User: Hamid Ghaedi
Hamid Ghaedi • 1.2k
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Genomic Data Science Enthusiastic
Posts by Hamid Ghaedi
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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 Ghaedi • 1.2k
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147
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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 Ghaedi • 1.2k
1
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167
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1
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... 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 Ghaedi • 1.2k
1
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1
answer
214
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1
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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 Ghaedi • 1.2k
1
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2
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171
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2
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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 Ghaedi • 1.2k
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159
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... 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 Ghaedi • 1.2k
0
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160
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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 Ghaedi • 1.2k
0
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1
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2.6k
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... Right, as:
> Sequencing depth correction is done automatically for the vst and rlog
...
written 3 months ago by
Hamid Ghaedi • 1.2k
2
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1
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214
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1
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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 Ghaedi • 1.2k
1
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2
answers
215
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... 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 Ghaedi • 1.2k
Latest awards to Hamid Ghaedi
Voter
8 weeks ago,
voted more than 100 times.
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
Popular Question
4 months ago,
created a question with more than 1,000 views.
For Methylation Analysis Tutorial in R_part1
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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5 months ago,
voted at least 25 times.
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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