User: m93

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m93150
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Posts by m93

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R: How to save Mart object (BiomaRt package)
... I am using the biomaRt package to obtain some annotation data in the context of an RNAseq pipeline. In my script I have the following commands: library(biomaRt) ensembl <- useMart("ENSEMBL_MART_ENSEMBL", dataset = "hsapiens_gene_ensembl", host = "www.ensembl.org") # Later on in the ...
R biomart rna-seq written 16 days ago by m93150 • updated 16 days ago by Mike Smith1.2k
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Comment: C: Is DAVID an over-representation (ORA) tool for pathway analysis
... Yes, it certainly seems like a lot of the terminology evolving around pathway analysis is loosely used. ...
written 4 months ago by m93150
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Is DAVID an over-representation (ORA) tool for pathway analysis
... I have been reading the following 2 reviews to get an overview of all pathway analysis tools: 1) https://www.nature.com/articles/nmeth.3963 2) https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002375 Am I right in thinking that DAVID is an ORA method? I was looking at the DA ...
david pathway-analysis written 4 months ago by m93150 • updated 4 months ago by h.mon26k
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edgeR: how to make contrasts with makeContrasts
... I am very new to RNAseq analysis and I am learning how to use edgeR to perform differential gene expression. I am quite confused about how contrasts work. According to the manual: > design <- model.matrix(~0+group, data=y$samples) > colnames(design) <- levels(y$samples$group) &g ...
ngs makecontrasts glm edger dge written 8 months ago by m93150
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UCSC hub: autoscale option for multiwig track
... I am making a hub on UCSC Genome Browser and I am aiming to display multiple bigWig files as a single track (multiwig container). I decided to use the autoscale option because I wanted a dynamic scale: y axis changing depending on the maximum values in the current observed window. However, I am con ...
multiwig autoscale track ucsc written 10 months ago by m93150
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Comment: C: variableStep vs fixedStep for range formats
... Thanks, that really helps! ...
written 10 months ago by m93150
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variableStep vs fixedStep for range formats
... I am reading the specifications of many range formats: BED, bigBED, bedGraph, Wig and BigWig. I am having a hard time summarizing which of these can store data that is either variableStep or fixedStep. For each format, there is an important parameter/characteristic to understand: - **Size of the ...
bedgraph ucsc bigwig formats range written 10 months ago by m93150 • updated 10 months ago by RamRS22k
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Comment: C: Reformating bedGraph files in shell script
... Was literally about to add an update with that :) Thanks! ...
written 10 months ago by m93150
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Reformating bedGraph files in shell script
... I have 100 bedGraph files that I need to reformat before converting them into bigWig files for display in UCSC Genome Browser. Briefly: - These bedGraph files were obtained using genomeCoverageBed on bam files (for which the SN tag did not have "chr" in front of the chromosome number). - Since t ...
bedgraph ucsc bigwig chr awk written 10 months ago by m93150 • updated 8 months ago by Biostar ♦♦ 20
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Comment: C: Output bedGraph from genomeCoverageBed is missing "chr"
... What do you mean? The awk command suggested by jared.andrews07 will not work within a script. I'm guessing this is maybe a simpler way than my awk command? I'm not very comfortable changing a BedGraph like this to be honest, I wish there was a way out outputting a bedGraph with what I want directly. ...
written 10 months ago by m93150

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