User: psm

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psm50
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1 month, 1 week ago
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2 years, 5 months ago
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Posts by psm

<prev • 23 results • page 1 of 3 • next >
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Comment: C: ChipQC doesn't run
... Thank you for reporting this! ...
written 5 weeks ago by psm50
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Comment: C: Seurat Violin Plot shows counts LESS than 0?
... That post has solved my problem. Thank you - I feel silly for not having found that myself! ...
written 3 months ago by psm50
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Seurat Violin Plot shows counts LESS than 0?
... Hi guys, When exploring certain genes on Single Cell RNAseq datasets, I've noticed that Seurat violin plots often show gene expression BELOW zero. Is this just a jitter effect? Because I've also noticed that in some cases the cells stack near the zero line too (which would be unexpected of jitter). ...
rna-seq written 3 months ago by psm50 • updated 3 months ago by Bastien Hervé4.8k
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Comment: C: Importing zUMI output of single nuclear RNA-seq data to Seurat: Introns, exons,
... Really appreciate the reply! ...
written 3 months ago by psm50
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Comment: C: Importing zUMI output of single nuclear RNA-seq data to Seurat: Introns, exons,
... Thank you for your reply. Would it be fair then to simply add the UMIs for intron, exon, and inex to get a final UMI counts matrix for downstream analysis, if I believe all of those to be informative? ...
written 3 months ago by psm50
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Importing zUMI output of single nuclear RNA-seq data to Seurat: Introns, exons, or both?
... Hello all, New to sequencing analysis but I have some familiarity with standard analysis pipelines on typical (non-nuclear) RNAseq datasets, bulk and single-cell. But I now need to analyze a public dataset of single nuclear RNA-sequencing data (from this paper https://www.pnas.org/content/116/39/19 ...
rna-seq written 3 months ago by psm50 • updated 3 months ago by rpolicastro2.1k
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Comment: C: Is the ssGSEA enrichment score affected by other samples in the analysis group?
... Thank you - I have since switched to GSVA because I find it much simpler to use in R. ...
written 3 months ago by psm50
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Comment: C: GSVA kernels: Gaussian or Poisson?
... Thank you Kevin - appreciate the response. ...
written 3 months ago by psm50
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GSVA kernels: Gaussian or Poisson?
... Hi all, this question has indirectly come up several times. What is the best kcdf setting to use for GSVA analysis on non-log or non-variance normalized TPM data? For GSVA analysis using RNAseq data, the GSVA manual states: "We calculate now GSVA enrichment scores for these gene sets using first ...
rna-seq written 3 months ago by psm50 • updated 3 months ago by Kevin Blighe66k
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Is the ssGSEA enrichment score affected by other samples in the analysis group?
... Hi all, I have an RNAseq data for 81 samples. I ran ssGSEA 2.0 (I cloned it from the Broad Institute's github repository and sourced the code through R). After running the analysis a first time, I was curious whether somehow the score generated for any given sample was affected by other samples pres ...
ssgsea R rna-seq written 4 months ago by psm50 • updated 4 months ago by lixuenan20080630

Latest awards to psm

Popular Question 24 months ago, created a question with more than 1,000 views. For RNA-seq: How to know which paired reads come from the same original fragment?
Popular Question 24 months ago, created a question with more than 1,000 views. For ENSEMBL annotation file for quantification: which file to use?
Popular Question 24 months ago, created a question with more than 1,000 views. For HISAT2: Extracting splice sites and exons for index

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