User: Biologist

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Biologist190
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Posts by Biologist

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Comment: C: Any R package to check the expression of single gene in multiple cancer types of
... But for TCGAbiolinks or RTCGA or other tools have to download all the complete data for all cancer types and then check the specific lncRNA expression. Is it possible to get only expression of that particular gene for all cancer types at a time? ...
written 8 weeks ago by Biologist190
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Any R package to check the expression of single gene in multiple cancer types of TCGA?
... I'm interested in one lncRNA. And would like to check its expression between tumor and normal in all cancer types of TCGA. Usually for protein coding genes I use `cbioportal`. But some genes and lncRNAs information is not found in that. So, are there any `R` packages to check the expression of an ...
R tcga geneexpression rna-seq written 8 weeks ago by Biologist190 • updated 8 weeks ago by Kevin Blighe52k
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Comment: C: Classifying the samples based on zscore of a specific gene
... Hey hi small help again. So, I have the data like below: df: Samples GABRD Gender Stage Sample1 0.002 Female A Sample2 0.233 Female A Sample3 1.527 Female B Sample4 -3.45 Male C Sample5 0.79 Male B Sample6 2.19 Male A Sample7 0.42 Female C Sample8 -1.01 Male ...
written 9 weeks ago by Biologist190
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Comment: C: Classifying the samples based on zscore of a specific gene
... Ok. sorry I misunderstood. But for my analysis division into groups is what I want. ...
written 9 weeks ago by Biologist190
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Comment: C: Classifying the samples based on zscore of a specific gene
... small help please. how this dichotomisation can be done on zscore values in R? Can you please give an example. ...
written 9 weeks ago by Biologist190
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Comment: C: Classifying the samples based on zscore of a specific gene
... So, basically I wanted to classify around 600 samples into GABRD high and GABRD low groups and check the association with some clinical parameters. I want to use all these 600 samples for the analysis. But if I take +1.96 and -1.96 as cutoff for high and low I may be able to use only 50 samples for ...
written 9 weeks ago by Biologist190
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Comment: C: Classifying the samples based on zscore of a specific gene
... Ok. I took the fpkm data of that gene and applied the below function to get the zscore. zscore<- function(x){ z<- (x - mean(x)) / sd(x) return(z) } gabrd_z <- zscore(gabrd_fpkm) And then made a density plot on `gabrd_z`. I see that it is right-skewed. ![dens ...
written 9 weeks ago by Biologist190
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Comment: C: Classifying the samples based on zscore of a specific gene
... Or else as I have fpkm expression data of that gene, can I take median as a cutoff and classify them into high and low? ...
written 9 weeks ago by Biologist190
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Comment: C: Classifying the samples based on zscore of a specific gene
... I took the zscore of the `GBARD` gene, and [density plot][1] looks like this. [1]: https://i.imgur.com/1PDVedW.png ...
written 9 weeks ago by Biologist190
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Comment: C: Classifying the samples based on zscore of a specific gene
... No, I didn't log transform. I thought I have to. But the `zFPKM` documentation there is a note saying that the data is not log2 transformed. ...
written 9 weeks ago by Biologist190

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Popular Question 8 weeks ago, created a question with more than 1,000 views. For Gene set enrichment analysis with edgeR output
Popular Question 8 weeks ago, created a question with more than 1,000 views. For Stringtie with Gencode gtf file doesn't give any gene_ids or transcript_ids?
Popular Question 4 months ago, created a question with more than 1,000 views. For Gene set enrichment analysis with edgeR output
Popular Question 5 months ago, created a question with more than 1,000 views. For Stringtie with Gencode gtf file doesn't give any gene_ids or transcript_ids?
Popular Question 5 months ago, created a question with more than 1,000 views. For Stringtie with Gencode gtf file doesn't give any gene_ids or transcript_ids?
Popular Question 5 months ago, created a question with more than 1,000 views. For Gene set enrichment analysis with edgeR output
Popular Question 5 months ago, created a question with more than 1,000 views. For Identifying differentially expressed lncRNA's from RNA-Seq data
Popular Question 6 months ago, created a question with more than 1,000 views. For Stringtie with Gencode gtf file doesn't give any gene_ids or transcript_ids?
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Popular Question 9 months ago, created a question with more than 1,000 views. For Stringtie with Gencode gtf file doesn't give any gene_ids or transcript_ids?
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