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User: Arindam Ghosh

gravatar for Arindam Ghosh
Arindam Ghosh • 200
Reputation:
200
Status:
Trusted
Location:
India
Website:
https://ag1805x.github...
Twitter:
ag1805x
Scholar ID:
Google Scholar Page
Last seen:
6 days, 23 hours ago
Joined:
4 years, 4 months ago
Email:
a******@outlook.in

I am a Junior Research Fellow (JRF) 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.

Looking forward for opportunities in Environmental Genomics.

Posts by Arindam Ghosh

<prev • 164 results • page 1 of 17 • next >
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Comment: C: WGCNA export Network To Cytoscape without trait data, error "Cannot determine no
... Any specific reason for choosing `threshold = 0.02`? ...
written 11 days ago by Arindam Ghosh • 200
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Comment: C: WGCNA and VisAnt
... Is there any specific reason to choose 0.02 as threshold. How to extract the network of only hub genes? ...
written 11 days ago by Arindam Ghosh • 200
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Comment: C: A good pipeline for GO term analysis on RNA-seq Clusters in R?
... I used PANTHER to identify enriched biological processes in ~4000 genes and obtained ~500 GO BP complete terms after FDR < 0.05. This I guess would not be good with heatmaps. REVIGO treemaps helped reduce the redundancy though and helped make a good figure for publication. ...
written 14 days ago by Arindam Ghosh • 200
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Comment: C: Question about gene ontology data visualization
... For my gene set I got ~160 terms from PANTHER. How do I display this? Should I show only the top 10 sorted by p-value? Have seen this , but not sure if this is logcal. ...
written 14 days ago by Arindam Ghosh • 200
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Comment: C: A good pipeline for GO term analysis on RNA-seq Clusters in R?
... DAVID is definitely good, but is there a way to present the results graphically instead of the standard tables? ...
written 14 days ago by Arindam Ghosh • 200
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Comment: C: genlist for clusterprofiler
... Is it necessary to use a ranked gene list for clusterProfiler. I have a gene list from different modules in a network for which I want to do annoation/ORA. ...
written 14 days ago by Arindam Ghosh • 200
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Compact visualisation of enrichment analysis
... What would be the best way to graphically represent GO enrichment analysis? I have performed the GO enrichment for two set of genes using PANTHER. For publication I want to put a graphical visualisation instead of usual table. I have tried REVIGO treemap and BinGO network. Putting 6 treemaps in a p ...
revigo panther gene ontology david rna-seq written 15 days ago by Arindam Ghosh • 200 • updated 15 days ago by grant.hovhannisyan • 1.9k
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Comment: C: What is the meaning of "weight" in the WGCNA Cytoscape edge output file?
... How to select an appropriate threshold for exporting network? Is it arbitrary and just to limit the number of connections to visualise or does it have any meaning? ...
written 5 weeks ago by Arindam Ghosh • 200
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Signed hybrid network vs up/down -reg network
... Is creating a signed hybrid weight co-expression network of differentially expressed genes similar to separate co-expression network reconstruction of upregulated and downregulated genes? Why would it be beneficial to create such network when combined network would give more biological meaningful in ...
wgcna network written 7 weeks ago by Arindam Ghosh • 200
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Comment: C: up regulated and down regulated genes in co expression network
... ".are you interested in identifying genes whose expression is upregulated or down regulated but follows the same direction (positive correlation)" Would it be logical construct a co-expression network of only upreg or downreg genes instead of accommodating genes of both types? ...
written 7 weeks ago by Arindam Ghosh • 200

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