代码语言:javascript 代码运行次数:0 运行 AI代码解释 ### 加载RNAseq数据load("TCGA-UCS-STARdata.Rdata")count=STARdata[["count"]]tpm=STARdata[["tpm"]] 我这里的演示数据,加载后的数据名称为STARdata,STARdata是一个list,包含count和tpm两个数据框。我这里查看一下前6行和前2列的数据。 再进行转换时...
Computational cell type identification is a fundamental step in single-cell omics data analysis. Supervised celltyping methods have gained increasing popularity in single-cell RNA-seq data because of the superior performance and the availability of high-
2022年3月29日,GDC官网(https://portal.gdc.cancer.gov/)发布了新的更新版本(Data Release 32.0)数据。此次数据更新范围广、变化大,导致许多网上的教程一夜之间不再直接可用。 具体的更新情况,在官网页面(https://docs.gdc.cancer.gov/Data/Release_Notes/Data_Release_Notes/)有详细介绍。对于应用最为广泛的RNA...
The count table, a numeric matrix of genes × cells, is the basic input data structure in the analysis of single-cell RNA-sequencing data. A common preprocessing step is to adjust the counts for variable sampling efficiency and to transform them so
Brown团队在《Genome Biology》发表标题为“Genotype inference from aggregated chromatin accessibility data reveals genetic regulatory mechanisms”的文章,提出了一种新的计算流程,从ATAC-seq数据中直接推断基因型并鉴定caQTL,从而阐释染色质可及性变异与复杂性状间的遗传调控机制。 一、研究方法 提出了通过ATAC-seq数据...
我们将这与多次实验的数据整合区分开来,我们称之为数据整合(data integration)。虽然批效应通常使用线性方法校正,但一般使用非线性方法进行数据整合。 最近对经典批次校正方法的比较显示,ComBat (Johnson et al,2006) 在低至中等复杂度的单细胞实验中也表现良好 (Buttner et al,2019)。ComBat 由基因表达的线性模型组成...
an automatic tool to annotate cell types from single-cell RNA-seq data, based on a score annotation model combining differentially expressed genes and confidence levels of cell markers in databases. Evaluation on real scRNA-seq datasets that SCSA is able to assign the cells into the correct types...
It is a challenging task to integrate scRNA-seq and scATAC-seq data obtained from different batches. Existing methods tend to use a pre-defined gene activity matrix to convert the scATAC-seq data into scRNA-seq data. The pre-defined gene activity matrix
cellassign automatically assigns single-cell RNA-seq data to known cell types across thousands of cells accounting for patient and batch specific effects. Information about a priori known markers cell types is provided as input to the model in the form of a (binary) marker gene by cell-type ma...
[ 2 ]. here, we focus on biases related to gc-content in the context of rna-seq data generated using the illumina genome analyzer platform. briefly, mrna is converted to cdna fragments which are then sequenced to produce millions of short reads (typically 25-100 bases). these reads are ...