data <- Read10X('path_to_data') #替换为您的数据路径 第二步:创建Seurat对象 接下来,我们将使用CreateSeuratObject函数创建一个Seurat对象。这个对象是我们进行后续分析的基础。 R seurat <- CreateSeuratObject(counts = data) 第三步:添加元数据 在这一步中,我们将使用AddMetaData函数向Seurat对象添加元数据...
Adding metadata to an integrated object works the same as adding to any other Seurat object. You just need a vector (or dataframe) that has the group information for each cell. In your particular example assuming you have the sample as a metadata column called sample, you could probably do ...
Preserve feature metadata when converting from SingleCellExperiment to SeuratObject class (#4205) Preserve multiple assays when converting from SingleCellExperiment to SeuratObject class (#3764) Fix passing of score.thresh parameter in ScoreJackStraw() (#4268) Fix FC calculation in FindMarkers() non...
第十一节:多个样本整合的单细胞数据分析 包括锚定和harmony两种主流的单细胞数据整合算法,同时讲解多线程运算原理和实操。 第十二节:单细胞差异分析 metadata理解 分组添加 可视化画图 热图 气泡图 第十三节:以nature文章为例系统auc算法计...
It contains a new module that uses a built-in function from seurat R package to automatically convert An easy choice for having this metadata indeed seems a direct conversion from.h5adto.rds. With that we can do in a single module for both sample-specific objects and the concatenated one,...
Hi Tim, when trying to build a motif matrix using macaca <- AddMotifs( object = macaca, genome = BSgenome.Mfascicularis.NCBI.5.0.renamed, pfm = pfm ) I get the following error: Error in loadFUN(x, seqname, ranges): trying to load regions...
After adding the score to the object metadata, I do a FeaturePlot with the specific gene and the gene set to check their co-expression: FeaturePlot(object, c('specificGene', 'geneSet1'), blend = TRUE, label = T, pt.size = 2)
## Step 7: Add results to metadata slot of original Seurat object seu <- Seurat::AddMetaData(seu, metadata = pANN, col.name = "pANN") predictions <- as.data.frame(rep("Singlet", n_real.cells), ncol = 1, stringsAsFactors = FALSE) rownames(predictions) <- real.cells doublet.predicti...
("https://research.nhgri.nih.gov/", "HydraAEP/download/scriptsdata/", "aepAtlasNonDub.rds") ) ) ## re-order meta.data according to cell order hvulgaris <- orderMetaData( seurat_obj = hvulgaris, seurat_data = hvulgaris@assays$SCT@data ) ## load Hydra vulgaris gene age estimation h...
seuratData <- FindVariableFeatures(seuratData, selection.method = "vst", x.cutoff=c(0.01,Inf),y.cutoff=0.01,nfeatures = 5000) seuratData <- ScaleData(object = seuratData, vars.to.regress = c("S.Score", "G2M.Score",'batcheffect','percent.mt','percent.ercc','nFeature_RNA')) seur...