with an error when using the diff.py. The chromosomes I chose for loop...

Visualize.py?

8

Hi, developers, Thanks a lot for providing such a powerful tool for us to analyze ONT data. I installed isoquant with version 3.4.2 by means of "conda create -c conda-forge...