User: TriS

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TriS4.2k
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Posts by TriS

<prev • 338 results • page 1 of 34 • next >
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Answer: A: Seurat "FindMarkers" and "FindallMarkers" v.s. Scanpy "rank_genes_groups"
... part of the answer can be found here for Seurat: https://www.biostars.org/p/409790/ for Scanpy's code (https://github.com/theislab/scanpy/blob/master/scanpy/tools/_rank_genes_groups.py): method The default method is `'t-test'`, `'t-test_overestim_var'` overestimates variance of ...
written 10 weeks ago by TriS4.2k
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Comment: C: Volcano plot for multiple clusters
... if those are the column names then you must have some sort of genes as row names. you gotta do a little bit of coding to define what genes belong to what cluster. 1- based on the cluster p.value and Log2FC define what belongs to what cluster 2- repeat that for all 20 clusters 3- color each gene base ...
written 10 months ago by TriS4.2k
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Answer: A: Volcano plot for multiple clusters
... or if you want to put them all together you can just color each group differently. library(ggplot2) ggplot(macrphage_list, aes(x = untreated.Log2.Fold.Change, y = -log10(untreated.P.Value), fill = myClusters)) + geom_point(size = 3) + geom_hline(yinterecept=-log10(10e-5)) + geom_vline(xi ...
written 10 months ago by TriS4.2k
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Comment: C: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
... this post is now pretty old, the data on cbioportal have been updated. that's why you see a difference ...
written 10 months ago by TriS4.2k
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Comment: C: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
... see comments above where I addressed this question ...
written 18 months ago by TriS4.2k
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Comment: C: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
... it's good practice to remove genes that have expression = 0 or very low expression in most samples. the % is up to you, this is an example, and I used 50% ...
written 18 months ago by TriS4.2k
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Comment: C: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
... that's because you are trying to assign a variable starting with the square bracket, which in R is used to subset variables. I'd suggest to get familiar with R first, instead of copy-paste the code above. that will help you preventing lethal mistakes ...
written 18 months ago by TriS4.2k
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Comment: C: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
... that will require quite a lil bit of coding, I'd suggest you to refine your question first and then contact a bioinformatician/statistician to help you coding it ...
written 18 months ago by TriS4.2k
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Comment: C: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
... you have to select patients based on the expression of two genes. - choose your two genes - classify patients based on the expression of both (i.e. `tp53 > 2 & pi3k > 2`) - that will be your altered class - the rest is not altered. or you can also count patients that are altered for one an ...
written 18 months ago by TriS4.2k
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Comment: C: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
... this code is a guideline, not a copy and paste document. I'd suggest you to read a bit more about basic R usage and survival analysis before digging into this. it'll be time well spent ...
written 2.8 years ago by TriS4.2k

Latest awards to TriS

Great Question 8 months ago, created a question with more than 5,000 views. For Plot average methylation levels across TSS region
Popular Question 10 months ago, created a question with more than 1,000 views. For artifact/false peaks visible in wiggle files
Scholar 11 months ago, created an answer that has been accepted. For C: limma results topTable vs toptable differ
Scholar 18 months ago, created an answer that has been accepted. For C: limma results topTable vs toptable differ
Scholar 18 months ago, created an answer that has been accepted. For A: How to split gene names in my list?
Good Answer 22 months ago, created an answer that was upvoted at least 5 times. For A: How to check whether two genomic regions contact in 3D?
Great Question 22 months ago, created a question with more than 5,000 views. For retrieve full TCGA datasets from cBioportal with R
Popular Question 24 months ago, created a question with more than 1,000 views. For artifact/false peaks visible in wiggle files
Appreciated 2.2 years ago, created a post with more than 5 votes. For A: How to check whether two genomic regions contact in 3D?
Popular Question 2.2 years ago, created a question with more than 1,000 views. For indel position in repetitive regions
Popular Question 2.2 years ago, created a question with more than 1,000 views. For breakdancer - cfg creation and chi square problem
Appreciated 2.3 years ago, created a post with more than 5 votes. For A: How to check whether two genomic regions contact in 3D?
Popular Question 2.3 years ago, created a question with more than 1,000 views. For breakdancer - cfg creation and chi square problem
Popular Question 2.4 years ago, created a question with more than 1,000 views. For breakdancer - cfg creation and chi square problem
Popular Question 2.4 years ago, created a question with more than 1,000 views. For breakdancer - cfg creation and chi square problem
Popular Question 2.5 years ago, created a question with more than 1,000 views. For breakdancer - cfg creation and chi square problem
Popular Question 2.8 years ago, created a question with more than 1,000 views. For filtering pileup file with samtools for SomaticSniper
Scholar 3.0 years ago, created an answer that has been accepted. For C: limma results topTable vs toptable differ
Teacher 3.1 years ago, created an answer with at least 3 up-votes. For A: How to split gene names in my list?
Commentator 3.1 years ago, created a comment with at least 3 up-votes. For C: Diagnose my daughter?
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: How to split gene names in my list?
Scholar 3.2 years ago, created an answer that has been accepted. For C: limma results topTable vs toptable differ
Commentator 3.2 years ago, created a comment with at least 3 up-votes. For C: Diagnose my daughter?
Teacher 3.3 years ago, created an answer with at least 3 up-votes. For A: How to split gene names in my list?
Scholar 3.3 years ago, created an answer that has been accepted. For C: limma results topTable vs toptable differ

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