User: Hamid Ghaedi
Hamid Ghaedi • 730
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Genomic Data Science Enthusiastic
Posts by Hamid Ghaedi
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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 Ghaedi • 730
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... 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 Ghaedi • 730
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... 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 Ghaedi • 730
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... Kallisto and Salmon are kind of mapper not aligner. So cant be used for variant calling. ...
written 9 days ago by
Hamid Ghaedi • 730
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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 Ghaedi • 730
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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 Ghaedi • 730
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... 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 Ghaedi • 730
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138
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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 Ghaedi • 730
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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 Ghaedi • 730
2
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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 Ghaedi • 730
Latest awards to Hamid Ghaedi
Appreciated
15 days ago,
created a post with more than 5 votes.
For Methylation Analysis Tutorial in R_part2
Popular Question
5 weeks ago,
created a question with more than 1,000 views.
For Methylation Analysis Tutorial in R_part1
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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