Nico Trummer
Nico Trummer
In my use case, there is one embedding for all cells and multiple embeddings for subsets of cells, which are non overlapping and of various sizes. Let's assume a structure...
When trying to use the package with FAISS-GPU installed, the GPU was not used automatically and also there was no option for enabling it manually. I added this functionality. However,...
Hello everyone, first of all, thanks for caring about Nix even if it is not the most widespread distro. Maybe you can help me with the problem I encountered? #...
Hey, this PR addresses 4 things: 1. Exclude overlong circRNAs from quantification as psirc-quant throws an error otherwise 2. Use only the circRNAs which pass the detection majority vote in...
### Description of feature Currently there is only a custom image available via dockerhub. We should find a cleaner solution, most likely via a bioconda recipe.
### Description of feature Currently, only the BSJs are detected and quantified, without knowing the exact sequences. There are several tools which can obtain the full length circRNA sequence from...
### Description of feature This should be an optional column in the samplesheet. If available, it should be used in detection tools like `CIRI`. The following things need to be...
### Description of feature Checking the detected circRNAs for their coding potential could open an additional perspective on deciphering the function of circRNAs. [This tool](https://pubmed.ncbi.nlm.nih.gov/28521017/) was suggested to me for...
### Description of the bug When using STAR indices from iGenomes, the versions are partly not compatible with the STAR version used by the pipeline. A workaround is setting manually...
This PR adds the [DoubletFiner](https://github.com/chris-mcginnis-ucsf/DoubletFinder) R package