Admixtools New Tool! - qpAdm Assistant

[Jovialis]

Download here

I created an HTML/Javascript-based tool with ChatGPT for easier qpAdm/qpWave R script production to help streamline downstream analysis. It lets users load an IND or FAM file, browse and search populations and samples, drag and drop populations into Target, Source, and Right/Outgroup groups, and customize the analysis settings.

The tool then generates a complete R pipeline covering F2 extraction, qpWave verification, and two qpAdm methods: precomputed common-SNP F2 analysis and an ALLSNPS sensitivity analysis. It generates the scripts locally; the user supplies their own dataset and runs the resulting code in R.

 

[Duarte]

View attachment 19929

Download here

I created an HTML/Javascript-based tool with ChatGPT for easier qpAdm/qpWave R script production to help streamline downstream analysis. It lets users load an IND or FAM file, browse and search populations and samples, drag and drop populations into Target, Source, and Right/Outgroup groups, and customize the analysis settings.

The tool then generates a complete R pipeline covering F2 extraction, qpWave verification, and two qpAdm methods: precomputed common-SNP F2 analysis and an ALLSNPS sensitivity analysis. It generates the scripts locally; the user supplies their own dataset and runs the resulting code in R.

Magnificent work, Jovialis, as always. Thank you for making the tool available to Eupedia members. The interface is very intuitive and easy to use. Unfortunately, I don't yet feel capable of generating a good merged dataset file using the PLINK 2.0 tool and the corresponding `--pmerge` command. I had to resort to a cloud-based processing site that runs tasks remotely. The merged dataset file remains hosted on the site for use with the online its own Admixtools, but I cannot download it to my PC. These are the limitations imposed by the site owner for the free service provided to the user. In exchange, they retain raw data of the user for analysis, while guaranteeing the security, integrity and no-sharing of the data that stay hosted on European servers.

 

[Jovialis]

Magnificent work, Jovialis, as always. Thank you for making the tool available to Eupedia members. The interface is very intuitive and easy to use. Unfortunately, I don't yet feel capable of generating a good merged dataset file using the PLINK 2.0 tool and the corresponding `--pmerge` command. I had to resort to a cloud-based processing site that runs tasks remotely. The merged dataset file remains hosted on the site for use with the online its own Admixtools, but I cannot download it to my PC. These are the limitations imposed by the site owner for the free service provided to the user. In exchange, they retain raw data of the user for analysis, while guaranteeing the security, integrity and no-sharing of the data that stay hosted on European servers.

If possible I would endeavor to create an interface for FASTQ to Eigenstrat/PLINK. It's a very complex process and it would be challenging to pin down.