-
If I run `computeDeviations` on a chromVARCounts object without providing annotations, then I expect the deviations thus computed are the chromatin accessibilities of the input peaks. But is it safe t…
-
Dear developers,
I found that there needs a PWM format text as input in the config file. However, Jaspar only provides PFM text and the R library construct a PWMatrixlist how to get the PWM format …
-
- [ ] swi6 chromatin adaptor activity for Dfp1 and Rad21
- [ ] scm3 recruits cnp1
- [ ] check how swi6 and rad21 are involved in mitotic telomere clustering
http://europepmc.org/article/MED/2…
-
Hello,
GO:0034724 DNA replication-independent nucleosome organization & assembly child term were merged into their respective chromatin organization and assembly parents, see https://github.com/ge…
-
Hi,
First of all: thanks for the great work. I was reading the paper (from your lab) "Two independent modes of chromatin organization revealed by cohesin removal." In the paper, the authors mentio…
-
According to the README.md, one can define and set up the various "soft LJ potentials" in a file called `LJsoft_RSQ.table` using the script `setup_ljsoft_potentials.py`. User should be able to modify …
-
### Data Owner Name
ALLEN INSTITUTE/Chan Zuckerberg Initiative/GeoNet
### Data Owner Country/Region
United States
### Data Owner Industry
Life Science / Healthcare
### Website
https://www.allen…
-
Hello~ This is a wonderful tool for people who are in the field~!
I already have the final outputs of HiCPro (such as .matrix and _abs.bed ), I don't need to run HiCPro again through 3d-genome-buil…
-
- Move length and quality trimming in bonus exercises in QC practical to gain a bit of time (day 1 morning)
- Move ChIP-seq lecture in the morning of day 1
- This will give more time to go explain a…
-
Hello. I believe ChromDiff is still recommended for finding out regions with differential chromatin state and linking it with different expression.
I'd like to give it a try, but I have not been able…