Software

 

Our gitlab group

https://gitlab.inria.fr/ml_genetics/public
For miscellaneous software, code, article data

DNADNA: Deep Neural Networks for DNA

https://www.lri.fr/logiciel.brevet.php?log=230

The beta version is out: https://gitlab.com/mlgenetics/dnadna 

There's a quickstart tutorial that you can try out! Please let us know what you think, we happily welcome feedback.

Preprint: T Sanchez*, EM Bray*, P Jobic, J Guez, A-C Letournel, G Charpiat, J Cury°, F Jay° (2021) Dnadna: Deep Neural Architecture for DNA - A deep learning framework for population genetic inference https://hal.archives-ouvertes.fr/hal-03352910v2

There is also a repo specific to the code from the Sanchez et al 2020 paper : repo ; prediction notebook

I'd like to highlight the excellent work by Erik Madison Bray and I'm very happy that they obtained a long-term position at LISN.  It should be easier for talented people to get such positions. The new French research plan (LPPR) does not seem to go in this direction!

Bacterial SLiMulator

by Jean Cury (LRI) et al
J Cury, B Haller, G Achaz, F Jay (2020). Simulation of bacterial populations with SLiM.   BioRxiv Preprint   Simulator
 

tfa: factor analysis of temporal samples

https://github.com/bcm-uga/tfa

with Olivier François (TIMC-IMAG)

PoPS: Predictions of Population Structure Version 1.2

Inferring population genetic structure and its relationships with environmental variables. Predicting changes in population structure


POPS is a method I developed during my PhD. It has a nice and friendly graphical interface. I also provide some post-processing R scripts to plot colorful maps.

The POPS program performs inference of ancestry distribution models. It uses a TESS-like interface to compute individual cluster membership and admixture proportions based on multilocus genotype data and their correlation with environmental and geographical variables. Similarly to species distribution models, POPS provides routines to project cluster memberships and admixture proportions under scenarios of environmental change. Typical uses of POPS are for evaluating how the population genetic structure of a species could be modified by climate change, or testing hypotheses about local adaptation and ecological speciation.

For more information or to download the software go to POPS page

Inscription à : Articles (Atom)