User: Renesh

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Renesh1.5k
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I am working as postdoctoral research associate at Texas A&M University. I have involved in several Bioinformatics projects, from small to large scale sequence analysis to address abiotic and biotic stresses in plants (Cotton, Sugarcane, Rice, Potato, Tomato, Spartina etc.). I have largely applied Next generation sequencing (NGS) RNA-seq approach to study molecular mechanisms and transcriptional regulation under various abiotic and biotic stresses in a model and non-model plant species. Additionally, I have developed algorithms and software pipeline for efficient analysis for large scale biological data generated from NGS instruments.

Posts by Renesh

<prev • 184 results • page 1 of 19 • next >
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Answer: A: WGCNA categorical trait with more than 2 levels.
... WGCNA works on correlation measure. You can not use categorical variables in WGCNA analysis. You need to have quantitative variables (samples) with a number of samples at least 15 for reliable results. ...
written 8 weeks ago by Renesh1.5k
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Answer: A: Benjamini+ Hochberg multiple testing p.adjust R
... Read this article about how to adjust P-values using Bonferroni and Benjamini and Hochberg in multiple testing https://reneshbedre.github.io/blog/mtest.html ...
written 8 weeks ago by Renesh1.5k
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Answer: A: WGCNA Network Analysis
... In WGCNA, power parameter is needed to reduce the spurious correlations in the data. To select a power from `pickSoftThreshold` function, choose reasonably high `R^2` (column 2), usually higher than say .85 and negative slope around -1 (column 4) to get an approximately scale-free network. Power is ...
written 9 weeks ago by Renesh1.5k
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Answer: A: What is the meaning of "weight" in the WGCNA Cytoscape edge output file?
... In Cytoscape Output Edge, the weight columns refer to the connection strength between two nodes (genes) in terms of the correlation value obtained from `TOMsimilarity` function. Topological Overlap Matrix (TOM) which obtained from `TOMsimilarity` will have these values for respective genes. This va ...
written 9 weeks ago by Renesh1.5k
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Comment: C: How to download raw sequence data from GEO/SRA
... Thanks for suggestions. NCBI SRA toolkit lastet release contains `fasterq-dump` which provides multithreading option for faster download. ...
written 9 weeks ago by Renesh1.5k
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Answer: A: Does .sra.cache file means failed download?
... If you see .sra.cache files under SRA directory, it means your download is not complete and got interrupted for some reason. `vdb-validate` command will fail for the corresponding accession. See this post for downloading SRA datasets: https://reneshbedre.github.io/blog/fqutil.html ...
written 9 weeks ago by Renesh1.5k
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Answer: A: How to download raw sequence data from GEO/SRA
... How to use NCBI SRA toolkit effectively: Read this post https://reneshbedre.github.io/blog/fqutil.html ...
written 9 weeks ago by Renesh1.5k
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Answer: A: Ma plot labelling
... Easy to understand and visualize MA plot for RNA-seq data: https://reneshbedre.github.io/blog/ma.html ...
written 9 weeks ago by Renesh1.5k
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Answer: A: Strange MA-plot using DESeq2
... Easy to understand and visualize MA plot for gene expression data: https://reneshbedre.github.io/blog/ma.html ...
written 9 weeks ago by Renesh1.5k
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Answer: A: Volcano Plot from DEseq2
... Easy Volcano plot for gene expression data in Python https://reneshbedre.github.io/blog/volcano.html ...
written 10 weeks ago by Renesh1.5k

Latest awards to Renesh

Epic Question 6 weeks ago, created a question with more than 10,000 views. For Extract specific patter from string in MySQL:
Scholar 8 weeks ago, created an answer that has been accepted. For A: Is there a way to know sequences length when querying ENA programmatically?
Scholar 9 weeks ago, created an answer that has been accepted. For A: Is there a way to know sequences length when querying ENA programmatically?
Good Answer 9 weeks ago, created an answer that was upvoted at least 5 times. For A: Volcano Plot from DEseq2
Appreciated 10 weeks ago, created a post with more than 5 votes. For A: Does read-depth refer to a fold?
Scholar 10 weeks ago, created an answer that has been accepted. For A: Is there a way to know sequences length when querying ENA programmatically?
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Masters Ideas in Computer Science that tackles Bioinformatics Problem
Librarian 11 weeks ago, created a post with more than 10 bookmarks. For Gene expression units explained: RPM, RPKM, FPKM and TPM
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Masters Ideas in Computer Science that tackles Bioinformatics Problem
Appreciated 8 months ago, created a post with more than 5 votes. For A: Does read-depth refer to a fold?
Prophet 8 months ago, created a post with more than 20 followers. For Gene expression units explained: RPM, RPKM, FPKM and TPM
Epic Question 8 months ago, created a question with more than 10,000 views. For Extract specific patter from string in MySQL:
Great Question 11 months ago, created a question with more than 5,000 views. For Gene expression units explained: RPM, RPKM, FPKM and TPM
Epic Question 11 months ago, created a question with more than 10,000 views. For Extract specific patter from string in MySQL:
Appreciated 15 months ago, created a post with more than 5 votes. For A: Does read-depth refer to a fold?
Popular Question 15 months ago, created a question with more than 1,000 views. For Cufflink p-value using blind dispersion method
Popular Question 15 months ago, created a question with more than 1,000 views. For How to use seek() with Biopython SeqIO object
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Masters Ideas in Computer Science that tackles Bioinformatics Problem
Scholar 16 months ago, created an answer that has been accepted. For A: Is there a way to know sequences length when querying ENA programmatically?
Scholar 16 months ago, created an answer that has been accepted. For A: Is there a way to know sequences length when querying ENA programmatically?
Guru 16 months ago, received more than 100 upvotes.
Scholar 16 months ago, created an answer that has been accepted. For A: Is there a way to know sequences length when querying ENA programmatically?
Scholar 17 months ago, created an answer that has been accepted. For A: Is there a way to know sequences length when querying ENA programmatically?
Scholar 17 months ago, created an answer that has been accepted. For A: Is there a way to know sequences length when querying ENA programmatically?
Scholar 17 months ago, created an answer that has been accepted. For A: Is there a way to know sequences length when querying ENA programmatically?

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