neherlab

Repositories

• covid19_scenarios

  Models of COVID-19 outbreak trajectories and hospital demand

  open-source science data opensource research simulation model
  TypeScript MIT 323 1,259 35 (32 issues need help) 11 Updated Jun 3, 2020

• ncov-swiss

  Forked from nextstrain/ncov

  Nextstrain build for novel coronavirus SARS-CoV-2
  Python MIT 274 0 0 0 Updated Jun 3, 2020

• HIVEVO_access
  Python MIT 3 4 2 0 Updated Jun 1, 2020

• treetime

  Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction

  phylogenetics
  Python MIT 28 73 6 1 Updated May 31, 2020

• covid19_scenarios_data Archived

  Data preprocessing scripts and preprocessed data storage for COVID-19 Scenarios project

  open-source science data opensource research simulation model
  Python 39 42 0 0 Updated Apr 1, 2020

• CoV_Seasonality

  Model coronavirus seasonality and explore consequences for nCoV dynamics
  TeX 4 11 0 0 Updated Mar 14, 2020

• 2019_Puller_SiteSpecificGTR
  TeX 1 1 0 0 Updated Jan 18, 2020

• SVVC

  simple viral variant caller
  Python MIT 2 2 0 0 Updated Jan 7, 2020

• EV-D68_sequence_mapping

  Code processing and analyzing data from Dyrdak et al, 2019
  Python MIT 1 1 0 0 Updated Jan 6, 2020

• 2018_evd68_paneurope_analysis

  Scripts producing figures and analysis of Hodcroft et al, 2020
  Python 1 1 0 0 Updated Jan 6, 2020

• pan-genome-analysis

  Processing pipeline for pan-genome visulization and exploration
  Python GPL-3.0 22 64 14 0 Updated Dec 28, 2019

• pan-genome-visualization

  Forked from wdingx/pan-genome-visualization

  Visualization of the pan-genome output by panX
  JavaScript GPL-3.0 15 37 1 0 Updated Nov 27, 2019

• treetime_web

  Forked from pausag/treetime_web
  JavaScript 2 1 0 0 Updated Sep 2, 2019

• gisaid_nextstrain
  Python 1 1 0 0 Updated Aug 27, 2019

• FluSpeciation

  Code for SIR models with antigenic evolution
  MATLAB GPL-3.0 6 2 0 0 Updated Aug 8, 2019

• 2019_Yan_RQS_flu_analysis
  Python 1 1 0 0 Updated Aug 8, 2019

• treetime_examples

  A collection of documented examples using TreeTime
  Python 8 5 1 0 Updated Jul 30, 2019

• python_morbidostat

  Control software for a morbidostat reactor based on arduino and python
  Python 2 3 0 0 Updated May 22, 2019

• allflu
  1 1 0 0 Updated Mar 14, 2019

• krisp

  visualization repository for the 2019 nextstrain workshop at KRISP
  1 1 0 0 Updated Jan 25, 2019

• ffpopsim

  FFPopSim is a collection of C++ classes and a Python interface for efficient simulation of large populations, in particular when the product of mutation rate and population size is larger than one. It consists of one library for individual-based simulations, and a complementary one for simulation of the entire genotype distribution. The latter i…
  C++ GPL-3.0 9 9 0 1 Updated Jan 17, 2019

• 2019-krisp-nextstrain-workshop

  Tutorials, data, and results of the 2019 KRISP nextstrain workshop
  Python 1 2 0 0 Updated Jan 16, 2019

• EV_D68_analysis

  scripts that generate figures for Dyrdak et al 2018 manuscript
  Python MIT 1 1 0 0 Updated Dec 19, 2018

• betatree

  Forked from rneher/betatree

  Generate and analyze beta coalescent trees
  Python MIT 4 0 0 0 Updated Dec 17, 2018

• enterovirus_nextstrain
  Python 1 1 0 0 Updated Sep 11, 2018

• HIV_fitness_landscape

  Forked from iosonofabio/HIV_fitness_landscape

  Analysis of fitness landscape of HIV-1 from longitudinal data
  Python 4 2 0 0 Updated Jul 1, 2018

• multiflu

  interactive flu trees side-by-side
  JavaScript MIT 2 2 1 0 Updated Jan 31, 2018

• treetime_validation
  Python MIT 1 1 1 0 Updated Oct 31, 2017

• HIV_time_of_infection

  Estimating time of HIV-1 infection from next-generation sequence diversity (code and data)
  Python MIT 2 3 0 0 Updated Sep 27, 2017

• HIVEVO_reservoir

  Establishment and stability of the latent HIV-1 DNA reservoir
  TeX MIT 2 1 0 0 Updated Feb 11, 2017