Explore @neherlab Open Source projects

@neherlab

neherlab

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Registered about 10 years ago
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Python
60.4 %

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Jupyter Notebook
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C++
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Java
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Location 🇨🇭 Switzerland
Country Total Rank 185
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C++
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covid19_scenarios

Models of COVID-19 outbreak trajectories and hospital demand

treetime

Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction

Jupyter Notebook

pan-genome-analysis

Processing pipeline for pan-genome visulization and exploration

SARS-CoV-2_variant-reports

Informal summaries of notable SARS-CoV-2 lineages

pangraph

A bioinformatic toolkit to align genome assemblies into pangenome graphs

covid19_scenarios_data

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

treetime_examples

A collection of documented examples using TreeTime

CoV_Seasonality

Model coronavirus seasonality and explore consequences for nCoV dynamics

nextalign

🧬 Viral genome reference alignment

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 is coded efficiently using Fast-Fourier Transforms to speed up recombination operations.

PoissonNMF

ImageJ plugins for blind decomposition of fluorencence microscopy data

ncov-europe

treetime-cloud

HIVEVO_access

python_morbidostat

Control software for a morbidostat reactor based on arduino and python

FluSpeciation

Code for SIR models with antigenic evolution

nextclade_data_workflows

genome-assembly

Bacterial genome assembly pipeline

HIVEVO_figures

SVVC

simple viral variant caller

HIV_time_of_infection

Estimating time of HIV-1 infection from next-generation sequence diversity (code and data)

synmut

Manuscript: Quantifying Selection against Synonymous Mutations in HIV-1 env Evolution.

timetree_viewer

treetool

tool to build and visualize annotated influenza phylogenies based on blab/nextflu

HIVEVO_reversion

Repository for the analysis and figures of Valentin Druelle's paper on HIV-1 reversion

flu_clades

2019-krisp-nextstrain-workshop

Tutorials, data, and results of the 2019 KRISP nextstrain workshop

treetime_validation

EV-D68_sequence_mapping

Code processing and analyzing data from Dyrdak et al, 2019

SC2_variant_rates

analyze substitution rate and mutation behavior within variants.

2019_Yan_RQS_flu_analysis

gisaid_nextstrain

2020_EU1_paper

demo-auspice-tree

Demonstrates how to embed Auspice tree into React application

ratchet

allflu

krisp

visualization repository for the 2019 nextstrain workshop at KRISP

spike-only

Spike-only SARS-CoV-2 Nextstrain build

ncov-simple

BA286

BA.2.86 project with Sigal lab

2018_evd68_paneurope_analysis

Scripts producing figures and analysis of Hodcroft et al, 2020

pid

Manuscript: Challenges with Using Primer IDs to Improve Accuracy of Next Generation Sequencing

nextstrain_base

pipeline components for realtime virus analysis

cluster-mutations

Get mutations in cluster by querying from LAPIS API

enterovirus_nextstrain

2019_Puller_SiteSpecificGTR

sequence_distances

multiflu

interactive flu trees side-by-side

reccoal

Manuscript: Coalescence and genetic diversity in sexual populations under selection

flu-ingest

CompBio2023

simple viral consensus assembly

ctlfit

Manuscript: Inferring HIV Escape Rates from Multi-Locus Genotype Data

EV_D68_analysis

scripts that generate figures for Dyrdak et al 2018 manuscript

TreeKnit-web

enterovirus_a71

HIVEVO_reservoir

Establishment and stability of the latent HIV-1 DNA reservoir

HIVEVO_recombination

Scripts created to analyse recombination in HIVEVO dataset

Jupyter Notebook