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I use the following command for big genome (wheat) scRNA-seq analysis:
PISA count -one-hit -@ 10 -cb CB -anno-tag GN -umi UB -outdir RawMatrix final.sorted.bam
An error occurred:
[error] [func: wri…
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To bump all modules to snakemake 8 (#12) we primarily need to document the libraries required to process the initial Snakemake file. These should be added to `envs/global.yaml` and cross-linked into t…
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Hello. Thank you for this package. I'm doing an integration analysis using more than 40 scATAC samples. However, I do not have scRNA data from the same cells. I tried doing the label transfer using th…
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Hi,
I have two questions:
1. I have a scRNA-seq dataset with 3 batches and I want to simulate a spatial dataset preserving the batch effect, is it better to simulate each batch separately or direc…
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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…
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### Project short name:
MyocardialInfarctionAmruteCITE
### Primary Wrangler:
Ida
### Secondary Wrangler:
### Associated files
* Google Drive: [folder](https://drive.google.com/drive/folders/12Lw3o…
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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
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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 …
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我已经跑完流程,得到了raw_matrix文件夹,我现在想自己进行从头的质控以及后续一系分析。但是我是进行了很多尝试使用 scanpy 读取总是会报错?不知道是否支持?
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- [x] [Single-cell transcriptomic atlas reveals increased regeneration in diseased human inner ear balance organs (nih.gov)](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11156867/pdf/41467_2024_Ar…