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Hi!
First of all, thank you for the great tool.
I have single-cell RNA sequencing (cell-ranger) data for e.g 3 donors (=> 3 bam files, one per donor), as well as pooled scRNA-seq data for the sa…
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Can you share any scripts that you have to convert an arbitrary scRNA-seq cell-by-gene matrix into the format your model inputs?
Thanks
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Hi,
I am trying to use Clipper to do the **differential analysis** on my data, which is a single-cell dataset collected from **multiple subjects**. I found the example data included in the package …
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Since the original publication is called _Feature selection and dimension reduction for single-cell RNA-Seq based on a multinomial model_, it would be nice to have a part of the vignette explaining ho…
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Dear Author,
I am using this script for analysis:
import SEVtras
SEVtras.sEV_recognizer(input_path='/home/yeziyang/Sc', sample_file='/home/yeziyang/Sc/Sc1_LN', out_path='/home/yeziyang/Sc/outputs…
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Hello,
Question about 'RNA sequencing assay' (OBI:0001177) and 'RNA-seq assay' (OBI:0001271). In OBI, 'RNA-seq assay' is a subclass of 'RNA sequencing assay'. Are there examples of assays that fal…
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Project UUID: 2043c65a-1cf8-4828-a656-9e247d4e64f1
Project Title: Single-cell RNA-seq analysis throughout a 125-day differentiation protocol that converted H1 human embryonic stem cells to a variety …
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Hi,
It is just a naive idea. According to the paper, you describe that scATAC-seq has the issue of "missingness" like the dropout in scRNA-seq data. So what if using a zero-inflated Bernoulli to char…
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Much like GSE100118 and GSE74355, the peturb-seq set has a variety of knockdown targets and functional effects. This could make for an excellent validation set.
https://www.ncbi.nlm.nih.gov/geo/que…
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| Name | Department/Program | Experties/Interests |GitHub ID |
| ------------- | ------------- | ------------- | ------------- |
| Annie Cavalla | Bioinformatics | Cancer genomics, single cell tra…