User: Hamid Ghaedi

gravatar for Hamid Ghaedi
Hamid Ghaedi730
Reputation:
730
Status:
Trusted
Location:
Canada
Website:
https://github.com/ham...
Twitter:
HaGhaedi
Scholar ID:
Google Scholar Page
Last seen:
4 minutes ago
Joined:
2 years, 2 months ago
Email:
q*******@gmail.com

Genomic Data Science Enthusiastic

Posts by Hamid Ghaedi

<prev • 94 results • page 1 of 10 • next >
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Comment: C: heatmap in R
... Came across this: https://www.nature.com/articles/nmeth.1902. You and others may find this helpful. > Hundreds of rows and columns can be displayed on a screen. Heat maps > rely fundamentally on color encoding and on meaningful reordering of > the rows and columns. When either of these co ...
written 3 days ago by Hamid Ghaedi730
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Answer: A: Survival analysis based on a set of genes for TCGA data
... You may need first to look at your gene one by one to know whether they are significantly associated with survival probability or not (univariate analysis). Then picking significant genes and make a model with those genes (multivariate Cox regression analysis). **For univariate analysis** check thi ...
written 6 days ago by Hamid Ghaedi730
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Comment: C: R or python packages for differential methylation levels analysis: case x contro
... You may want to check these posts: 1- https://www.biostars.org/p/465230/ 2-https://www.biostars.org/p/465232/ ...
written 7 days ago by Hamid Ghaedi730
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Comment: C: Best aligner to identify single point mutation
... Kallisto and Salmon are kind of mapper not aligner. So cant be used for variant calling. ...
written 9 days ago by Hamid Ghaedi730
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Comment: C: Alignment in WES
... Agreed with @ATpoint, suppose you have included high-quality unpaired read and made a BAM file, further processing would be needed to proceed with this file in your workflow. Indeed 1% would not add much sensetivity to your discovery. ...
written 10 days ago by Hamid Ghaedi730
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Comment: C: Alignment in WES
... It is interesting to know why the pipeline is designed in this way. What is the benefit of doing this? It may be designed to deal with a very specific situation. For sure it is not wise to include *unpared.fastq.gz into the mapping step for variant discovery at least in clinical related analysis. A ...
written 11 days ago by Hamid Ghaedi730
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Comment: C: annotation - biomaRt - Error in UseMethod
... Your code seems Ok to me and using that I got the intended result. Mybe you need to update some of your package installation (see this [post][1] )or detach all package except biomaRt, and do analysis. [1]: https://support.bioconductor.org/p/p132709/ ...
written 13 days ago by Hamid Ghaedi730
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Comment: C: WGCNA - what is it for
... Hi, Would you please share a reference- published article for this? Looks intresting ...
written 16 days ago by Hamid Ghaedi730
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Comment: C: HT-Seq count data coding gene
... Then make sure you have `rna` file , it complained that you have not such file. See the very end of error message: ....object 'rna' not found ...
written 21 days ago by Hamid Ghaedi730
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Comment: C: HT-Seq count data coding gene
... Dear rhasanvandj , As far as I know, there is no code for doing this at the download step. You need to download data and perform your analysis. Then you can select those genes you are interested (here coding gene). Having a list of genes you can retrieve data on their Biotype (including coding and ...
written 21 days ago by Hamid Ghaedi730

Latest awards to Hamid Ghaedi

Appreciated 15 days ago, created a post with more than 5 votes. For Methylation Analysis Tutorial in R_part2
Appreciated 4 weeks ago, created a post with more than 5 votes. For Gene Set Enrichment Analysis
Popular Question 5 weeks ago, created a question with more than 1,000 views. For Methylation Analysis Tutorial in R_part1
Appreciated 6 weeks ago, created a post with more than 5 votes. For Gene Set Enrichment Analysis
Scholar 9 weeks ago, created an answer that has been accepted. For A: How to embed known cell information into Seurat object? AddMetaData?
Supporter 10 weeks ago, voted at least 25 times.
Scholar 10 weeks ago, created an answer that has been accepted. For A: How to embed known cell information into Seurat object? AddMetaData?
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Is definition of differentially methylated region (DMR) biologically meaningful?
Teacher 10 weeks 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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