User: DrAcula
DrAcula • 40
- 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
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... 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
DrAcula • 40
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... 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
DrAcula • 40
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... 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
DrAcula • 40
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... 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
DrAcula • 40
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... 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 ...
written 13 days ago by
DrAcula • 40
• updated
12 days ago by
rpolicastro ♦ 3.2k
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... **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! ...
written 15 months ago by
DrAcula • 40
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... 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
DrAcula • 40
1
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... 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. ...
written 22 months ago by
DrAcula • 40
• updated
22 months ago by
Charles Warden ♦ 8.0k
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... I already have a csv file of genes and counts for my selected cells, How should I proceed?? ...
written 2.8 years ago by
DrAcula • 40
1
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... 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 ...
written 2.8 years ago by
DrAcula • 40
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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