User: spacemorrissey

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Posts by spacemorrissey

<prev • 36 results • page 1 of 4 • next >
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How do I specify a background gene list on reactome?
... Hello, I want to look at annotation enrichments for a set of genes using reactome, but I can't figure out how to specify the background to use. All human genes would not be a good background for me as only 5000 genes were measured. ...
gene written 14 months ago by spacemorrissey240
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Answer: A: What is the reasonable proportion of zero counts in single-cell RNA-Seq data
... Unfortunately the answer to this would be very organism and cell type specific. It would also depend on the depth of sequencing that you performed. From normal RNA-seq from a population of cells there are often 1/3 to 1/2 of genes that are not expressed at levels above noise. I would think that i ...
written 2.1 years ago by spacemorrissey240
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Answer: A: What is the "sliding window" in a bio statistical analysis, e.g. in a genome seq
... Very simply, you take a window of some size, 10, 100, 1000 base pairs. You can then answer some question about what happens in that window. How many mutation occur in this window, how many reads align to this window, etc. The you slide the window by moving the window by some number of basepaires. ...
written 2.1 years ago by spacemorrissey240
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Answer: A: How can I look at find 'open chromatin' from ATAC-seq data using MACS2
... You can use MACS, but it is not the best tool for identifying open chromatin regions. I would recommend using Fseq: http://fureylab.web.unc.edu/software/fseq/ It was designed to analyze DNase -seq data, the predecessor of ATAC-seq. When analyzing data from either experiment, you do not really wa ...
written 2.1 years ago by spacemorrissey240
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Comment: C: Analyzing CRISPR and RNAi genome wide screens
... I found this paper "Systematic comparison of CRISPR-Cas9 and RNAi screens for essential genes" https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4900911/ Has anyone used this? Has anyone found anything better? ...
written 2.1 years ago by spacemorrissey240
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Analyzing CRISPR and RNAi genome wide screens
... I have data from genome wide CRISPR and RNAi gene knockdown screens. These were pooled experiments where genes were either knocked out with CRISPR or knocked down with RNAi, and then the surviving cells were sequenced. Tags corresponding to lethal knockouts would therefore be depleted in the resul ...
crispr meta analysis rnai written 2.1 years ago by spacemorrissey240
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Metabolomics Analysis - missing value imputation
... Hello, I am looking for some guidance on metabolomics analysis. I have a data set that has missing values for many of the metabolites, and I am wondering what the best method for dealing with that is. If I limit myself to metabolites with no missing values I drop a huge amount of my data, but ...
metabolomics written 2.2 years ago by spacemorrissey240 • updated 2.2 years ago by Kevin Blighe63k
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Comment: C: how many columns does F-seq need in the bed file
... Oops the text editor wrapped the lines of data. Just give it: Chrom start stop . . strand ...
written 3.1 years ago by spacemorrissey240
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Answer: A: how many columns does F-seq need in the bed file
... All F-seq really needs is the chrome, start position, and strand, but it expects to find that in bed format. So you should send it a file with 6 columns as below. Columns 4 and 5 are ignored, so you can put what ever you want in there. Also, since F-seq works on the density of cut sites, not an o ...
written 3.1 years ago by spacemorrissey240
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Comment: C: How to report differentially expressed transcription factors in scatter plot
... plotting FPKM in men vs women should give you what you wanted. I do not think you want to be plotting the FDR values. ...
written 3.7 years ago by spacemorrissey240

Latest awards to spacemorrissey

Teacher 14 months ago, created an answer with at least 3 up-votes. For A: How can I look at find 'open chromatin' from ATAC-seq data using MACS2
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: I'M Looking For A Bioinformatics Problem Which Could Benefit From A New Or Impro
Scholar 2.0 years ago, created an answer that has been accepted. For A: How can I look at find 'open chromatin' from ATAC-seq data using MACS2
Popular Question 3.1 years ago, created a question with more than 1,000 views. For What Is The Best Software For Finding Footprints In Mouse Dnase-Seq Data?
Popular Question 4.1 years ago, created a question with more than 1,000 views. For What Is The Best Software For Finding Footprints In Mouse Dnase-Seq Data?
Popular Question 5.5 years ago, created a question with more than 1,000 views. For What Is The Best Software For Finding Footprints In Mouse Dnase-Seq Data?
Teacher 6.3 years ago, created an answer with at least 3 up-votes. For A: I'M Looking For A Bioinformatics Problem Which Could Benefit From A New Or Impro

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