-
Hi,
I find ANANSE rather useful in inferring regulatory interactions. I would like to use it to connect the peaks to the target genes directly. Is there a way to do that? Can I somehow extract the p…
-
Hello,
Following on the Signaling workshop of the Fall 2017 (see slides here: https://docs.google.com/presentation/d/1xR6EFbRyCSwruXVeMYZtJfwWEbIr6U8zei8IwGG3OrA/edit#slide=id.g26be66c50c_0_6) and…
-
For my project I am wanting to look at how specific genes are regulated, so will likely need gff and fasta files that include full UTRs rather than just a buffer.
Pombase has separate fasta files fo…
-
For MGI gene model Zfp750 (MGI:MGI:2442210)(model ID: gomodel:653b0ce600001157 ), I noticed that:
annotation preview missing the ISO annotations:
Zap750
promoter-specific chromatin binding GO:19…
-
Here is how the reaction [R-HSA-163743](https://reactome.org/content/detail/R-HSA-163743) "Transcriptional activation of ACACA by ChREBP:MLX" (the middle box) is currently converted:
![image](https:/…
-
I think it would be a useful exercise to find a paper or two which use one of the existing tools (UCSC, Wash U epigenome browser) to test hypotheses related to gene regulation (ideally using some Cist…
-
Found some problems with example notebooks. Making a list here:
1. In Notebook 1 (CRNs) the text doesn't quite match the code for the new way propensities work.
2. Notebook 4 (Gene Regulation) Exa…
-
Gene.mirna was used for 37, not used in 38. Do we still need these data? `mirna.txt` is not on the download list, so it's not being loaded anymore.
- [ ] remove mirna from [GeneParser.java](https:/…
-
Right now the[ URL for MotifFeatures.gff.gz is incorrect](https://github.com/opencb/cellbase/issues/466). However the file is still created with a size of zero:
```
-rw-r--r-- 1 julie julie …
-
Once mentioned in wechat but forget to submit here.
Cannot apply to simplify() on compare cluster result.
It simplifies independently.
something reproducible:
file: https://drive.google.com/…