User: Hamid Ghaedi

gravatar for Hamid Ghaedi
Hamid Ghaedi1.2k
Reputation:
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Canada
Website:
https://github.com/ham...
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HaGhaedi
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11 hours ago
Joined:
2 years, 5 months ago
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Genomic Data Science Enthusiastic

Posts by Hamid Ghaedi

<prev • 106 results • page 1 of 11 • next >
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Comment: C: RNA seq analysis with TCGA
... There are lots of tutorials here and there for this job. Strongly recommend to pick one and follow accordingly for this kind of job. always it would be helpful for one to get familiarize them self with concepts before doing analysis. Anyway expression values could not be in RSEM and FPKM at the sa ...
written 4 weeks ago by Hamid Ghaedi1.2k
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Comment: C: whole exome variant filtering
... Maybe duplicate of this thread: https://www.biostars.org/p/475995/#480774 You can find a list of tools there. ...
written 9 weeks ago by Hamid Ghaedi1.2k
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Answer: A: Barplot in R for differential expression analysis
... This would create what you asked for, BUT for gene expression visualization bar plot is NOT a smart way to do so. Please follow @ATpoint comment (volcano plot) for visualization. [Here][1] is sample code for making volcano plot using ggplot package. df <- data.frame(gene = c("A", "B", "C", ...
written 9 weeks ago by Hamid Ghaedi1.2k
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Comment: C: Variant filtration software
... If you found this helpful, please upvote and whether this is a sort of answer for your question please approve the answer. ...
written 10 weeks ago by Hamid Ghaedi1.2k
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Comment: C: SNPs name (protein change)
... **EDIT: @Pierrre answered your question. I have assumed you have a list of common name for SNPs and want to retrieve rs#**. Having had a similar problem-Having a list of variants in non-standard format and wanna have relevant rs#- a couple of years ago I went through it by using [Variant Name Map ...
written 12 weeks ago by Hamid Ghaedi1.2k
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Comment: C: Creating an interaction network in R
... If you have your data in `maf` format or you convert them into this format, `maftools` packages do such a job very well. ...
written 12 weeks ago by Hamid Ghaedi1.2k
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Comment: C: SNPEff output meaning
... This is a more genetic question than a bioinformatic related question. Anyway I do recommend checking the website for Sequence Variant Nomenclature available here: https://varnomen.hgvs.org/. There, under DNA section check for deletion : https://varnomen.hgvs.org/recommendations/DNA/variant/deletio ...
written 3 months ago by Hamid Ghaedi1.2k
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Comment: C: Questions regarding VST/rlog correction to plot sample distances between RNA-seq
... Right, as: > Sequencing depth correction is done automatically for the vst and rlog ...
written 3 months ago by Hamid Ghaedi1.2k
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Answer: A: Variant filtration software
... There are tools like [ANNOVAR][1], [SnpEff][2], and [VEP][3] that are widely used for variant annotation. Most variant filtration/prioritization software work on the output from these three main software. Appended below is a list of software that one can use to do variant annotation, filtration, a ...
written 3 months ago by Hamid Ghaedi1.2k
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Answer: A: Can we use SNPs for diagnostics?
... Lets me take a look at your question in a bit different view than what Kevin did: It depends on what do you mean by SNP: By SNP if you mean those single nucleotide variants that are present in a relatively large fraction of the population ( > 1%), the **answer is a big NO!** These markers are u ...
written 3 months ago by Hamid Ghaedi1.2k

Latest awards to Hamid Ghaedi

Voter 8 weeks ago, voted more than 100 times.
Librarian 9 weeks ago, created a post with more than 10 bookmarks. For Gene Set Enrichment Analysis
Prophet 9 weeks ago, created a post with more than 20 followers. For Gene Set Enrichment Analysis
Popular Question 10 weeks ago, created a question with more than 1,000 views. For Methylation Analysis Tutorial in R_part1
Guru 11 weeks ago, received more than 100 upvotes.
Commentator 11 weeks ago, created a comment with at least 3 up-votes. For C: Best aligner to identify single point mutation
Commentator 11 weeks ago, created a comment with at least 3 up-votes. For C: HT-Seq count data coding gene
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: Is definition of differentially methylated region (DMR) biologically meaningful?
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: How to embed known cell information into Seurat object? AddMetaData?
Centurion 12 weeks ago, created 100 posts.
Appreciated 3 months ago, created a post with more than 5 votes. For Methylation Analysis Tutorial in R_part2
Appreciated 4 months ago, created a post with more than 5 votes. For Gene Set Enrichment Analysis
Popular Question 4 months ago, created a question with more than 1,000 views. For Methylation Analysis Tutorial in R_part1
Appreciated 4 months ago, created a post with more than 5 votes. For Gene Set Enrichment Analysis
Scholar 5 months ago, created an answer that has been accepted. For A: How to embed known cell information into Seurat object? AddMetaData?
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Scholar 5 months ago, created an answer that has been accepted. For A: How to embed known cell information into Seurat object? AddMetaData?
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Is definition of differentially methylated region (DMR) biologically meaningful?
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Is definition of differentially methylated region (DMR) biologically meaningful?

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