User: m93

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m93170
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Posts by m93

<prev • 54 results • page 1 of 6 • next >
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Software design book/resource recommendation for bioinformaticians
... 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 ...
best-practise python rna-seq software-design written 26 days ago by m93170
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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 4 months ago by m93170 • updated 4 months ago by Mike Smith1.4k
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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 8 months ago by m93170
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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 8 months ago by m93170 • updated 8 months ago by h.mon28k
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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 12 months ago by m93170
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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 14 months ago by m93170
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Comment: C: variableStep vs fixedStep for range formats
... Thanks, that really helps! ...
written 14 months ago by m93170
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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 14 months ago by m93170 • updated 14 months ago by RamRS24k
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Comment: C: Reformating bedGraph files in shell script
... Was literally about to add an update with that :) Thanks! ...
written 14 months ago by m93170
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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 14 months ago by m93170 • updated 12 months ago by Biostar ♦♦ 20

Latest awards to m93

Great Question 3 months ago, created a question with more than 5,000 views. For FastQC with multiple FASTQ files
Popular Question 3 months ago, created a question with more than 1,000 views. For edgeR: how to make contrasts with makeContrasts
Popular Question 3 months ago, created a question with more than 1,000 views. For Which skills are most required to become a good bioinformatician?
Popular Question 3 months ago, created a question with more than 1,000 views. For Obtaining hazard ratio from beta and chi-square values
Popular Question 3 months ago, created a question with more than 1,000 views. For Understanding subsampling with Samtools
Popular Question 4 months ago, created a question with more than 1,000 views. For Which skills are most required to become a good bioinformatician?
Popular Question 5 months ago, created a question with more than 1,000 views. For R: How to test for trend of risk scores
Popular Question 6 months ago, created a question with more than 1,000 views. For FastQC with multiple FASTQ files
Popular Question 6 months ago, created a question with more than 1,000 views. For Trim_galore on multiple fast.qz files: syntax problem
Student 9 months ago, asked a question with at least 3 up-votes. For Any suggestions for basic intro to submitting jobs to an HPC cluster?
Student 10 months ago, asked a question with at least 3 up-votes. For Which skills are most required to become a good bioinformatician?
Student 14 months ago, asked a question with at least 3 up-votes. For Which skills are most required to become a good bioinformatician?
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Student 17 months ago, asked a question with at least 3 up-votes. For Which skills are most required to become a good bioinformatician?

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