User: Hamid Ghaedi

gravatar for Hamid Ghaedi
Hamid Ghaedi230
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

<prev • 36 results • page 1 of 4 • next >
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Answer: A: How I can study cross-talk from two different tissue using gene expression profi
... 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 Ghaedi230
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Comment: C: Pipeline for Genomics WES raw data
... Try [this][1] one. [1]: https://github.com/hamidghaedi/pipeline_whole_exome_sequencing_analysis ...
written 3 days ago by Hamid Ghaedi230
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Comment: C: Cross-platform of microarray or analysis separately
... 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 Ghaedi230
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Comment: C: kegg enrichment and pathway analysis
... 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 Ghaedi230
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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 Ghaedi230
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Comment: C: Variant Call Format (.vcf) conversion to .bam
... Upvoted your answer because I supposed, @abyssaldharok has not idea about what he/she asked. ...
written 5 days ago by Hamid Ghaedi230
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Comment: C: Is there a database of haploinsufficiency scores or status for each gene?
... 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 Ghaedi230
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Answer: A: Clustering of genes using FPKM
... 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 Ghaedi230
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Comment: C: K Means Clustering Two Matrices for ComplexHeatmap
... > I then try to run > > rows = hclust(templogs)$order `hclust` should be run on a dissimilarity matrix calculated by `dist` , not your data frame! use `?hclust` to find more. ...
written 9 days ago by Hamid Ghaedi230
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Comment: C: Adding the csv file names as a separate column to the csv file
... Use (edit) `lapply` to read and adding an id column to your files. Then do rbind on the files. This would give you what you want: f <- list.files() # suppose you have your files in your current directory file <- lapply(f, function(x){ df <- read.csv(x) df$id <- x ...
written 9 days ago by Hamid Ghaedi230

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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