然后这些计数被合并成一个单独的矩阵来构建一个单独的SingleCellExperiment对象。为了方便起见,所有cell的元数据都存储在同一个对象中,供以后访问。 library(SingleCellExperiment)all.counts<-rbind(endo.data$counts,mito.data$counts,spike.data$counts)sce<-SingleCellExperiment(list(counts=all.counts),colData=endo...
4:Saiful Islam, et al. Quantitative single-cell RNA-seq with unique molecular identifiers. Nature Methods. 2014, 11:163-166. 5: Kivioja T, et al. Counting absolute numbers of molecules using unique molecular identifiers. Nat Methods. 2011, 9(1):72-4....
Benchmarking UMI-based single-cell RNA-seq preprocessing workflowsdoi:10.1186/s13059-021-02552-3You, YueTian, LuyiSu, ShianDong, XueyiJabbari, Jafar S.Hickey, Peter F.Ritchie, Matthew E.Genome Biology
Single-cell RNA-Seq (scRNA-Seq) profiles gene expression of individual cells. Recent scRNA-Seq datasets have incorporated unique molecular identifiers (UMIs). Using negative controls, we show UMI counts follow multinomial sampling with no zero inflation. Current normalization procedures such as log of...
gene expression, high-throughput analysis, and single-cell RNA-seq specifically formulated for cells with ultra-low RNA content (e.g., peripheral blood mononuclear cells [PBMC], T cells, and B cells). The SMART-Seq mRNA kits have become the industry st...
cellranger pipeline基本是对的,但想要更原始的数据还是得自己手动count。 这两批perturb-seq的问题在于,Plasmid的设计,无法区分原始的和编辑后的Plasmid,长度一样,于是做cell sorting的时候一大堆dummy cells就被筛选出来了,真正有gRNA的就很少。 以下是手动counting的代码,建议用linux命令,python很慢很慢很慢。
However, conventional analysis is based exclusively on the relative abundance of integrated single guide RNAs (sgRNAs) between populations, which does not discern distinct phenotypes and editing outcomes generated by identical sgRNAs. Here we present CRISPR-UMI, a single-cell lineage-tracing methodology...
[1] Svensson V, Vento-Tormo R, Teichmann S A. Exponential scaling of single-cell RNA-seq in the past decade[J]. Nature Protocols, 2018, 13(4):599-604. [2] Malte D L., Fabian J T.. Current best practices in single‐cell RNA‐seq analysis: a tutorial. Molecular Systems Biology. ...
scruff(SingleCellRNA-SeqUMIFilteringFacilitator) is a package for processing single cell RNA-seq (scRNA-seq) FASTQ reads generated by CEL-Seq and CEL-Seq2 protocols. It demultiplexes scRNA-seq FASTQ files, aligns reads to reference genome usingRsubread, and generates UMI filtered count matrix. ...
•功能较为单一:虽然在单细胞RNA-seq处理上表现出色,但对于其他类型的数据支持较少。 总结 处理UMI数据是提高测序数据质量的重要步骤。选择合适的工具取决于你的项目需求。如果你需要一个功能全面、适应性强的工具,UMI-tools是个不错的选择;如果你的项目涉及单细胞RNA测序数据,Drop-seq Tools和Je-Suite提供了更为...