User: Renesh
Renesh • 1.9k
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- Joined:
- 5 years, 11 months ago
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Posts by Renesh
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128
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... Can you please provide the one or few sequences containing "TT[TA]TTGC..CCCACTG"? ...
written 3 days ago by
Renesh • 1.9k
1
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2
answers
162
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2
answers
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 3 days ago by
Renesh • 1.9k
0
votes
1
answer
108
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1
answers
... 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 4 weeks ago by
Renesh • 1.9k
1
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4
answers
4.4k
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 4 weeks ago by
Renesh • 1.9k
0
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0
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394
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0
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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 11 weeks ago by
Renesh • 1.9k
0
votes
1
answer
191
views
1
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... https://onlinelibrary.wiley.com/doi/full/10.1002/pld3.191 ...
written 8 months ago by
Renesh • 1.9k
0
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16
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48k
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16
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... Try this for proportional Venn diagrams https://reneshbedre.github.io/blog/venn.html ...
written 8 months ago by
Renesh • 1.9k
0
votes
1
answer
219
views
1
answers
... You need to add a new line character `\n` explicitly. Which programming language you are using? Provide your code to answer your question perfectly. ...
written 8 months ago by
Renesh • 1.9k
0
votes
1
answer
186
views
1
answers
... As I mentioned in my answer, you can use the similarity approach (BLAST) to identify gene families. But you will miss a lot of genes that can be grouped into gene families. The similarity approach would not able to identify divergent or distantly related homologs effectively. The domain-based approa ...
written 8 months ago by
Renesh • 1.9k
0
votes
1
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1.0k
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1
answers
... Yes, you can choose a career as data analysts with your Msc Bioinformatics degree. It is a good choice. You can work in Academics, Industries, Hospitals, and genomics research centers. In addition, you can also opt to pursue a Ph.D. in Bioinformatics. ...
written 8 months ago by
Renesh • 1.9k
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For A: Does read-depth refer to a fold?
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For Cufflink p-value using blind dispersion method
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For A: Microarray to Protein Interaction Network
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For A: Is there a way to know sequences length when querying ENA programmatically?
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For A: Volcano Plot from DEseq2
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For Gene expression units explained: RPM, RPKM, FPKM and TPM
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For Gene expression units explained: RPM, RPKM, FPKM and TPM
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For A: Does read-depth refer to a fold?
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