User: Arindam Ghosh

gravatar for Arindam Ghosh
Arindam Ghosh150
Reputation:
150
Status:
Trusted
Location:
India
Website:
https://ag1805x.github...
Twitter:
ag1805x
Last seen:
3 days, 6 hours ago
Joined:
3 years, 3 months ago
Email:
a******@outlook.in

I am currently working as a Junior Research Fellow at the Centre of Bioinformatics, University of Allahabad. I hold an undergraduate (B.Sc.) degree in Biotechnology from West Bengal University of Technology, India and a postgraduate (M.Sc.) degree in Bioinformatics from Alagappa University, India. My current research interests include stem cell bioinformatics, RNA-seq data analysis and network biology.

Posts by Arindam Ghosh

<prev • 117 results • page 1 of 12 • next >
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How to efetch specific attributes from BioSamples?
... I need to extract the sample source for a list of sample ids. I tried using efetch as follows: efetch -db biosample -id SAMN04383980 -format xml | xtract -pattern BioSampleSet -division BioSample -group Attributes -element Attribute The problem here is that there are often more than two attri ...
ncbi xml eutils written 10 days ago by Arindam Ghosh150 • updated 10 days ago by Pierre Lindenbaum116k
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Comment: C: Data selection for RNA-seq data analysis
... I have tried the approach 2 and as you mentioned the overlap is very less but to some extent has biological relevance. One major shortcoming of approach 2 is the number of replicates within each experiment. This now compels me to move towards approach 1. Can you help me with some papers that have u ...
written 11 days ago by Arindam Ghosh150
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Comment: C: What does cluster number in ClusterMaker represent?
... That's my concern. Even in their [example][1] problem in their [paper][2] I saw a similar situation. [1]: https://www.ncbi.nlm.nih.gov/core/lw/2.0/html/tileshop_pmc/tileshop_pmc_inline.html?title=Click%20on%20image%20to%20zoom&p=PMC3&id=2995124_btq596f1.jpg [2]: https://www.ncbi.nlm.n ...
written 16 days ago by Arindam Ghosh150
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What does cluster number in ClusterMaker represent?
... While clustering a network using Community Cluster (GLay) in ClusterMaker it gives a cluster number for each cluster. What does this represent? I Initially thought it to simple numbers to distinguish between two clusters but I saw that the cluster with highest node is at #2 while the other major clu ...
network clustermaker cytoscape clustering written 18 days ago by Arindam Ghosh150 • updated 16 days ago by scooter80
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Comment: C: How to construct GCN?
... But constructing only network with gene expression for single condition will give how the genes are correlated between the samples of a single condition. It won't tell much if any two genes are correlated across conditions. Again, for any given condition the gene expression values should be same ac ...
written 7 weeks ago by Arindam Ghosh150
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How to construct GCN?
... I have gene expression values for TEST and CONTROL samples from RNA-seq. I have determined the differentially expressed genes (DEG). Now I need to prepare a co-expression network of only the DEG. I did this by calculating the Pearson Correlation Coefficient (PCC) values using the corr.test() in R an ...
network gene coexpression network rna-seq written 7 weeks ago by Arindam Ghosh150 • updated 7 weeks ago by Kevin Blighe37k
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Comment: C: Low Sample For Coexpression
... Ok sorry. I missed to mention. 90% of the maximum possible correlation between n genes given by (n*(n-1))/2. ...
written 8 weeks ago by Arindam Ghosh150
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Comment: C: Low Sample For Coexpression
... A bit of clarification. While doing WGCNA or any other co-expression network, do we have to use the expression values for both the conditions of only a single condition? I used Pearson Correlation Coefficients to create an unweighted network. Using 0.9 as threshold, I found that ~90% of interaction ...
written 8 weeks ago by Arindam Ghosh150
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Comment: C: Any coexpression tools for RNAseq expression data
... A bit of clarification. While doing WGCNA or any other co-expression network, do we have to use the expression values for both the conditions of only a single condition? ...
written 8 weeks ago by Arindam Ghosh150
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Comment: C: Questions about DAVID
... Which one is best suggested to annotate a set of up-regulated ges? ...
written 4 months ago by Arindam Ghosh150

Latest awards to Arindam Ghosh

Autobiographer 11 days ago, has more than 80 characters in the information field of the user's profile.
Epic Question 18 days ago, created a question with more than 10,000 views. For C program to find complementary of DNA sequence
Popular Question 4 weeks ago, created a question with more than 1,000 views. For Non-bonded atoms in PDB
Student 5 weeks ago, asked a question with at least 3 up-votes. For Can anyone suggest a good tutorial to learn RNA-seq analysis?
Popular Question 3 months ago, created a question with more than 1,000 views. For Non-bonded atoms in PDB
Great Question 3 months ago, created a question with more than 5,000 views. For Can anyone suggest a good tutorial to learn RNA-seq analysis?
Popular Question 3 months ago, created a question with more than 1,000 views. For Non-bonded atoms in PDB
Popular Question 5 months ago, created a question with more than 1,000 views. For Non-bonded atoms in PDB
Centurion 6 months ago, created 100 posts.
Voter 7 months ago, voted more than 100 times.
Popular Question 9 months ago, created a question with more than 1,000 views. For C program to find complementary of DNA sequence
Scholar 11 months ago, created an answer that has been accepted. For A: What is the difference between gene FPKM and transcript FPKM values?
Great Question 11 months ago, created a question with more than 5,000 views. For C program to find complementary of DNA sequence
Supporter 15 months ago, voted at least 25 times.
Popular Question 2.6 years ago, created a question with more than 1,000 views. For C program to find complementary of DNA sequence

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