-
Hi!
Our scRNA-seq data was processed using the Seurat package. In order to run scDRS with our scRNA-seq data, I first converted the Seurat object saved as an RDS file to an h5ad file using the foll…
-
Hello, developer!
I have been using the Methykit package for analyzing differential methylation, and I want to express my gratitude for developing such a helpful tool for methylation research. Howe…
-
I am using R Markdown to create a report using R chunks.
When loading `bsplus` package and `mtcars` dataset, I try to create an accordion. Here is the example:
head %
bs_append(title …
-
We are trying to implement proBatch into our data analysis pipelines, but our data has a lot of NAs. We've found that batch correction only works when we filter out peptides containing NAs which leav…
-
Do you suggest any easy way to plot input data and fitted clusters?
Thank you
-
### Please describe your wishes and possible alternatives to achieve the desired result.
https://data-apis.org/dataframe-protocol/latest/index.html
It could be nice if AnnData supported the `_…
-
Hello,
I was wondering if there is a "good" / "correct" way for tweaking the number of discovered modules? I.e. I'm running a dataset of 300k cells, but I only end up with 5 modules, of which 3 ar…
-
Hi Shuangbin,
I'm wondering how to set the aesthetic mapping of PCoA use the _mapping_ parameter in the _ggordpoint_ function. It seems to be that I can change the shape, size, or alpha of the p…
-
(nllp) MacBook-Air-3:lnlp user$ python main.py tests/test_data/data.csv
Welcome to the NLLP CLI!
Loaded data from tests/test_data/data.csv
1. Run a Topic Model
2. Run an Optimization routine fo…
-
Hello,
I have some methlyation EPICv2 data that I am trying to perform differential methylation regional (DMR) analysis on, and am having some trouble using the customized packages (specifically t…