好久没用Cellranger做10X分析了。 今天有需要用一次,Bug频出,浪费时间。 不如在知乎上记录一下,以后也帮助自己节省时间了。 1.装Cellranger软件 这一步根据官网提示,下载下来解压缩即可。 这里遇到一个小bug, 提示cellranger:command not found (base) [@login04 bin]$ cellranger bash: cellranger: command ...
f GO enrichment analysis performed on the gene sets associated with neuronal (green), non-neuronal (red), and pancellular (orange) KAT3 peaks. g Volcano plots of RNA-seq analysis for the subset of genes classified as neuronal. Red: upregulated genes; blue: downregulated genes. h BETA ...
#每个细胞类型的marker gene set为元素组成的list对象 2.3AUCell计算 首先需提前使用GSEABase包整理marker gene sets的对象为指定的GeneSetCollection对象格式 library(GSEABase) all.sets <- lapply(names(markers.z),function(x) { GeneSet(markers.z[[x]], setName=x) }) all.sets <- GeneSetCollection(all...
We obtained similar or better prediction results compared to commonly used methods for cell type assignment in independent benchmarking datasets. Our gene signature set yields higher prediction scores than other published immune cell type gene sets in random forest-based cell type c...
Complex gene regulatory mechanisms underlie differentiation and reprogramming. Contemporary single-cell lineage-tracing (scLT) methods use expressed, heritable DNA barcodes to combine cell lineage readout with single-cell transcriptomics. However, relian
2C). Based on hallmark gene set enrichment analysis, we identified B-ISG15 as an interferon-stimulated B-cell subtype. B-ISG15 was enriched in interferon-α and interferon-γ response gene sets. We also found that B-ISG15 was enriched in the IL2 STAT5 signaling and IL6 JAK STAT3 ...
Data Integration step - part 6 - Exclusion of specific gene categories Data integration step - part 7 - Downsampling Data Exploration Data Exploration - part 1 - Embedding Data Exploration - part 2 - Clustering Data Exploration - part 3 - Cell sets ...
The single sample gene set enrichment analysis (ssGSEA) algorithm was used to quantify the relative abundance of each cell infiltration in the TME of BC patients [22]. We obtained the signature gene sets indicating a wide range of human immune cell subtypes from Charoentong’s research, includi...
A challenge in bulk gene differential expression analysis is to differentiate changes due to cell type-specific gene expression and cell type proportions. SCADIE is an iterative algorithm that simultaneously estimates cell type-specific gene expression p
This study builds a DNN-based CCD model that is trained by using the simulated gene signature matrix derived from the Harmony-normalized scRNA-seq data. Materials and methods The workflow This study used the harmonized expression data of scRAN-seq to develop a CCD model, HASCAD (HArmonized ...