wangmhan

Hi, I wonder if the runHomer function can also return matrix for de novo motif discovery as mentioned in the tutorial, step 17: https://github.com/r3fang/SnapATAC/blob/master/examples/10X_PBMC_15K/README.md#homer Now seems can only return the...

how to add custome genome

5

Hi, I work with chicken data. So that I create reference through snaptools index-genome, while fetchChromSizes didn't work so I use .fai file to generate chromesome size. But encountered problem...

degPatterns error

8

Hi, I tried to use degPatterns with consensusCluster = TRUE, cannot get a result but end fraction message. Does anyone know how to fix it? Thanks!

error when using the new version: Train your own predictor

8

Hi, I tried to run the new version Train your own predictor. And got several errors: 1) when run this line: "ensemble = subset_genes_ensemble(clf=clf, class_size=20, subset_fold=5,subset_min=5,subset_logT=True,verbose=True)", it seems subset_logT is...

could this pipeline used for other datasets

11

Hi, This .ipynb file is only for generate the figure in your paper. I wonder if there is a general version, which could be used for other dataset? As you...

ask for updating Cis-bp

1

**Is your feature request related to a problem? Please describe.** Now Cis-bp has changed to version 2.0.0, while the version in GimmeMotifs is still 1.0.2 **Describe the solution you'd like**...