We introduce Halfpipe, a tool for analyzing RNA-seq data from metabolic RNA labeling experiments. Its main features are the absolute quantification of 4-thiouridine-labeling-induced T>C conversions in the data as generated by SLAM-seq, calculating the proportion of newly synthesized transcripts, and...
Analyzing RNA-seq data with DESeq2翻译(1) 为了深入学习DESeq包以及差异基因表达分析,我开始对Bioconductor网站上的DESeq包的说明进行翻译。以下是部分选译内容。 Quick startDESeq2分析的基本步骤如下: dds <- DESeqDataSetFro… 信息就是力...发表于学习·持续... SPSS因子分析载荷系数表结果如何解读?简...
Analyzing RNA-seq data with DESeq2翻译(2) 差异表达分析标准的差异表达分析已经被打包整合到DESeq这一个函数中。其具体分析过程可以通过“?DESeq”在DESeq包的帮助页面查看。 差异表达分析的结果可以用results函数进行提取,该函数导… 信息就是力...发表于学习·持续... Analyzing RNA-seq data with DESeq2翻...
The vast amount of RNA-seq data deposited in Gene Expression Omnibus (GEO) and Sequence Read Archive (SRA) is still a grossly underutilized resource for biomedical research. To remove technical roadblocks for reusing these data, we have developed a web-a
而本文的思路是在分析scRNAseq的数据的第二步使用到了MFL: gene selection, manifold learning, cell organization, Dimensionality reduction and visualization, Density estimation and clustering。 而整体的前三步统称为pseudotime methods。 下图清晰的展示出了文章的分析思路,图也草鸡美。我觉得我还要修炼些时日再做...
RNA-seq Multiple Sequence Alignment Database Management System Genome Assembly Programming Language Genome Alignment Antibodies Protein Experimental Models Kits Arabidopsis lyrata Arabidopsis thaliana Brassica rapa Chlamydomonas reinhardtii Zea mays Medicago truncatula Setaria italica Physcomitrella patens Popu...
Details of the installation and additional software packages for the analysis of small RNA-seq data are described in the user manual (Additional file 1). There are seven tabs in the main window. Each tab corresponds to a specific step in the workflow. Users can set the parameters, upload a...
Analyzing data from two large-scale CRISRPi screens in iPSCs with single-cell RNA-seq read-out. - claudiafeng123/crispri_scrnaseq_hipsci
et al. Integration of single-cell RNA-seq data into population models to characterize cancer metabolism. PLoS Comput. Biol. 15, e1006733 (2019). Article CAS PubMed PubMed Central Google Scholar Hartmann, F. J. et al. Single-cell metabolic profiling of human cytotoxic T cells. Nat. ...
标准的差异表达分析已经被打包整合到DESeq这一个函数中。其具体分析过程可以通过“?DESeq”在DESeq包的帮助页面查看。 差异表达分析的结果可以用results函数进行提取,该函数导出一个结果表格,结果包括log2 fold change值、p值(Wald检验)以及校正后的p值。如果不指定额外的参数,结果表格会输出disign公式中最后一个变量...