User: Prakash

gravatar for Prakash
Prakash730
Reputation:
730
Status:
Trusted
Location:
India
Twitter:
gprakash047
Last seen:
1 day, 11 hours ago
Joined:
3 years, 6 months ago
Email:
j********@gmail.com

Posts by Prakash

<prev • 80 results • page 1 of 8 • next >
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Comment: C: How to determine fibroblast contamination by expression profile
... Here I would suggest to do some gene enrichment analysis for set of genes expressed from your sample against expression profile of fibrobalst. May be that will give idea about the fibroblast component in your sample ...
written 18 days ago by Prakash730
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Comment: C: How to perform GSEAPreranked analysis in a proper manner?
... Generally people take account of both fold change and p-value together for ranking gene list. Have a look at this [post][1] [1]: https://www.biostars.org/p/279097/ ...
written 18 days ago by Prakash730
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Answer: A: Dividing the groups on the same axis using ggplot2
... You need to just use facet_wrap(Group ~ .) instead of facet_grid ...
written 23 days ago by Prakash730
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Answer: A: showing specific GO pathways in the dotplot or cnetplot
... This has been discussed [here][1]. I have modified the code posted by [Ming Tang][2] you can plot selected pathway using ggplot2 from the enrichplot result x <- enrichPathway(gene=de,pvalueCutoff=0.05, readable=T) y <- as.data.frame(x) head(y) ggplot(y[c(1,4,5,7,8),], # you ...
written 24 days ago by Prakash730
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Comment: C: Differential gene expression in edgeR
... On what basis you are saying 110 genes are deferentially expressed ? I think if you know the answer, you can filter the DE object based on fold change and significance level. pardon me If i am missing something. ...
written 24 days ago by Prakash730
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Answer: A: Tools To Do the Alternative Splicing Analysis
... I would like to add one more tool recently out is [Annotation-free quantification of RNA splicing using LeafCutter][1] [1]: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5742080/ ...
written 24 days ago by Prakash730
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Answer: C: Regular expression to extract mutations type
... using simple grep command you can extract the line based on pattern. for e.g grep "C>T" file.txt >output.txt and grep can be done in R as well a <- c("c.2455C>T","c.2455C>G","c.2455C>A") b <- grep(pattern = "[C]>[TG]",a,perl = TRUE,value = TRUE) # as Pierre ...
written 25 days ago by Prakash730
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Comment: C: Identify genes with chip signal > input prior to peak calling
... what I understood that you want to narrow down ChIPseq signal having enrichment > input (but how much 1.5 fold or 2 fold?), and then use look for enrichment near TSS. I think you need keep one thing fixed either all the TSS or ChIPseq enrichment. I would suggest to to reduce the fold change c ...
written 26 days ago by Prakash730
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Comment: C: Strange output of samtools flag stat?
... why you think it has not aligned successfully based on samtool flagstat output? compare both the output. ...
written 26 days ago by Prakash730
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Answer: A: Filtering, Summerizing, and plotting from big data frame
... See, if this help library(ggplot2) library(ggpubr) library(reshape2) # a is list created from your post df <- do.call(cbind.data.frame, a) melted <- melt(df) head(melted) melted$variable<- str_replace_all(melted$variable, '_[0-9]$', '') melted$varia ...
written 26 days ago by Prakash730

Latest awards to Prakash

Popular Question 4 days ago, created a question with more than 1,000 views. For Finding instances of motifs near peaks
Appreciated 21 days ago, created a post with more than 5 votes. For A: How to add colors to bar chart?
Teacher 21 days ago, created an answer with at least 3 up-votes. For A: How to add colors to bar chart?
Scholar 22 days ago, created an answer that has been accepted. For A: How to add colors to bar chart?
Teacher 23 days ago, created an answer with at least 3 up-votes. For A: How to add colors to bar chart?
Teacher 24 days ago, created an answer with at least 3 up-votes. For A: How to add colors to bar chart?
Teacher 25 days ago, created an answer with at least 3 up-votes. For A: How to add colors to bar chart?
Good Answer 11 weeks 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 3 months ago, created a question with more than 1,000 views. For Finding instances of motifs near peaks
Appreciated 3 months ago, created a post with more than 5 votes. For A: Gene Set Enrichment Analysis after DESeq2
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Gene Set Enrichment Analysis after DESeq2
Scholar 5 months ago, created an answer that has been accepted. For A: Gene Set Enrichment Analysis after DESeq2
Appreciated 5 months ago, created a post with more than 5 votes. For A: Gene Set Enrichment Analysis after DESeq2
Good Answer 5 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 5 months ago, created an answer that has been accepted. For A: Gene Set Enrichment Analysis after DESeq2
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Gene Set Enrichment Analysis after DESeq2
Appreciated 5 months ago, created a post with more than 5 votes. For A: Gene Set Enrichment Analysis after DESeq2
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Gene Set Enrichment Analysis after DESeq2
Scholar 5 months ago, created an answer that has been accepted. For A: Gene Set Enrichment Analysis after DESeq2
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Appreciated 6 months ago, created a post with more than 5 votes. For A: Gene Set Enrichment Analysis after DESeq2
Appreciated 7 months ago, created a post with more than 5 votes. For A: Gene Set Enrichment Analysis after DESeq2
Popular Question 8 months ago, created a question with more than 1,000 views. For Finding instances of motifs near peaks
Scholar 16 months ago, created an answer that has been accepted. For A: Gene Set Enrichment Analysis after DESeq2
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: Gene Set Enrichment Analysis after DESeq2

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