User: Renesh

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Renesh1.9k
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Posts by Renesh

<prev • 204 results • page 1 of 21 • next >
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Answer: A: Extract sequences from a list of ID
... You can also try Python package `bioinfokit` (v1.0.2 or later) for extracting the sequences from the FASTA file (check how to install https://reneshbedre.github.io/blog/howtoinstall.html#how-to-install) `from bioinfokit.analys import fasta` `fasta.extract_seq(file='Trinity.fasta', id='id.txt')` C ...
written 5 days ago by Renesh1.9k
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Comment: C: EdgeR analysis with CPM normalzed counts
... Hi, If you have CPM normalized counts from edgeR, then it should be already normalized for library size. You do not need to again calculate `calcNormFactors` you can see here https://reneshbedre.github.io/blog/expression_units.html#tmm-trimmed-mean-of-m-values ...
written 4 weeks ago by Renesh1.9k
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Comment: C: Plant orthologous genes
... You can have the orthologous genes in Arabidopsis for all rice genes at Phytozome database (https://phytozome.jgi.doe.gov/pz/portal.html#) The best way is to do the reciprocal BLAST analysis of the transcript sequences and retain the best hits from two species to identify the orthologous genes. ...
written 10 weeks ago by Renesh1.9k
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Comment: C: Python: regular expression searching error
... Can you please provide the one or few sequences containing "TT[TA]TTGC..CCCACTG"? ...
written 11 weeks ago by Renesh1.9k
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Answer: A: Heatmap for gene expression
... Hi akashagri19, Thank you for using the bioinfokit for heatmap. You need to first import your data as a pandas dataframe. You can not use `get_data` as it is for internal example datasets. Import your dataset as import pandas as pd df = pd.read_csv('your_data.csv') # for CSV file df ...
written 11 weeks ago by Renesh1.9k
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Answer: A: Confused about the AF tag in VCF from samtools/bcftools mpileup
... The AF in bcftools and GATK should be the same. AF is calculated as AC/AN, where AC is total ALT allele count and AN is total allele called in genotypes. If you have only one genotype or sample, AF = 1 for GT = 1/1 refers to you have 2 ALT allele and the total is also 2 alleles. Similarly, AF=0.5 fo ...
written 3 months ago by Renesh1.9k
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Answer: A: perplexity value in t-sne algorithm
... In most cases, the default value of the perplexity parameter in t-SNE is 30. The standard range for the perplexity parameter is between 10-100. But, you can change this value based on the size of your datasets. In the context of scRNA-seq, setting a perplexity value of 1% of sample size (number of ...
written 3 months ago by Renesh1.9k
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Comment: A: DeSeq2 error: counts matrix should be numeric, currently it has mode: character
... `all(is.numeric(cts))` should return True count matrix should be numeric (integer). How did you import your table? using `read.csv` only (for CSV file)? Try this: Import your table for CSV file as cts = as.matrix(read.csv('table_file', row.names='gene_column_name')) ...
written 5 months ago by Renesh1.9k
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Comment: C: Assigning proteins to pre-computed gene families
... https://onlinelibrary.wiley.com/doi/full/10.1002/pld3.191 ...
written 10 months ago by Renesh1.9k
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Answer: A: Tool to generate proportional Venn Diagrams?
... Try this for proportional Venn diagrams https://reneshbedre.github.io/blog/venn.html ...
written 10 months ago by Renesh1.9k

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Appreciated 4 weeks ago, created a post with more than 5 votes. For A: Does read-depth refer to a fold?
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: Masters Ideas in Computer Science that tackles Bioinformatics Problem
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Scholar 22 months ago, created an answer that has been accepted. For A: Is there a way to know sequences length when querying ENA programmatically?
Scholar 22 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 23 months ago, created an answer that was upvoted at least 5 times. For A: Volcano Plot from DEseq2
Scholar 23 months ago, created an answer that has been accepted. For A: Is there a way to know sequences length when querying ENA programmatically?
Appreciated 23 months ago, created a post with more than 5 votes. For A: Does read-depth refer to a fold?
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