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3 votes

Filtering columns from large file based on a column list

It's really just count[,col$V1]. Please learn about basic subsetting of columns and rows, it's simple yet powerful.
ATpoint's user avatar
  • 1,078
3 votes

Filtering columns from large file based on a column list

You can save time and memory by preprocessing your file before loading it into R. Use miller toolkit to manipulate csv or tab-delimited files using column names. ...
Timur Shtatland's user avatar
1 vote

PANTHER FUNCTIONAL CLASSIFICATION in R

One approach is to get the gene's sequence (DNA/AA) and use the interproscan API (e.g., https://www.ebi.ac.uk/Tools/common/tools/help/index.html?tool=iprscan5) with the httr2 library in R to POST ...
Jacob Krol's user avatar
1 vote

getting NCBI TAXname by R

I developed the function and it worked perfectly, ...
Farzad Beikpour's user avatar
1 vote

biomarRT conversion of symbols

My background in coding is more extensive in Python. If you have Python skills, I can say for sure, use the Bioservices library: from bioservices import BioMart ...
Rachel Sweeney's user avatar
1 vote

Intepreting and applying ordinal logistic regression coefficients to calculate probabilities?

Its a while since I've done GLM because ML is the method of choice. Question1 Yes multi-linear regression is an approximate description of GLM. Generally the weights simply mean whether a feature is ...
M__'s user avatar
  • 11.9k
1 vote

Filtering columns from large file based on a column list

Below code works perfectly of me. ...
bioinfonext's user avatar
1 vote

Mendelian randomization

I understand linkage disequilibrium (LD) versus panmixia, which the technical term for Mendelian randomisation and for humans PLINK is a population package. The best outcome is a correlation between ...
M__'s user avatar
  • 11.9k
1 vote

error in downloading the annotation of sequences on NCBI

You could use the tryCatch function to handle inputs that throw an error. A good example on how to write them can be found here. Though the message indicates it's a ...
dthorbur's user avatar
  • 111

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