User: prakash

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prakash530
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Posts by prakash

<prev • 69 results • page 1 of 7 • next >
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Comment: C: How to make k-means clustering plot for relative expression?
... Hi Chirag and Kevin, A simple and naive question on this thread. How do you choose a particular number of cluster (k) before performing kmeans clustering?. I know there are several methods such as pvclust or nbclust to find optimal number of k, but in my experience those doesn't always work better ...
written 7 weeks ago by prakash530
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Comment: C: Is it possible to visualize ChIP peaks of three different samples in one plot us
... well [HOMER][1] has everything what you need. merge peaks from all the files and calculate enrichment over merged files. [1]: http://homer.ucsd.edu/homer/ngs/quantification.html ...
written 9 weeks ago by prakash530
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Comment: C: Finding DE genes in a group compared to all groups
... kudos ! Somehow I just missed to mention about resultsName ...
written 9 weeks ago by prakash530
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Comment: C: Finding DE genes in a group compared to all groups
... Well I have also recently did analysis on interaction type of design in DESeq2, what I would do in this case, I would use contrast and perform comparison keeping one condition as reference (as you are doing) and extract all the genes that are DE (log2FC >=1 || log2FC <=-1 && padj < ...
written 9 weeks ago by prakash530
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Comment: C: How different is rlog transformation from vst transformation in DESeq2
... In my understanding, vst takes two things into account while normalization, one is size factor(depth normalization) and another is mean dispersion across the sample. while rld only accounts for size factor. ...
written 11 weeks ago by prakash530
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Comment: C: Plot factors by specific column in ggplot
... factor every column which you want to order, then feed combination in facet_grid(), you can take help from this [post][1] [1]: https://www.biostars.org/p/336799/#336804 ...
written 11 weeks ago by prakash530
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Comment: C: Correlating gene expression with traits for multiple treatments
... My suggestion would be try WGCNA on you datasets. you can identify modules based on gene expression correlation and also can perform module-trait relationship. you can find details [here][1] [1]: https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/Tutorials/ ...
written 12 weeks ago by prakash530
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Comment: C: Motif location for enriched motif in HOMER
... Thanks Kevin ! Actually I performed de novo motif analysis of peaks using findMotifsGenome.pl and it showed enrichment for a motif, say 20 % of total target. I was interested to know the genomic regions for this enriched motif. So I used findMotifsGenome.pl to extract the regions and it extracted g ...
written 3 months ago by prakash530
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Comment: C: Delete numbers in the tables column
... See edit, answer updated. ...
written 3 months ago by prakash530 • updated 3 months ago by zx87546.0k
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Answer: A: Delete numbers in the tables column
... Read the file, and filter out any row where SNP column is more than or equal to 10: data <- read.table("SNP.txt", header = TRUE) data <- data[ data$SNP >= 10, ]) To exclude 1st BP column, and to add 20KB to BP column: data <- data[ , -3 ] data$BP <- data$BP + 20000 ...
written 3 months ago by prakash530 • updated 3 months ago by zx87546.0k

Latest awards to prakash

Good Answer 7 days ago, created an answer that was upvoted at least 5 times. For A: How to add gene symbol to RNA-Seq data using R
Popular Question 28 days ago, created a question with more than 1,000 views. For Finding instances of motifs near peaks
Appreciated 6 weeks ago, created a post with more than 5 votes. For A: Gene Set Enrichment Analysis after DESeq2
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: Gene Set Enrichment Analysis after DESeq2
Scholar 3 months ago, created an answer that has been accepted. For A: Gene Set Enrichment Analysis after DESeq2
Appreciated 3 months ago, created a post with more than 5 votes. For A: Gene Set Enrichment Analysis after DESeq2
Good Answer 3 months ago, created an answer that was upvoted at least 5 times. For A: How to add gene symbol to RNA-Seq data using R
Scholar 3 months ago, created an answer that has been accepted. For A: Gene Set Enrichment Analysis after DESeq2
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Gene Set Enrichment Analysis after DESeq2
Appreciated 3 months ago, created a post with more than 5 votes. For A: Gene Set Enrichment Analysis after DESeq2
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Gene Set Enrichment Analysis after DESeq2
Scholar 3 months ago, created an answer that has been accepted. For A: Gene Set Enrichment Analysis after DESeq2
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Appreciated 4 months ago, created a post with more than 5 votes. For A: Gene Set Enrichment Analysis after DESeq2
Appreciated 4 months ago, created a post with more than 5 votes. For A: Gene Set Enrichment Analysis after DESeq2
Popular Question 5 months ago, created a question with more than 1,000 views. For Finding instances of motifs near peaks
Scholar 13 months ago, created an answer that has been accepted. For A: Gene Set Enrichment Analysis after DESeq2
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Gene Set Enrichment Analysis after DESeq2
Popular Question 14 months ago, created a question with more than 1,000 views. For how to get p value for a set of fdr value
Popular Question 15 months ago, created a question with more than 1,000 views. For how to get p value for a set of fdr value

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