User: DrAcula

gravatar for DrAcula
DrAcula40
Reputation:
40
Status:
New User
Location:
University of Miami
Last seen:
2 days, 23 hours ago
Joined:
2 years, 9 months ago
Email:
f********@gmail.com

Posts by DrAcula

<prev • 10 results • page 1 of 1 • next >
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Comment: C: Merging multiple single cell gene expression matrices (in .txt format) into one
... WOW. That was dumb of me. I just realized what was going on... just to clarify the sequence of events: file_list <- list.files("~/Rawdata") #where list.files points towards a dir containing 'x number of' .txt files names(file_list) <- basename(file_list) seu <- imap(file_l ...
written 12 days ago by DrAcula40
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Comment: C: Merging multiple single cell gene expression matrices (in .txt format) into one
... Ok, so this may be incorrect but I think it may be a solution. Using the `Reduce` base R function: merged.nhp = Reduce(function(...) merge(..., all=T), list_of_files) tail(merged.nhp) However I know that `Reduce()` combines from the left, and since the first column is a gene list, its eas ...
written 12 days ago by DrAcula40
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Comment: C: Merging multiple single cell gene expression matrices (in .txt format) into one
... Ok, so sorry I didn't read the first two lines of your first comment, just to elaborate, my goal is to perform non-linear multidimensional reduction, on this dataset GSE120180, via either merging or integrating each of the donors. This dataset consists of 16 donors that were single-cell sequenced in ...
written 12 days ago by DrAcula40
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Comment: C: Merging multiple single cell gene expression matrices (in .txt format) into one
... Thanks for the comment @rpolicastro ! When I run your code, I get the following error: Error in column_to_rownames(., "Gene") : is.data.frame(.data) is not TRUE Traceback: 13. stop(simpleError(msg, call = if (p <- sys.parent(1L)) sys.call(p))) 12. stopifnot(is.data.frame ...
written 12 days ago by DrAcula40
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Merging multiple single cell gene expression matrices (in .txt format) into one .txt/.csv/df
... Dear All, First of all my apologies if this has been answered somewhere else and I haven't understood it properly, but I am having a somewhat irritating problem with merging single-cell RNA seq datasets. I know that across donors it's probably best to perform integration, but I wanted to see what ...
R rna-seq sequencing written 13 days ago by DrAcula40 • updated 12 days ago by rpolicastro3.2k
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Tool: 3D UMAP and 3D tSNE visualization for Seurat
... **scRNAseq 3D Visualization Tool** I got a lot of help from these posts, Thought id share this tool for anyone working with a Seurat object to use for visualization: https://github.com/Dragonmasterx87/Interactive-3D-Plotting-in-Seurat-3.0.0/blob/master/3D%20UMAP%20Plotting%20v1.3.R Enjoy! ...
tool tsne scrnaseq 3d umap rna-seq written 15 months ago by DrAcula40
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Answer: A: Making a 3d tSNE Plot in Seurat for scRNA-seq
... I know this is old now. But Ive written some code which will help you create a 3D expression plot using plotly out of a seurat v3.0.0 object. Dont forget to star and fork :) Find the complete solution here: https://github.com/Dragonmasterx87/3D-Plotting-in-Seurat-3.0.0 Update: The code now support ...
written 20 months ago by DrAcula40
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How can you merge more than two 10x datasets in Seurat?
... I am trying to merge 3 datsets in seurat. I use the vignette on the seura website to merge 2 datasets however when I merge the 3rd t seems like the metadata isnt saved, however the head and tail of the data seem that its all being merged. ...
10x rna-seq scrnaseq written 22 months ago by DrAcula40 • updated 22 months ago by Charles Warden8.0k
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Comment: A: single cell RNAseq: From counts or RPKM > PCA > tSNE visualization of PCA
... I already have a csv file of genes and counts for my selected cells, How should I proceed?? ...
written 2.8 years ago by DrAcula40
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single cell RNAseq: From counts or RPKM > PCA > tSNE visualization of PCA
... Hello! I am a beginner at RNA seq analysis, I was hoping someone would point me in the direction of how I can take a data set (~50K genes in rows + 200 cells in columns, I have gene counts), perform a differential gene expression analysis (i don't know if this is needed for a PCA) and subsequently a ...
rna-seq written 2.8 years ago by DrAcula40

Latest awards to DrAcula

Popular Question 15 months ago, created a question with more than 1,000 views. For 3D UMAP and 3D tSNE visualization for Seurat
Popular Question 15 months ago, created a question with more than 1,000 views. For single cell RNAseq: From counts or RPKM > PCA > tSNE visualization of PCA
Popular Question 22 months ago, created a question with more than 1,000 views. For single cell RNAseq: From counts or RPKM > PCA > tSNE visualization of PCA

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