User: m98
m98 • 280
- Reputation:
- 280
- Status:
- Trusted
- Location:
- Last seen:
- 1 month, 1 week ago
- Joined:
- 3 years, 6 months ago
- Email:
- m***********@gmail.com
Posts by m98
<prev
• 58 results •
page 1 of 6 •
next >
1
vote
1
answer
177
views
1
answer
... 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 ...
0
votes
1
answer
234
views
1
answer
... 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. ...
0
votes
0
answers
241
views
0
answers
... 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 ...
0
votes
0
answers
247
views
0
answers
... 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. ...
written 12 months ago by
m98 • 280
0
votes
0
answers
247
views
0
answers
... 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 15 months ago by
m98 • 280
5
votes
1
answer
676
views
1
answer
... 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 18 months ago by
m98 • 280
• updated
18 months ago by
Mike Smith • 1.6k
0
votes
0
answers
813
views
0
answers
... Yes, it certainly seems like a lot of the terminology evolving around pathway analysis is loosely used. ...
written 22 months ago by
m98 • 280
1
vote
0
answers
813
views
0
answers
... 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 ...
1
vote
0
answers
3.5k
views
0
answers
... 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 2.2 years ago by
m98 • 280
1
vote
0
answers
852
views
0
answers
... 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 2.3 years ago by
m98 • 280
Latest awards to m98
Epic Question
12 weeks ago,
created a question with more than 10,000 views.
For Definition of minor and major allele and connection with risk, effect, wildtype and reference allele
Popular Question
3 months ago,
created a question with more than 1,000 views.
For Obtaining hazard ratio from beta and chi-square values
Prophet
3 months ago,
created a post with more than 20 followers.
For Definition of minor and major allele and connection with risk, effect, wildtype and reference allele
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
Appreciated
11 months ago,
created a post with more than 5 votes.
For Definition of minor and major allele and connection with risk, effect, wildtype and reference allele
Good Question
11 months ago,
asked a question that was upvoted at least 5 times.
For Definition of minor and major allele and connection with risk, effect, wildtype and reference allele
Epic Question
13 months ago,
created a question with more than 10,000 views.
For Definition of minor and major allele and connection with risk, effect, wildtype and reference allele
Great Question
17 months ago,
created a question with more than 5,000 views.
For Bash: find duplicates based on 2 columns and keep duplicate with lowest value in a different column
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
17 months ago,
created a question with more than 1,000 views.
For Bash: find duplicates based on 2 columns and keep duplicate with lowest value in a different column
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
Great Question
20 months ago,
created a question with more than 5,000 views.
For Definition of minor and major allele and connection with risk, effect, wildtype and reference allele
Popular Question
21 months ago,
created a question with more than 1,000 views.
For Definition of minor and major allele and connection with risk, effect, wildtype and reference allele
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1857 users visited in the last hour