User: Renesh

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Renesh1.6k
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5 years, 1 month ago
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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 • 186 results • page 1 of 19 • next >
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Answer: A: Merge vcf files with multiple samples into one vcf with all variants
... Check this link if you want to merge multiple vcf files https://reneshbedre.github.io/blog/mergevcf.html ...
written 7 months ago by Renesh1.6k
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Answer: A: How to merge vcf files with different variants but same samples?
... Check this link to merge vcf files https://reneshbedre.github.io/blog/mergevcf.html ...
written 7 months ago by Renesh1.6k
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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 10 months ago by Renesh1.6k
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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 10 months ago by Renesh1.6k
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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 10 months ago by Renesh1.6k
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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 10 months ago by Renesh1.6k
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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 10 months ago by Renesh1.6k
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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 10 months ago by Renesh1.6k
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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 10 months ago by Renesh1.6k
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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 10 months ago by Renesh1.6k

Latest awards to Renesh

Epic Question 9 months ago, created a question with more than 10,000 views. For Extract specific patter from string in MySQL:
Scholar 10 months ago, created an answer that has been accepted. For A: Is there a way to know sequences length when querying ENA programmatically?
Scholar 10 months ago, created an answer that has been accepted. For A: Is there a way to know sequences length when querying ENA programmatically?
Good Answer 10 months ago, created an answer that was upvoted at least 5 times. For A: Volcano Plot from DEseq2
Appreciated 10 months ago, created a post with more than 5 votes. For A: Does read-depth refer to a fold?
Scholar 10 months ago, created an answer that has been accepted. For A: Is there a way to know sequences length when querying ENA programmatically?
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Masters Ideas in Computer Science that tackles Bioinformatics Problem
Librarian 10 months ago, created a post with more than 10 bookmarks. For Gene expression units explained: RPM, RPKM, FPKM and TPM
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Masters Ideas in Computer Science that tackles Bioinformatics Problem
Appreciated 16 months ago, created a post with more than 5 votes. For A: Does read-depth refer to a fold?
Prophet 16 months ago, created a post with more than 20 followers. For Gene expression units explained: RPM, RPKM, FPKM and TPM
Epic Question 16 months ago, created a question with more than 10,000 views. For Extract specific patter from string in MySQL:
Great Question 19 months ago, created a question with more than 5,000 views. For Gene expression units explained: RPM, RPKM, FPKM and TPM
Epic Question 19 months ago, created a question with more than 10,000 views. For Extract specific patter from string in MySQL:
Appreciated 23 months ago, created a post with more than 5 votes. For A: Does read-depth refer to a fold?
Popular Question 23 months ago, created a question with more than 1,000 views. For Cufflink p-value using blind dispersion method
Popular Question 23 months ago, created a question with more than 1,000 views. For How to use seek() with Biopython SeqIO object
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: Masters Ideas in Computer Science that tackles Bioinformatics Problem
Scholar 2.0 years ago, created an answer that has been accepted. For A: Is there a way to know sequences length when querying ENA programmatically?
Scholar 2.0 years ago, created an answer that has been accepted. For A: Is there a way to know sequences length when querying ENA programmatically?
Guru 2.1 years ago, received more than 100 upvotes.
Scholar 2.1 years ago, created an answer that has been accepted. For A: Is there a way to know sequences length when querying ENA programmatically?
Scholar 2.1 years ago, created an answer that has been accepted. For A: Is there a way to know sequences length when querying ENA programmatically?
Scholar 2.1 years ago, created an answer that has been accepted. For A: Is there a way to know sequences length when querying ENA programmatically?
Scholar 2.1 years 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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