User: Hamid Ghaedi
Hamid Ghaedi • 230
- Reputation:
- 230
- Status:
- Trusted
- Location:
- Queens university
- Website:
- https://github.com/ham...
- Twitter:
- HaGhaedi
- Scholar ID:
- Google Scholar Page
- Last seen:
- 40 minutes ago
- Joined:
- 2 years ago
- Email:
- q*******@gmail.com
Genomic Data Science Enthusiastic
Posts by Hamid Ghaedi
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... To me, your question (hypothesis) is not valid with regards to biology/genetics.
Cells in different tissue for sure have different expression profiles and because of that, you have "two" different tissues!. Indeed what makea a given "tissue identity" is a process (or chain of processes) having ge ...
written 2 days ago by
Hamid Ghaedi • 230
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... Try [this][1] one.
[1]: https://github.com/hamidghaedi/pipeline_whole_exome_sequencing_analysis ...
written 3 days ago by
Hamid Ghaedi • 230
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... The second option is more robust here. you can undertake a ranked-based meta-analysis approach like [This package][1] do was intorduced to resolve similar issues.
[1]: https://cran.r-project.org/web/packages/RobustRankAggreg/RobustRankAggreg.pdf ...
written 3 days ago by
Hamid Ghaedi • 230
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... Have you tried [DAVID][1]? It does functional gene enrichment analysis and other intresting analysis for you.
[1]: https://david.ncifcrf.gov/ ...
written 3 days ago by
Hamid Ghaedi • 230
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Comment:
C: Unused argument in R
... Paria, please use "code sample" option to indicate your code lines. ...
written 4 days ago by
Hamid Ghaedi • 230
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... Upvoted your answer because I supposed, @abyssaldharok has not idea about what he/she asked. ...
written 5 days ago by
Hamid Ghaedi • 230
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... Not sure about a well-stablished dedicated databse for HI. However, [Decipher][1] database is using a sort of dosage-sensitivity scores, I used to use this score as a metric of HI.
[1]: https://decipher.sanger.ac.uk/browser ...
written 8 days ago by
Hamid Ghaedi • 230
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... Old question but this may be of help for those dealing with the same issue:
For clustering, you need to transform your data into a z-score. There is a Bioconductor package, [zFPKM][1] do this on FPKM reads.
[1]: https://www.bioconductor.org/packages/release/bioc/vignettes/zFPKM/inst/doc/zFPKM. ...
written 9 days ago by
Hamid Ghaedi • 230
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... > I then try to run
>
> rows = hclust(templogs)$order
`hclust` should be run on a dissimilarity matrix calculated by `dist` , not your data frame! use `?hclust` to find more. ...
written 9 days ago by
Hamid Ghaedi • 230
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... Use (edit) `lapply` to read and adding an id column to your files. Then do rbind on the files. This would give you what you want:
f <- list.files() # suppose you have your files in your current directory
file <- lapply(f, function(x){
df <- read.csv(x)
df$id <- x
...
written 9 days ago by
Hamid Ghaedi • 230
Latest awards to Hamid Ghaedi
Supporter
6 days ago,
voted at least 25 times.
Scholar
12 days ago,
created an answer that has been accepted.
For A: How to embed known cell information into Seurat object? AddMetaData?
Teacher
12 days ago,
created an answer with at least 3 up-votes.
For A: Is definition of differentially methylated region (DMR) biologically meaningful?
Teacher
12 days 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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