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Hi, I am working on a single cell DNA dataset (10x genomics) and I managed to run cellsnp-lite and vireo and now I am generating the clustering using the example [here](https://nbviewer.org/github/sin…
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`STAR --runThreadN 8 \
--genomeDir /Users/plab/Desktop/Fasta_scRNAseq/STAR_Genome_Indices/Intact/ \
--readFilesIn CP18S_L001_R2.fastq,CP18S_L002_R2.fastq,CP18S_L003_R2.fastq,CP18S_L004_R2.…
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- download a data of choice from 10x genomics with `sc.datasets_visium_sge()` (you can browse them [here](https://support.10xgenomics.com/spatial-gene-expression/datasets))
- run the scanpy tutorial,…
giovp updated
3 years ago
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I used VarTrix to extract single cell variant information from our 10x Genomics single cell data
$vartrix --bam $out_bam --cell-barcodes $barcodes --fasta $fasta_file --vcf $out_vcf --out-variants $o…
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_Our analysis re- veals that the BTD-trained SenCID is applicable to both Dropseq- (Figures 2A, 2C, 2D, and 2F) and Smart-seq- (Figure 2B) generated single-cell data._
Is there any difference betwe…
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Hi Cutadapt team,
This is not a standard "issue" but an inquiry regarding sn/scATAC-seq data preprocessing (10x Genomics multiome). I'm using Cutadapt to trim snATAC-seq data reads before alignment…
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Dear team,
Thanks a lot for providing scGPT for biological researchers. You provide a tutorial for perturbation prediction using Adamson or Norman's datasets. However, I am still confused about h…
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Hey @labrazil and @tiagochst
I have scRNA Seq (10X genomics) data from a cancer and want to quantify the stemless indices for each cell type or cluster. Do you recommend this approach for the same…
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Hi Dr. Zhang,
I read your Polarbear paper and planned to run the model on some multiomics data for the Human Brain to see how well your model performs on human brain tissue. Do you have a pretraine…
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Hi Christophe.
I got this error after installing version 1.15. It is even on the mock example in the package
This is my code
infercnv_obj2 = infercnv::run(infercnv_obj2,
…