User: Renesh
Renesh • 1.9k
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Posts by Renesh
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... 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
Renesh • 1.9k
0
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1
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... 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
Renesh • 1.9k
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3
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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
Renesh • 1.9k
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225
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... Can you please provide the one or few sequences containing "TT[TA]TTGC..CCCACTG"? ...
written 11 weeks ago by
Renesh • 1.9k
1
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2
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428
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2
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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
Renesh • 1.9k
0
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1
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210
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1
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... 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
Renesh • 1.9k
1
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4
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4.7k
views
4
answers
... 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
Renesh • 1.9k
0
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0
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798
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... `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
Renesh • 1.9k
0
votes
1
answer
217
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1
answers
... https://onlinelibrary.wiley.com/doi/full/10.1002/pld3.191 ...
written 10 months ago by
Renesh • 1.9k
0
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17
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49k
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17
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... Try this for proportional Venn diagrams https://reneshbedre.github.io/blog/venn.html ...
written 10 months ago by
Renesh • 1.9k
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