User: prakash

gravatar for prakash
prakash510
Reputation:
510
Status:
Trusted
Location:
Last seen:
an hour ago
Joined:
3 years, 2 months ago
Email:
j********@gmail.com

Posts by prakash

<prev • 69 results • page 1 of 7 • next >
0
votes
2
answers
213
views
2
answers
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 3 days ago by prakash510
1
vote
1
answer
139
views
1
answers
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 15 days ago by prakash510
1
vote
1
answer
173
views
1
answers
Comment: C: Finding DE genes in a group compared to all groups
... kudos ! Somehow I just missed to mention about resultsName ...
written 16 days ago by prakash510
1
vote
1
answer
173
views
1
answers
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 17 days ago by prakash510
0
votes
1
answer
160
views
1
answers
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 29 days ago by prakash510
0
votes
0
answers
204
views
0
answers
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 4 weeks ago by prakash510
0
votes
0
answers
172
views
0
answers
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 4 weeks ago by prakash510
0
votes
1
answer
214
views
1
answers
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 5 weeks ago by prakash510
0
votes
2
answers
195
views
2
answers
Comment: C: Delete numbers in the tables column
... See edit, answer updated. ...
written 5 weeks ago by prakash510 • updated 5 weeks ago by zx87545.4k
4
votes
2
answers
195
views
2
answers
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 5 weeks ago by prakash510 • updated 5 weeks ago by zx87545.4k

Latest awards to prakash

Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: Gene Set Enrichment Analysis after DESeq2
Scholar 5 weeks ago, created an answer that has been accepted. For A: Gene Set Enrichment Analysis after DESeq2
Appreciated 5 weeks ago, created a post with more than 5 votes. For A: Gene Set Enrichment Analysis after DESeq2
Good Answer 5 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
Scholar 5 weeks ago, created an answer that has been accepted. For A: Gene Set Enrichment Analysis after DESeq2
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: Gene Set Enrichment Analysis after DESeq2
Appreciated 5 weeks ago, created a post with more than 5 votes. For A: Gene Set Enrichment Analysis after DESeq2
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: Gene Set Enrichment Analysis after DESeq2
Scholar 5 weeks ago, created an answer that has been accepted. For A: Gene Set Enrichment Analysis after DESeq2
Supporter 8 weeks ago, voted at least 25 times.
Appreciated 11 weeks ago, created a post with more than 5 votes. For A: Gene Set Enrichment Analysis after DESeq2
Appreciated 12 weeks ago, created a post with more than 5 votes. For A: Gene Set Enrichment Analysis after DESeq2
Popular Question 4 months ago, created a question with more than 1,000 views. For Finding instances of motifs near peaks
Scholar 12 months ago, created an answer that has been accepted. For A: Gene Set Enrichment Analysis after DESeq2
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Gene Set Enrichment Analysis after DESeq2
Popular Question 12 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 14 months ago, created a question with more than 1,000 views. For how to get p value for a set of fdr value

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 626 users visited in the last hour