User: m93
m93 • 170
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Posts by m93
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... I am a bioinformatician looking to improve my skills in software design (things like error handling, object-orientated design, unit testing and best practises in general).
My background is biology (my degree was in biology) and I am self taught in Bash, R and Python. Most software design books look ...
written 26 days ago by
m93 • 170
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... 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 ...
written 4 months ago by
m93 • 170
• updated
4 months ago by
Mike Smith • 1.4k
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... Yes, it certainly seems like a lot of the terminology evolving around pathway analysis is loosely used. ...
written 8 months ago by
m93 • 170
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... 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 ...
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... 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 ...
written 12 months ago by
m93 • 170
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... 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 ...
written 14 months ago by
m93 • 170
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... Thanks, that really helps! ...
written 14 months ago by
m93 • 170
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... 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 ...
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... Was literally about to add an update with that :) Thanks! ...
written 14 months ago by
m93 • 170
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... 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 ...
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