molpopgen/devnotes

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Created almost 10 years ago
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molpopgen/devnotes

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Notes/tips/tricks/obscure hints related to software development.

libsequence

libsequence: a C++ class library for evolutionary genetic analysis

BigDataFormats

Tutorial on programming or "big data"/bioinformatics

fwdpy11

Forward-time simulation in Python using fwdpp

fwdpp

fwdpp is a C++ template library for implementing efficient forward-time population genetic simulations

gimp_scripts

Plugins for GIMP

fwdpy

forward-time population genetic simulation in python

msstats

msstats calculates many common popgen summary statistics from the output of the coalescent simulation "ms".

pylibseq

Python interface to libsequence via pybind11

pecnv

C++ tools for calling structural variants from PE mapping of short reads.

md2Canvas

Examples of canvas questions written in Markdown

Rcode4teaching

R code that I use for teaching and illustration of population genetic concepts.

fwdpy11_arg_example

Example of tracking the ARG during forward simulations. Implementation is a Python package using fwdpp, fwdpy11, msprime, and pybind11.

cython_mcpp

Glue layer between Cython and C++11/14/17

buRden

Rcpp functions for performing "burden" tests.

ABCreg

Automating approximate Bayesian computation by local linear regression

sweepsims

A collection of coalescent simulations of selective sweeps written over the years. (See wiki for citation info, please.)

analysis

Programs for the (pre-NGS-era) analysis of population-genetic data.

newgene

The simulation code used in doi:10.1534/genetics.107.074948

landscape

Explicit landscape simulations using fwdpp

text2qti_example

text2qti_example

sequtils

Tools for manipulation of (pre-NGS-era) sequence data. (Probably only for old folks at this point in time...)

travis_test

How to get a travis yml file to do what I want.