-
Hi Alex,
I have a question about best practices for dealing with multi-mapping reads in scRNA-seq data analysis, particularly when looking at transposable elements (TEs). Due to the nature of TEs,…
-
Hello,
I really enjoyed your paper (great method!), and I am applying spaCET for deconvolution of a lung cancer ST Visium data set. For validation, I would like to know how to find the marker genes …
-
# Contribution Guidelines
1. **Initial Setup**
- Clone the repository: `git clone `
2. **Update Local Content**
- Ensure you’re up to date with the development branch:
```bash
git ch…
-
Hello DcjComm developers,
First, thank you for your excellent work on the DcjComm package!
I am currently working on a project using Seurat to analyze single-cell RNA-seq data, and I would like …
-
Dear all,
What is the corresponding table in case of mouse genome in this command?
genes.df = read.table("gencode.v19.annotation.gene.bed");
Thanks
-
Hi
I recently used scMTNI for my scRNA-seq data analysis. I have few question about it.
The first question is about the input gene expression table. I saw one github discussion about it, but I a…
-
i analysis the scrna-seq of two conditions and used the DotPlot functions to show the average expression levels in different conditions. however, i found there is an opposite trend between the DotPlot…
-
This is a question about the .table file. I understand that LIGER integrates the scATAC and scRNA-seq. What exactly does this .table contain, and how can I generate it from other pipelines (Seruat, sc…
-
Hello SPROD author!
Tools like Tangram or gimVI can utilize scRNA-seq data to predict and impute spatial data, but they seem to be unable to denoise contaminated data. Therefore, I am considering u…
-
To prepare scRNA-seq data for BAF analysis, xcltk is used. However, xcltk current does not support mm10 mouse scRNA-seq data at the baf_pre_phase.sh step, as it only permits usage of a Sanger-phasing …