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User: Kristin Muench

gravatar for Kristin Muench
Reputation:
380
Status:
Trusted
Location:
United States
Twitter:
kristin_muench
Last seen:
8 hours ago
Joined:
4 years, 7 months ago
Email:
k******@stanford.edu

Posts by Kristin Muench

<prev • 111 results • page 1 of 12 • next >
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Answer: A: Normal to have high variability in Broad Institute's GSEA Output?
... It seems the problem is either that I needed to run more permutations or just that I had a very weak phenotype. Pablo Tamayo at UCSD wrote the following in response to my question on the gsea-help listserv: " If you explicitly set the seed and get the same results then that is the expected behavior ...
written 18 days ago by Kristin Muench • 380
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Comment: C: Normal to have high variability in Broad Institute's GSEA Output?
... [Moved this text to an answer - see below] ...
written 19 days ago by Kristin Muench • 380
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Comment: C: Seurat on both pooled and unpooled samples
... Thank you for the tip. ...
written 7 weeks ago by Kristin Muench • 380
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Seurat on both pooled and unpooled samples
... Hello, I'm analyzing an scRNA-Seq dataset that includes both pooled and unpooled samples. Additionally, the number of cells per sample is different between the unpooled and pooled samples. The overall number of pooled and unpooled samples is balanced across conditions, however. It's like this: ...
scrna-seq rna-seq seurat written 7 weeks ago by Kristin Muench • 380 • updated 7 weeks ago by RamRS ♦ 20k
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Normalizing using Seurat with large numbers of samples
... Hello, I am trying to run Seurat on a fairly large scRNA-Seq experiment, with 16 samples ranging from 1000-10,000 cells. In my first run of the pipeline, I merged all of the samples into a single Seurat object, like so: data.combined <- MergeSeurat(object1 = J, object2 = E, add.cell.id1 = ...
scrna-seq R single cell written 8 weeks ago by Kristin Muench • 380
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Answer: A: In Seurat, what data is VlnPlot() plotting?
... UPDATE: It looks like the issue lied in confusing a combined Seurat object representing multiple samples and using an object that had a single sample. Previously, I had been plotting VlnPlot on combined sample, but accidentally trying to extract data from a single sample, which I'm guessing had not ...
written 8 weeks ago by Kristin Muench • 380
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In Seurat, what data is VlnPlot() plotting?
... Hello, I'm using the Seurat function VlnPlot() to visualize some of my data. VlnPlot(object = data.combined, features.plot = c( 'Xist' ) When I plot it, the values range between 0 and 5. I then wanted to extract the expression value matrix used to generate VlnPlot. By peeking inside the Vln ...
scrna-seq seurat rna-seq single cell written 8 weeks ago by Kristin Muench • 380
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Comment: C: Handling biological replicates across batches in DESeq2
... Hello - I posted his reply below, hope it helps ...
written 4 months ago by Kristin Muench • 380
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Comment: C: Handling biological replicates across batches in DESeq2
... Thank you for clarifying. I wonder if there might still be an issue that individual samples are correlated to each other that might not be accounted for in the design/might still influence results? Mike Love suggested one strategy (post below) but I think I'll try this to see how much of a differenc ...
written 4 months ago by Kristin Muench • 380
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Answer: A: Handling biological replicates across batches in DESeq2
... Hello, Back-propagating the answer that Mike Love suggested on Bioconductor forums: If there is not a lot of technical variation across replicates > consider treating the samples like technical replicates, and collapse them in DESeq using the collapseReplicates() function. If there is a lot of ...
written 4 months ago by Kristin Muench • 380

Latest awards to Kristin Muench

Teacher 18 days ago, created an answer with at least 3 up-votes. For A: Normal to have high variability in Broad Institute's GSEA Output?
Scholar 18 days ago, created an answer that has been accepted. For A: Handling biological replicates across batches in DESeq2
Scholar 8 weeks ago, created an answer that has been accepted. For A: Handling biological replicates across batches in DESeq2
Popular Question 4 months ago, created a question with more than 1,000 views. For Is it problematic to use ANOVA in microarray meta-analysis?
Scholar 4 months ago, created an answer that has been accepted. For A: Handling biological replicates across batches in DESeq2
Popular Question 4 months ago, created a question with more than 1,000 views. For Is it problematic to use ANOVA in microarray meta-analysis?
Centurion 4 months ago, created 100 posts.
Popular Question 4 months ago, created a question with more than 1,000 views. For Is it problematic to use ANOVA in microarray meta-analysis?
Popular Question 6 months ago, created a question with more than 1,000 views. For Is it problematic to use ANOVA in microarray meta-analysis?
Popular Question 9 months ago, created a question with more than 1,000 views. For Is it problematic to use ANOVA in microarray meta-analysis?
Popular Question 9 months ago, created a question with more than 1,000 views. For Why can't I replicate DESeq's Log2FC calculation?
Popular Question 11 months ago, created a question with more than 1,000 views. For How many reads should I expect for paired end reads when coverage = 30 million?
Great Question 13 months ago, created a question with more than 5,000 views. For Bowtie2: Why won't it recognize my index files?
Supporter 13 months ago, voted at least 25 times.
Popular Question 20 months ago, created a question with more than 1,000 views. For How many reads should I expect for paired end reads when coverage = 30 million?
Popular Question 20 months ago, created a question with more than 1,000 views. For How to make lumi accept .txt data?
Popular Question 20 months ago, created a question with more than 1,000 views. For Could a "complete" RNA-Seq database feasibly exclude some protein-coding transcripts?
Popular Question 20 months ago, created a question with more than 1,000 views. For Determining gene expression with 2 biological replicates and RPKM data only
Popular Question 20 months ago, created a question with more than 1,000 views. For Is it possible to compare 3SEQ and RNA-Seq data?
Great Question 2.2 years ago, created a question with more than 5,000 views. For Bowtie2: Why won't it recognize my index files?
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Determining gene expression with 2 biological replicates and RPKM data only
Popular Question 2.8 years ago, created a question with more than 1,000 views. For Determining gene expression with 2 biological replicates and RPKM data only
Popular Question 2.8 years ago, created a question with more than 1,000 views. For I have demultiplexed files for a single biological replicate. When to combine them in pipeline?
Appreciated 3.2 years ago, created a post with more than 5 votes. For How do I explain to my non-bioinformatician labmates how to interpret principal components?
Popular Question 3.4 years ago, created a question with more than 1,000 views. For I have demultiplexed files for a single biological replicate. When to combine them in pipeline?
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