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pophelper

pophelper is an R package and web app to analyse and visualise population structure. See the project website for more details.

Disclaimer

The pophelper R package is offered free and without warranty of any kind, either expressed or implied. I will not be held liable to you for any damage arising out of the use, modification or inability to use this program. pophelper R package can be used, redistributed and/or modified freely for non-commercial purposes subject to the original source being properly cited. Licensed under GPL-3. Please make sure you verify all your results.

Contact

If you have an comments, suggestions, corrections or ideas on ways to improve or extend this package, feel free to contact me. Submit a report on the Github issues page.

2019 | Roy M Francis

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Version

Version

2.3.0

License

GPL-3

Issues

25

Pull Requests

1

Stars

150

Forks

37

Maintainer

Roy Francis

Last Published

December 29th, 2020

Functions in pophelper (2.3.0)

readQ

Convert run files (q-matrices) to qlist.
mergeQ

Merge replicate runs of the same K
joinQ

Combine two or more qlist objects into one
readQClumpp

Convert CLUMPP format numeric text files to qlist.
readQBasic

Convert delimited text files to qlist.
readQTess3

Convert TESS3 R object to pophelper qlist.
readQStructure

Convert STRUCTURE run files to qlist.
readQTess

Convert TESS cluster files to qlist.
sortQ

Sort runs in a qlist based on an attribute
clumppExport

Generate CLUMPP output from a qlist
plotQ

Generate barplots from qlists.
splitQ

Split a qlist into sublists by attribute
summariseQ

Summarise a tabulated dataframe
plotQMultiline

Plot a qlist as individual-level multiline barplot
tabulateQ

Tabulate runs from a qlist
verifyGrplab

Verify a grplab dataframe
readQBaps

Convert BAPS cluster files to qlist.
distructColours

Vector of 90 Distruct colours
is.qlist

Verify if a qlist is formatted correctly.
collectClumppOutput

Collect CLUMPP output files from multiple folders
distructExport

Generate files for DISTRUCT.
as.qlist

Convert a qlist or qlist-like list to a valid qlist.
collectRunsTess

Collect TESS cluster run files from multiple folders
analyseQ

Analyse STRUCTURE, TESS, BAPS or BASIC text runs. Wrapper around several smaller functions.
evannoMethodStructure

Perform the Evanno method for STRUCTURE runs.
alignK

Align clusters