User: m98

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m98280
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Posts by m98

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PRSice: how to obtain exact list of SNPs used for PRSice.best
... I have run a standard PRSice analysis as follows: PRSice.R \\ --prsice /usr/local/bin/PRSice_linux \\ --base !{base} \\ --snp SNPID \\ --chr CHR \\ --bp POS \\ --A1 Allele1 \\ --A2 Allele2 \\ --stat BETA \\ --pvalue p.value \\ --beta \\ --target !{nam ...
prsice prs plink written 3 months ago by m98280 • updated 3 months ago by Sam3.3k
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IMPUTE2: how to dynamically obtain chunks for each chromosome
... I would like to run IMPUTE2 on some pre-phased data (made using SHAPEIT). The command I would like to use is like the example one given by IMPUTE2: ./impute2 \ -known_haps_g gwas_data_chr10_phased.haps \ -h pilot1.jun2010.b36.CEU.chr10.snpfilt.haps \ -l pilot1.jun2010.b36.CEU.chr10. ...
impute2 chunks written 6 months ago by m98280 • updated 6 months ago by jmukisa9030
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How to do pathway analysis on kinome Drosophila dataset
... I am familiar with gene set enrichment analysis (GSEA - Broad Institute) using sequencing data but I am fairly unexperienced in pathway and/or GO analysis in other contexts. My questions are: - Is it possible at all to perform gene set enrichment/pathway analysis/GO analysis on data from a drosophi ...
pathway-analysis go kinome statistical-power written 10 months ago by m98280 • updated 8 months ago by Biostar ♦♦ 20
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Resources recommendations for cloud computing (AWS) beginners
... I am a bioinformatician looking to improve my skills in cloud computing (mainly AWS). I have experience in HPC. I was wondering if anyone has recommendations for bioinformaticians for beginner courses in AWS. Thanks. ...
hpc aws cloud bioinformatics written 12 months ago by m98280
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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 15 months ago by m98280
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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 18 months ago by m98280 • updated 18 months ago by Mike Smith1.6k
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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 22 months ago by m98280
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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 22 months ago by m98280 • updated 22 months ago by h.mon32k
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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 2.2 years ago by m98280
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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 2.3 years ago by m98280

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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 Obtaining hazard ratio from beta and chi-square values
Popular Question 5 months ago, created a question with more than 1,000 views. For Obtaining hazard ratio from beta and chi-square values
Popular Question 6 months ago, created a question with more than 1,000 views. For edgeR: how to make contrasts with makeContrasts
Popular Question 9 months ago, created a question with more than 1,000 views. For edgeR: how to make contrasts with makeContrasts
Popular Question 9 months ago, created a question with more than 1,000 views. For edgeR: how to make contrasts with makeContrasts
Popular Question 9 months ago, created a question with more than 1,000 views. For edgeR: how to make contrasts with makeContrasts
Great Question 17 months ago, created a question with more than 5,000 views. For FastQC with multiple FASTQ files
Popular Question 17 months ago, created a question with more than 1,000 views. For edgeR: how to make contrasts with makeContrasts
Popular Question 17 months ago, created a question with more than 1,000 views. For Which skills are most required to become a good bioinformatician?
Popular Question 17 months ago, created a question with more than 1,000 views. For Obtaining hazard ratio from beta and chi-square values
Popular Question 17 months ago, created a question with more than 1,000 views. For Understanding subsampling with Samtools
Popular Question 19 months ago, created a question with more than 1,000 views. For Which skills are most required to become a good bioinformatician?
Popular Question 19 months ago, created a question with more than 1,000 views. For R: How to test for trend of risk scores
Popular Question 20 months ago, created a question with more than 1,000 views. For FastQC with multiple FASTQ files
Popular Question 20 months ago, created a question with more than 1,000 views. For Trim_galore on multiple fast.qz files: syntax problem

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