User: Renesh

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Renesh1.9k
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Posts by Renesh

<prev • 201 results • page 1 of 21 • next >
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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 3 days 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 3 days 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 4 weeks 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 4 weeks 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 11 weeks 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 8 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 8 months ago by Renesh1.9k
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Comment: C: Moving sequence in to next line in multi fasta file
... 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 Renesh1.9k
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Comment: C: How to group genes in a single genome into gene families?
... 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 Renesh1.9k
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Answer: A: Bioinformatics to Data Analyst
... 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 Renesh1.9k

Latest awards to Renesh

Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Masters Ideas in Computer Science that tackles Bioinformatics Problem
Appreciated 7 months ago, created a post with more than 5 votes. For A: Does read-depth refer to a fold?
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Does read-depth refer to a fold?
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: How do you organize your articles?
Popular Question 17 months ago, created a question with more than 1,000 views. For Cufflink p-value using blind dispersion method
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Microarray to Protein Interaction Network
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Masters Ideas in Computer Science that tackles Bioinformatics Problem
Epic Question 19 months ago, created a question with more than 10,000 views. For Extract specific patter from string in MySQL:
Scholar 20 months ago, created an answer that has been accepted. For A: Is there a way to know sequences length when querying ENA programmatically?
Scholar 20 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 20 months ago, created an answer that was upvoted at least 5 times. For A: Volcano Plot from DEseq2
Scholar 20 months ago, created an answer that has been accepted. For A: Is there a way to know sequences length when querying ENA programmatically?
Appreciated 20 months ago, created a post with more than 5 votes. For A: Does read-depth refer to a fold?
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: Masters Ideas in Computer Science that tackles Bioinformatics Problem
Librarian 20 months ago, created a post with more than 10 bookmarks. For Gene expression units explained: RPM, RPKM, FPKM and TPM
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: Masters Ideas in Computer Science that tackles Bioinformatics Problem
Appreciated 2.2 years ago, created a post with more than 5 votes. For A: Does read-depth refer to a fold?
Prophet 2.2 years ago, created a post with more than 20 followers. For Gene expression units explained: RPM, RPKM, FPKM and TPM
Epic Question 2.2 years ago, created a question with more than 10,000 views. For Extract specific patter from string in MySQL:
Epic Question 2.4 years ago, created a question with more than 10,000 views. For Extract specific patter from string in MySQL:
Great Question 2.4 years ago, created a question with more than 5,000 views. For Gene expression units explained: RPM, RPKM, FPKM and TPM
Teacher 2.8 years ago, created an answer with at least 3 up-votes. For A: Masters Ideas in Computer Science that tackles Bioinformatics Problem
Popular Question 2.8 years ago, created a question with more than 1,000 views. For How to use seek() with Biopython SeqIO object
Popular Question 2.8 years ago, created a question with more than 1,000 views. For Cufflink p-value using blind dispersion method
Appreciated 2.8 years ago, created a post with more than 5 votes. For A: Does read-depth refer to a fold?

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