Tag: tSNE

rna seq – How will Seurat handle pre-normalized and pre-scaled data?

I don’t do transcriptome analysis, it ain’t my thing, however I do understand statistical analysis as well as the underlying issue regarding the public availability of molecular data … I agree with the OP its not ideal. However, yes the OP can continue with ‘clustering’, personally I definitely prefer it…

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One-step induction of photoreceptor-like cells from human iPSCs by delivering transcription factors

Introduction of CRX and NEUROD1 using piggyBac vector into iPSCs and differentiation to induced photoreceptor-like cells (iPRCs) (A) Design of polycistronic piggyBac vector for CRX and NEUROD1 mediated conversion under control of the tetracycline operator rtTA and neomycin resistance gene. Dox: doxycycline, rtTA: reverse tetracycline transactivator, neo: neomycin resistance gene….

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scrnaseq – Arrange ggplot Figure for scRNA-seq data

I have generated a ggplot for 8 single-cell libraries, with the purpose of visualizing the tSNE facet plot by sample, colored by cell type — with percentages. The best I could get to is this – however, it looks too crowded, and I also want the cell types to be…

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Labeling Clusters in ggplot

Labeling Clusters in ggplot 1 I have a data matrix I extracted from seurat and I want to plot the tSNE plot by using ggplot. I don’t know how to label the clusters on the plot with 0..15. Help is appreciated. ggplot single cell • 1.3k views This is what…

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tSNE and UMAP of scATAC-seq data looks like spaghetti

tSNE and UMAP of scATAC-seq data looks like spaghetti 0 I would like to use R to generate cluster my 20k cells from a single cell ATAC-seq experiment. I ran PCA then selected the first 50 components, which were put into tSNE’s normalize_input() then Rtsne(). This is the result I…

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A question about scRNA-seq analysis

A question about scRNA-seq analysis 0 Dear all, please may I ask for a suggestion : I have a scRNA-seq dataset, which has 2 groups (Control and Model). I would like to process all the samples into cluster by tSNE or UMAP , then classification or differentiation the cell types….

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How to display TCR data in tsne space via seurat object

How to display TCR data in tsne space via seurat object 1 Hi Guys, I am trying to work out how I can display by VDJ usage within my tsne plot for some 10x data. I added everything to the Seurat object and tried to do a feature plot to…

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