User: Diwan

gravatar for Diwan
Diwan560
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560
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United States
Twitter:
@curephile
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1 year, 1 month ago
Joined:
6 years, 4 months ago
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m************@gmail.com

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Posts by Diwan

<prev • 76 results • page 1 of 8 • next >
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Answer: A: Protein-protein Docking Software?
... Check Zdock software. They also have a webserver: http://zdock.umassmed.edu/ Also haddock: https://haddock.science.uu.nl/ ...
written 17 months ago by Diwan560
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Comment: C: network analysis of genes using R
... check igraph package Google gives many tutorials: http://kateto.net/networks-r-igraph http://statmath.wu.ac.at/research/friday/resources_WS0708_SS08/igraph.pdf ...
written 17 months ago by Diwan560
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Comment: C: How to download REVIGO TreeMap as Image? Also need help for Python script
... check ?treemap as tmPlot is deprecated. It says dataframe, index, and vsize are required parameters for treemap (also tmPlot) function. ...
written 21 months ago by Diwan560
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Comment: C: How to download REVIGO TreeMap as Image? Also need help for Python script
... Good. So that is the source of error. The usual input is GO IDs and associated p-value. Since you don't have pvalue you are getting error where ever it is mentioned. You should comment that line in the script too. As you can see, the Rscript creates a dataframe called *stuff* with GO terms, pvalues ...
written 21 months ago by Diwan560
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Comment: C: How to download REVIGO TreeMap as Image? Also need help for Python script
... As it works for the example, its difficult to understand the error message without further details. I can only guess. Based on the script, there is an assignment: vSize = "abslog10pvalue" Can you check if you get some results for : stuff$abslog10pvalue In example #1, you get something like [1] 22 ...
written 21 months ago by Diwan560
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Answer: A: How to download REVIGO TreeMap as Image? Also need help for Python script
... If you want the treemap for publication purposes, it is best to use "make R script" option. Just run the script in R and you will get the image inside R which you can save as figure or pdf. Moreover, it will also allow you to modify font/color etc. If you need it for presentation, just print screen ...
written 21 months ago by Diwan560
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Comment: C: Identifying interactors of hub genes using Cytoscape Network Analyzer plugin
... Networkanalyzer is just to calculate the properties of network. If your goal is getting clusters of subnetwork you can explore other clustering plugins such as clusterviz etc. As Jean has pointed out, if you just want to focus on hub, use the option "select first neighbours of a node" in cytoscape w ...
written 21 months ago by Diwan560
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Comment: C: Semantic Similarity selection in REVIGO: which is better? many clusters or few?
... As others have noted above, the semantic similarity measure in revigo is just a neat way to summarize/highlight the long list of significantly enriched GO terms. It is a better way to summarize the whole picture of GO analysis rather than listing few top enriched GO terms. The choice of the similar ...
written 21 months ago by Diwan560
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Answer: A: Is there way to do batchquery and obtain ATC codes for pubchem CIDs?
... Hi RF, My solution is given below. HTH #install.packages('httr') library(httr) #install.packages("RCurl") library(RCurl) #install.packages("RJSONIO") library(RJSONIO) #install.packages("plyr") library(plyr) getATC <- function(cidnum){ pubchem_url_in<-paste('https://pubchem.ncbi. ...
written 21 months ago by Diwan560
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Comment: C: node degree in cytoscape to find hub proteins
... Just add a new node property and fill it with 1's and 0's, i.e., put hub nodes as 1's. Then in cytoscape, viewer panel, you can color according to this property. If there are few nodes, just select them manually and override default color for that hub node only. HTH Another way to highlight a hub ...
written 22 months ago by Diwan560

Latest awards to Diwan

Popular Question 17 months ago, created a question with more than 1,000 views. For Is there way to do batchquery and obtain ATC codes for pubchem CIDs?
Voter 19 months ago, voted more than 100 times.
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: What Are The Most Influential Bioinformatics/Computational Biology Papers Of 201
Scholar 21 months ago, created an answer that has been accepted. For A: How to predict cancer-related proteins in Protein-Protein Interaction networks
Scholar 21 months ago, created an answer that has been accepted. For A: How to predict cancer-related proteins in Protein-Protein Interaction networks
Scholar 22 months ago, created an answer that has been accepted. For A: How to predict cancer-related proteins in Protein-Protein Interaction networks
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Is there any open proteomics repository like GEO?
Popular Question 2.4 years ago, created a question with more than 1,000 views. For How Can We Get Tissue Specific Genes?
Good Answer 2.5 years ago, created an answer that was upvoted at least 5 times. For A: Converting Affymetrix Probes To Gene Ids
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: Converting Affymetrix Probes To Gene Ids
Epic Question 2.6 years ago, created a question with more than 10,000 views. For How Can We Get Tissue Specific Genes?
Scholar 2.6 years ago, created an answer that has been accepted. For A: How to predict cancer-related proteins in Protein-Protein Interaction networks
Popular Question 2.8 years ago, created a question with more than 1,000 views. For How To Show A Ppi Subnetwork/Cluster Is Not Obtained By Random Chance?
Appreciated 3.2 years ago, created a post with more than 5 votes. For A: Converting Affymetrix Probes To Gene Ids
Good Question 3.2 years ago, asked a question that was upvoted at least 5 times. For How Can We Get Tissue Specific Genes?
Popular Question 3.2 years ago, created a question with more than 1,000 views. For How To Use Present/Absent Calls Based Filtering Of Probes?
Popular Question 3.2 years ago, created a question with more than 1,000 views. For How To Show A Ppi Subnetwork/Cluster Is Not Obtained By Random Chance?
Appreciated 3.4 years ago, created a post with more than 5 votes. For A: Converting Affymetrix Probes To Gene Ids
Scholar 3.6 years ago, created an answer that has been accepted. For A: How to predict cancer-related proteins in Protein-Protein Interaction networks
Great Question 3.7 years ago, created a question with more than 5,000 views. For How Can We Get Tissue Specific Genes?
Popular Question 3.7 years ago, created a question with more than 1,000 views. For How Can We Get Tissue Specific Genes?
Popular Question 3.8 years ago, created a question with more than 1,000 views. For How Can We Get Tissue Specific Genes?

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