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why PCA for RNA-Seq but tSNE for scRNA-seq?

scrna-seq pca tsne rna-seq written 8 months ago by CY • 270 • updated 8 weeks ago by Minstein • 60

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295

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How to reproduce MATLAB tsne('algorithm', 'exact') result in R?

tsne pca matlab R rtsne written 4 months ago by mk • 70

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1.1k

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Why different tSNE plot with Seurat and Monocle if they'r using the same R package?

single-cell R monocle tsne seurat written 7 months ago by jgarces • 0 • updated 7 months ago by dppb05 • 70

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464

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How to fix (find) number of dimensions while reducing dimensions in tSNE method?

tsne pca rna-seq R written 10 months ago by sciencer • 70

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3.2k

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5 follow

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Making a 3d tSNE Plot in Seurat for scRNA-seq

scrna-seq tsne rna-seq seurat written 17 months ago by asyndeton17 • 20 • updated 15 months ago by garyhokawai • 30

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792

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scRNA-seq: how to visualize SNN-Cliq clustering result

single-cell snn-cliq snn tsne scrnaseq written 17 months ago by pacman • 50

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2.4k

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R script - Error: protect(): protection stack overflow

tsne bigdata pca R written 19 months ago by Chen Mor • 0

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1.1k

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Determining Cluster Criteria From FlowSOM/RtSNE

R tsne written 2.3 years ago by CMosychuk • 20

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Recent Replies

C: snpEff building new database ERROR by Anastasia A. • 0
Yes, you were right, that worked! Thank you!! (hate when it is just a typo)
C: snpEff building new database ERROR by Vitis • 1.8k
Is the command you used? java -jar snpEff.jar build -gtf22 -v Zea_Mays_B73 Make sure the n...
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Actually this is a HTG EdgeSeq assay. In this assay we have 4 negative probes by which we can ch...
C: snpEff building new database ERROR by Anastasia A. • 0
Thank you for your reply, and yes I did add the genome to the snpEff config file and still receiv...
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Pysam is a good tool to manipulate SAM/BAM with various attributes like CIGAR and mapping quality...
A: snpEff building new database ERROR by Vitis • 1.8k
Similar problem with this: https://www.biostars.org/p/182267/ Have you added your genome entry...
C: Error while building new database for SnpEff by Anastasia A. • 0
I'm currently running on the same issue. How were you able to fix it? Is it that it requires the ...
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One possible approach is described below, which involves some manual work, but which facilitates ...
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using samjdk: http://lindenb.github.io/jvarkit/SamJdk.html java -jar dist/samjdk.jar -e 're...
C: Getting an error whilst trying to import Biopython SeqIO by jrj.healey ♦ 10.0k
Never seen that before either. Have you tried reinstalling the module? Can you import anything e...
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There are two reasons for not filtering genes when performing co-expression network analysis: 1)...
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What error do you get? What is it that you would like to get out of the loop? The same files but ...

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