Pf7 Package by https://padlet.com/km222/9eag2neeilcixsjs Prioritising further work for the pf7 package en-us 2022-02-15 11:45:54 UTC 2022-02-16 16:46:30 UTC hello@padlet.com https://padlet.net/icons/png/1f33f.png FWS values Notebook km222 https://padlet.com/km222/9eag2neeilcixsjs/wish/2048384250 Convert current FWS code into a notebook that can be easily followed so people can reproduce FWS values

]]> 2022-02-15 11:49:21 UTC https://padlet.com/km222/9eag2neeilcixsjs/wish/2048384250 Regenerate genetic distance matrix km222 https://padlet.com/km222/9eag2neeilcixsjs/wish/2048385953 Notebook showing how to regenerate genetic distance matrix with own parameters

]]> 2022-02-15 11:50:28 UTC https://padlet.com/km222/9eag2neeilcixsjs/wish/2048385953 Tutorial on using pf7 package km222 https://padlet.com/km222/9eag2neeilcixsjs/wish/2049022685 There is a draft of this notebook, but needs reviewed]]> 2022-02-15 16:45:16 UTC https://padlet.com/km222/9eag2neeilcixsjs/wish/2049022685 Why indels are important km222 https://padlet.com/km222/9eag2neeilcixsjs/wish/2049034307 There is an example in the readme explaining why indels are important to include in analysis. There are specific locations used, could translate this example to a notebook

https://www.malariagen.net/sites/default/files/File8_Pf_6_README_20191010.txt]]> 2022-02-15 16:50:07 UTC https://padlet.com/km222/9eag2neeilcixsjs/wish/2049034307 Exploring Metadata km222 https://padlet.com/km222/9eag2neeilcixsjs/wish/2049047244 Something similar to the pf6+ notebooks, giving the data a narrative.

This might already be sufficiently covered by web app]]> 2022-02-15 16:55:23 UTC https://padlet.com/km222/9eag2neeilcixsjs/wish/2049047244 Add own data km222 https://padlet.com/km222/9eag2neeilcixsjs/wish/2049051180 Adding users own data into analysis 
(This could be joint with some of the tasks under reproducing analysis)]]> 2022-02-15 16:56:54 UTC https://padlet.com/km222/9eag2neeilcixsjs/wish/2049051180 Prevalence of drug resistance geographically km222 https://padlet.com/km222/9eag2neeilcixsjs/wish/2049056055 2022-02-15 16:58:58 UTC https://padlet.com/km222/9eag2neeilcixsjs/wish/2049056055 Most common haplotypes km222 https://padlet.com/km222/9eag2neeilcixsjs/wish/2049060461 2022-02-15 17:00:52 UTC https://padlet.com/km222/9eag2neeilcixsjs/wish/2049060461 Genotypes to resistance classification km222 https://padlet.com/km222/9eag2neeilcixsjs/wish/2049066017 something that we already do in Pf6+ (with phenotyper)]]> 2022-02-15 17:03:09 UTC https://padlet.com/km222/9eag2neeilcixsjs/wish/2049066017 Opening the genetic distance matrix km222 https://padlet.com/km222/9eag2neeilcixsjs/wish/2050944030 how to open the npy genetic distance matrix, what is on there and what can you use that info]]> 2022-02-16 14:18:59 UTC https://padlet.com/km222/9eag2neeilcixsjs/wish/2050944030 Generate aa haplotypes from genes km222 https://padlet.com/km222/9eag2neeilcixsjs/wish/2050957748 2022-02-16 14:24:27 UTC https://padlet.com/km222/9eag2neeilcixsjs/wish/2050957748 FWS plot km222 https://padlet.com/km222/9eag2neeilcixsjs/wish/2050976512 Notebook for visualising FWS values]]> 2022-02-16 14:30:13 UTC https://padlet.com/km222/9eag2neeilcixsjs/wish/2050976512 Allele Frequency in gene km222 https://padlet.com/km222/9eag2neeilcixsjs/wish/2051206545 2022-02-16 15:59:54 UTC https://padlet.com/km222/9eag2neeilcixsjs/wish/2051206545 Exporting data as tabular file https://padlet.com/km222/9eag2neeilcixsjs/wish/2051218773 Tutorial on how to export data from Pf7 as a tabular file (for a gene or region of the genome) as many software tools expect tabular genotype files as input.]]> 2022-02-16 16:04:43 UTC https://padlet.com/km222/9eag2neeilcixsjs/wish/2051218773 Produce PCoA plot and add in own samples gw161 https://padlet.com/km222/9eag2neeilcixsjs/wish/2051218966 2022-02-16 16:04:48 UTC https://padlet.com/km222/9eag2neeilcixsjs/wish/2051218966 Quick start https://padlet.com/km222/9eag2neeilcixsjs/wish/2051248206 2022-02-16 16:16:32 UTC https://padlet.com/km222/9eag2neeilcixsjs/wish/2051248206