User: Renesh
Renesh • 1.5k
- Reputation:
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- Location:
- United States
- Last seen:
- 5 days, 17 hours ago
- Joined:
- 4 years, 5 months ago
- Email:
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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
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... 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
Renesh • 1.5k
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... 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
Renesh • 1.5k
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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
Renesh • 1.5k
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... 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
Renesh • 1.5k
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... Thanks for suggestions. NCBI SRA toolkit lastet release contains `fasterq-dump` which provides multithreading option for faster download. ...
written 9 weeks ago by
Renesh • 1.5k
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2
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... 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
Renesh • 1.5k
1
vote
9
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... How to use NCBI SRA toolkit effectively: Read this post https://reneshbedre.github.io/blog/fqutil.html ...
written 9 weeks ago by
Renesh • 1.5k
1
vote
2
answers
1.2k
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2
answers
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
Renesh • 1.5k
0
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2
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1.5k
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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
Renesh • 1.5k
6
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2
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7.7k
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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
Renesh • 1.5k
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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