Lindsay Clark

Get annotation from TxDb?

9

I work for a biotech center where we get a lot of projects in honeybee, so we have our own custom GTF and transcriptome for _Apis mellifera_ that includes several...

Support pedigreed populations

3

I'd like to make a new pipeline that uses pedigree information. Genotype estimates of parents and offspring will iteratively influence genotype priors of parents and offspring. Even for biparental populations,...

Export to additional population genetics formats

3

## Overview There has been some interest in using genotypes called by polyRAD for population genetics analysis. Two pieces of software that have long supported polyploid genotypes are [Structure](https://web.stanford.edu/group/pritchardlab/structure.html) and...

Export to and import from updog

2

It would be nice to have some convenience functions to convert between a `RADdata` object and the input and output of [`updog`](https://github.com/dcgerard/updog). This would allow users to take advantage of...

Getting more than two axes with `ordinate`

10

I'm doing NMDS with `ordinate` and trying to get three axes rather than two. I see in the documentation that I can set `k = 3`. This works with the...

Problem using covariates with mmDS

2

If I run the code: ``` mmDS_res fitVarPartModel -> .fitVarPartModel In addition: Warning message: In DGEList(counts(x), norm.factors = 1/sizeFactors(x)) : norm factors don't multiply to 1 ``` I have checked...