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#1CreateSeuratObject: Create a Seurat object - RDocumentation
Create a Seurat object from a feature (e.g. gene) expression matrix. The expected format of the input matrix is features x cells. Usage. CreateSeuratObject( ...
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#2Create a 'Seurat' object - Search in: R
Create a Seurat object. Description. Create a Seurat object from raw data. Usage. CreateSeuratObject( counts, project = "CreateSeuratObject", assay = "RNA", ...
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#3Seurat 4 源码解析5: step2 创建Seurat 对象CreateSeuratObject()
(3) CreateSeuratObject() 函数. 这个函数就是根据输入矩阵/数据框，创建Seurat对象的。重要步骤是设置ident 和添加meta.data。 我们 ...
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#4CreateSeuratObject: Create a Seurat object in lambdamoses ...
CreateSeuratObject : Create a Seurat object. In lambdamoses/SeuratBasics: Slimmed down version of Seurat. Description Usage Arguments Details ...
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#5R语言Seurat包CreateSeuratObject函数使用说明 - 爱数吧
返回R语言Seurat包函数列表. 功能\作用概述: 从原始数据创建Seurat对象. 语法\用法：. CreateSeuratObject( counts, project = "CreateSeuratObject", assay = "RNA",
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#6Problem trying Create Seurat Object #5982 - GitHub
The only thing that CreateSeuratObject requires is data in a data.frame or matrix where the rows are the features/genes and the columns are the cells. The ...
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#7No cell names (colnames) names present in the input matrix
I had the exact same problem, doing the exact same experiment, haha. Reading your question though got me to the answer. Replace: CreateSeuratObject(counts ...
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#8Seurat - Guided Clustering Tutorial - Satija Lab
... raw (non-normalized data). pbmc <- CreateSeuratObject(counts = pbmc.data, project = "pbmc3k", min.cells = 3, min.features = 200) pbmc.
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#9CreateSeuratObject issue in R - when first column is gene ...
I'm completely new to the analysis of scRNA data and have been having issues with the CreateSeuratObject command in R.
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#10创建Seurat对象_createseuratobject - CSDN博客
+ CreateSeuratObject(counts = Read10X(folder),project = pro). + }). > scList. [[1]]. An object of class Seurat.
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#11Seurat包标准流程 - Huisheng Liu
scRNA_data1 <- Read10X(data.dir = "data/scType1/") # 构建Seurat对象srt1 <- CreateSeuratObject(counts = scRNA_data1, # 表达矩阵，可以是稀疏 ...
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#12Seurat Example - RPubs
pbmc <- CreateSeuratObject(counts = pbmc.data, project = "pbmc3k", min.cells = 3, min.features = 200) ## Warning: Feature names cannot have underscores ...
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#13非10X单细胞测序数据创建Seurat对象CreateSeuratObject - 简书
首先读入txt文件，转成table； 生成matrix矩阵，再转成sparse matrix稀疏矩阵； 最后CreateSeuratObject即可。 library ...
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#14用Seurat包分析文章数据（二） - 腾讯云
使用Seurat V3版本（以下简写"V3"）(版本3有大量的参数从之前的genes改成了features) sce <- CreateSeuratObject(counts = counts, meta.data = meta, ...
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#15Seurat CreateSeuratObject - Galaxy | Tool Shed
Seurat CreateSeuratObject (version 2.3.1+galaxy0). Seurat object: RDS file from Seurat read10x module. What it does. Seurat is a toolkit for quality control ...
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#16Single-cell RNA-seq | Griffith Lab
... First create an empty list to hold the Seurat objects scrna.list[[1]] = CreateSeuratObject(counts = data.10x[[1]], min.cells=100, min.features=700, ...
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#17Standard Preprocessing using Seurat | IRTG Course
We create a Seurat object using the CreateSeuratObject function as follows. Use the ?function helper in R to get information about the ...
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#18Seurat with normalized count matrix? - ECHEMI
I know that in Seurat we have the function CreateSeuratObject from which the analysis starts, but it accepts raw count matrix according to the documentation ...
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#19Roadmap to prepare the input matrix for scTensor
... PBMC data of Cell Ranger can be imported by the Read10X function and DGE matrix of UMI-count is available by the output of CreateSeuratObject function.
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#20GSM5839473 - GEO Accession viewer
2) using the 'Read10x' and 'CreateSeuratObject' functions with the parameters min.cells = 3, min.features = 200. Cells with > 15,000 total RNA ...
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#21umap highlighting two different models - Posit Community
#create the Seurat object OD_10K_HUMAN <- CreateSeuratObject(counts = HUMAN_OD_10K.data, min.cells = 0, project = "human") SD_5K_HUMAN ...
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#22Chapter 2 Seurat Pre-process | Single Cell Multi-Omics Data ...
2.1 Load count matrix from CellRanger ; CreateSeuratObject · counts = ; project = '11002C' ; min.cells = 3 ...
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#23Data structures and object interaction • Signac - Stuart Lab
create a Seurat object containing a ChromatinAssay object <- CreateSeuratObject(counts = chromatinassay). ## Warning: Keys should be one or ...
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#24Seurat object from count matrix
2020 · 非10X单细胞测序数据创建Seurat对象CreateSeuratObject. ... A Seurat object can be created from our sparse matrix using the CreateSeuratObject function.
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#25Seurat V3 Interface - Broad Institute
With Harmony integration, create only one Seurat object with all cells. In [88]:. pbmc <- CreateSeuratObject( ...
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#26Seurat part 2 – Cell QC - NGS Analysis - NYU
While the CreateSeuratObject imposes a basic minimum gene-cutoff, you may want to filter out cells at this stage based on technical or biological parameters ...
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#27seurat objects {OFYMTC}
CreateSeuratObject : Create a Seurat object Description Create a Seurat object from a feature (e. CreateSeuratObject: Create a Seurat object Description ...
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#28230212_SCH.R - myCompiler
MB7 <- CreateSeuratObject(counts = C$MB7 , min.cells = 3, min.features=200); MB7 <- AddMetaData(object=MB7, metadata = meta, ...
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#29Seurat get raw counts
... CreateSeuratObject function - RDocumentation WebCreate a Seurat object from ... matrix as follows: srat <- CreateSeuratObject(counts = filt.matrix) srat ...
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#30シングルセルデータ解析 - DBKERO Home
... できた遺伝子を使用し、200以上のUMIを持つ細胞を使用 > lung <- CreateSeuratObject(counts = lung.data, project = "lung", min.cells = 3, min.features = 200) ...
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#31Single cell analysis of iPSC-derived midbrain organoids
MUT3 <-CreateSeuratObject(counts = MUT3.data). MUT3. # Merge more than two objects MUT.combined <-Reduce(function(x,y) merge (x,y, all=T), list (GC1, MUT1, ...
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#32Loading a dataset — cellbrowser v1.2.1+3.g0cb0a1c ...
+[|]", "", genes) mat = data.frame(mat[,-1], row.names=genes) so <- CreateSeuratObject(counts = mat, project = "adultPancreas", meta.data=meta).
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#33Use of SpatialDecon in a Spatial Transcriptomics dataset
... put into a seurat object: andersson_g1 = CreateSeuratObject(counts = raw, assay="Spatial") [email protected]$x = x [email protected]$y = y ...
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#34createseuratobject function - 시보드
to R environment by "Read10X" function, and convert the data to Seurat object by "CreateSeuratObject" function. However, I found out that some publicly ...
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#35单细胞转录组|Seurat 4.0 使用指南 - 阿里云开发者社区
参数解释CreateSeuratObject( counts, #未标准化的数据，如原始计数或TPMs project = "CreateSeuratObject",#设置Seurat对象的项目名称 assay = "RNA" ...
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#36Making Seurat object from a processed file [closed]
The function you need is CreateSeuratObject() and not Read10X() as you start from TPMs.
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#37No cell names (colnames) names present in the input matrix
Making Seurat object from a processed file [closed] Ağ21 May 2021 · CreateSeuratObject (getwd (),gene.column = 2,cell.column = 1,unique.features = TRUE ...
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#38Analyze Single-cell with AI-based pipeline (in R) - UAB
Data <- Read10X(data.dir = "10XFormat/Fetal" ); seuratObj <- CreateSeuratObject(counts = Data) Data <- Read10X(data.dir = "10XFormat/CTL-P56" ); seuratObj2 ...
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#39Seurat raw data
R Create a Seurat object from raw data CreateSeuratObject( counts, ... hessen https://mojaveazure.github.io/seurat-object/reference/CreateSeuratObject.html ...
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#40integrating single-cell datasets - Swarup Lab
... cur_data <- Read10X(paste0(in_data_dir,sample,'/outs/filtered_feature_bc_matrix/')) cur_seurat <- CreateSeuratObject( counts = cur_data, min.cells=3, ...
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#41Importing a merged Seurat dataset into Monocle
... naive <- CreateSeuratObject(raw.data = naive.data, min.cells = 3, ... and then creating the Seurat object with CreateSeuratObject .
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#42SARS-CoV-2 gene expression studies | Max Delbrück Center
seu <- CreateSeuratObject(counts =t(raw_counts), meta.data = meta_data). Note on viral transcripts: reads within viral genes were counted separately, ...
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#43Homework Week 10
Create a Seurat object (function: Seurat::CreateSeuratObject ) (1pt); Perform the same filtering that you chose to do on the SCE object.
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#44Visualizing single cell data - YuLab@SMU
library(Seurat) dir = "filtered_gene_bc_matrices/hg19" pbmc.data <- Read10X(data.dir = dir) pbmc <- CreateSeuratObject(counts = pbmc.data, ...
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#45超好用的单细胞测序数据合并（3'和5'数据合并）（一） - Seurat
srat_3p <- CreateSeuratObject(matrix_3p,project = "pbmc10k_3p") srat_5p <- CreateSeuratObject(matrix_5p,project = "pbmc10k_5p") srat_3p
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#46scRNA-10X免疫治疗学习笔记-2-配置Seurat的R语言环境
library(Seurat) sce.10x <- Read10X(data.dir = '~/four-PBMC-mtx/SRR7722939/') sce1 <- CreateSeuratObject(raw.data = sce.10x, min.cells = 60, ...
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#47NBIS系列单细胞转录组数据分析实战（一） - OmicShare
使用CreateSeuratObject函数构建seurat对象 sdata.cov15 <- CreateSeuratObject(cov.15, project = "covid_15")
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#48Seurat from matrix
思路：执行三个命令(1) 使用Read10x ()读取计数数据；（2）使用CreateSeuratObject ()从读取的数据中创建Seurat对… https://www.jianshu.com/p/37d2e8d68c91 seurat ...
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#49Seurat-CreateSeuratObject Example - Program Talk
NewPeakSeurat < - function(peak.data, annot.info, project.name = "PolyA", cell.idents = NULL, tsne.coords = NULL, umap.coords = NULL, min.cells = 10, ...
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#50Developers - $ operator not defined for this S4 class when ...
... $ operator not defined for this S4 class when using CreateSeuratObject. seurat. 04 May 2021 Posted by lkqnaruto. I'm trying to load the 10X data using ...
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#51翻车实录之Nature Medicine新冠单细胞文献|附全代码-陈同的博文
C141<-CreateSeuratObject(counts = C141, project = "C141",min.cells = 3, min.features = 200) C142<-CreateSeuratObject(counts = C142, ...
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#52Bioconductor | DNA confesses Data speak
... Initialize the Seurat object with the raw (non-normalized data). pbmc <- CreateSeuratObject(counts = pbmc.data, project = "pbmc3k", min.
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#53How to convert between Seurat/SingleCellExperiment object ...
seo <- CreateSeuratObject(counts = t(counts), project = "min", min.cells = 3, min.features = 200) ### Set the meta data [email protected]<-cbind(cellMeta ...
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#54毕业救星！这个R包在高分文章常见，实用！好学！
... "~/Downloads/pbmc3k/filtered_gene_bc_matrices/hg19/") pbmc <- CreateSeuratObject(counts = pbmc.counts) pbmc <- NormalizeData(object ...
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#55Seurat - scRNA Tutorial - Amazon AWS
... the raw (non-normalized data). pbmc <- CreateSeuratObject(counts = pbmc.data, project = "pbmc3k", min.cells = 3, min.features = 200)
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#56iPSC residue detection method based on single cell ...
pbmc1<-CreateSeuratObject(counts＝pbmc.data,project＝project_name,min.cells＝QC_min_cells,min.features＝QC_min_features).
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#57Seurat conda安装
使用CreateSeuratObject 创建对象。. sce <- CreateSeuratObject(counts,min.cells = 10,min.features = 200) 过滤检测min.features = 200：一个细胞最少要检测到200个 ...
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#582023 Seurat Object From Matrix - esdikgeliyoruz.online
Create a Seurat object — CreateSeuratObject • SeuratObject. I'm trying to do a cross-species comparison between the patient TME vs.
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#59R中seurat处理流程中的函数说明 - 博客园
1.CreateSeuratObject 转自：https://cloud.tencent.com/developer/article/1055892 # Initialize the Seurat object with the raw (non-normalized ...
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#602023 Seurat Object From Matrix - naberbeya.online
Create a Seurat object — CreateSeuratObject • SeuratObject. I'm trying to do a cross-species comparison between the patient TME vs.
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#61Seurat Remove Genes. ercc <- grep("ERCC_",rowname
Create Seurat object CTC_seurat <- CreateSeuratObject (counts = counts, min. features is to filter genes and cells Step 2: Filtering A) Mitochondrial Create ...
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#62Seurat Object From Matrix 2023 - helalbe.online
Create a Seurat object — CreateSeuratObject • SeuratObject. I'm trying to do a cross-species comparison between the patient TME vs.
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#63Merge Seurat Objects - ITHACA
Then we can take advantage of the monocle function importCDS to import the combined object into monocle. pancreas <- CreateSeuratObject (counts = pancreas.
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#64Doheatmap Seurat Color - xparts66
0)) rownames (data) <- c ("gene1", "gene2") test <- CreateSeuratObject (data) test@scale. 4 ColorPalette for discreate groups. Seurat object.
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#65Transcriptomics in Health and Disease - 第 97 頁 - Google 圖書結果
... grep(pattern = "P3|P10", dim(p3_and_p10_data) # dimensions for selected data The function CreateSeuratObject() initializes the Seurat object with the ...
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#66Drosophila: Methods and Protocols - 第 416 頁 - Google 圖書結果
... ...........................285 Controlled vocabularies ................................................6, Conventional CLIP CreateSeuratObject ...
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#67Skeletal Muscle Stem Cells: Methods and Protocols
Use the CreateSeuratObject function to create a Seurat object from the count matrix. The object produced is a container for data (e.g., the count matrix), ...
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#68Dendritic Cells: Methods and Protocols - 第 327 頁 - Google 圖書結果
Create the Seurat object, perform some QC, and normalize: ➤GSE131957_data <- CreateSeuratObject(counts, min.cells = 5, min.features = 600, ...
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#69Chromatin Accessibility: Methods and Protocols
Create a Seurat object via the ChromatinAssay functionality. seurat_obj <- CreateSeuratObject(counts = Create- ChromatinAssay(counts, ...), ...) 3.
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