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Installation: Tax4Fun2 package are not found and github repository is not maintained anymore

Hi everyone!

I have tried to find the R package Tax4Fun2 from the paper (https://pubmed.ncbi.nlm.nih.gov/33902725/) . This R package lets analizes the microbiome in an easy way to predict functional profiles from metagenomic 16S rRNA data.

However, I have not found the package in R CRAN packages, neither in the github refered in the original paper (https://github.com/bwemheu/Tax4Fun2) or the Tax4Fun page (http://tax4fun.gobics.de/).

I am looking for Tax4Fun2 because gives higher accuracies than PICRUSt and Tax4Fun.

Any help will be grateful!

Best,

E

tax4fun2
• 10,336 views • link
updated by Ram Ram • written by Elsa • Elsa

Tax4Fun2 because gives higher accuracies than PICRUSt

They tested Tax4Fun2 (2020) against PICRUSTt version 1, which is very old (2013). In this paper on the other hand, Tax4Fun2 actually performs worse than PICRUSt2

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updated by Ram Ram • written by andres.firrincieli andres.firrincieli

Hello , I also have the same problem. Did you find repositories for installing T4F2 and T4F please ? if not what did you use as an alternative and are you satisfied with the results of the alternative tool ? please answer !!

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written by safeassli • safeassli

Thank you so much. I downloaded it and renamed it, now I need to download and install prodigal_v2.6.3

Thank so much

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written by Mai Abdelmonem • Mai Abdelmonem 
assignFunction(genome_file = "OneProkaryoticGenome.fasta", 
               file_extension = "fasta", 
               path_to_reference_data = "Tax4Fun2_ReferenceData_v2", 
               num_of_threads = 1, fast = TRUE)

chmod: Tax4Fun2_ReferenceData_v2/TOOLS/prodigal_v2.6.3/prodigal.macos: No such file or directory
chmod: Tax4Fun2_ReferenceData_v2/TOOLS/diamond_v0.9.24/diamond.macos: No such file or directory

Error in system(command = paste(path_to_diamond, "help"), intern = T,  : 
  error in running command

what should i do? I have Tax4Fun2_ReferenceData_v2/TOOLS/prodigal_v2.6.3/prodigal.macos (renamed it prodigal), Tax4Fun2_ReferenceData_v2/TOOLS/diamond_v0.9.24/diamond.macos (renamed it: diamond)

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updated by GenoMax GenoMax • written by Mai Abdelmonem • Mai Abdelmonem

Mai Abdelmonem : Stop posting errors and comments as new answers. Submit answer is only for new answers to the original question.

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written by GenoMax GenoMax

2 answers

I searched GitHub for Tax4Fun2 and found this:

https://github.com/ZihaoShu/Tax4Fun2

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written by Mensur Dlakic Mensur Dlakic

This is a repository for a project that uses tax4fun2, not the repository that documents T4F and provides it for download/installation. All repositories for installing T4F2 and T4F seem to have been removed from the internet in the last few months.

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written by djeppschmidt • djeppschmidt

Hello , I also have the same problem. Did you find repositories for installing T4F2 and T4F please ? if not what did you use as an alternative and are you satisfied with the results of the alternative tool ? please answer !!

• 0 views • link
written by safeassli • safeassli

Hello! I was confused as well.

When installing Tax4Fun2, Follow this: https://github.com/songweizhi/Tax4Fun2_short_tutorial?search=1

• 0 views • link
written by Viviane • Viviane

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