Antigenic Cartography

slurm-pipeline

A Python class for scheduling SLURM jobs

Racmacs

Racmacs R package for performing antigenic cartography

dark-matter

Virus discovery

ncbi-taxonomy-database

How to make a mysql or sqlite database of NCBI taxonomy data for use with the dark-matter lineage fetcher

ablandscapes

An R package for making antibody landscapes

acmacs-build

acmacs-py

Python module for acmacs

acutilsLite

lispmds

LispMDS

mapping_SARS-CoV-2_antigenic_relationships_and_serological_responses

roessler_netzl_et_al2023

This repository contains the code for the manuscript "Characterizing SARS-CoV-2 neutralization profiles after bivalent boosting using antigenic cartography" by Annika Rössler, Antonia Netzl, et. al., 2023

acmacs-api

API (mostly for websockets based interface in acmacs-webserver) to access acmacs-c database

acmacs-base

Scripts and utilities for acmacs-d modules

acmacs-chart-2

Accessing chart data

acmacs-draw

Drawing on an image

acmacs-map-draw

Drawing antigenic maps

acmacs-tal

Tree et al.

acmacs-whocc

Programs and scripts for WHO CCs chains

acmacs-whocc-data

Data files with WHO CC related data and library to read them

branche_et_al2023

This repository contains the code to construct antibody landscapes for the CoVAIL clinical trial.

comparison_of_sars-cov-2_antigenic_characteristics

hidb-5

HiDb maker

midtools

Multiple Infection Detection - Python for detecting multiple infections from sequence reads and trying to pick them apart

omicron-neutralization-paper

antigenic cartography and antibody landscapes related code and figures for the paper Analysis of SARS-CoV-2 Omicron Neutralization Data up to 2022-28-01

roessler_netzl_et_al2022

Code repository for "BA.2 and BA.5 omicron differ immunologically from both BA.1 omicron and pre-omicron variants" by Roessler, A., Netzl, A., et al.

roessler_netzl_et_al2023a

This repository holds the code for the species comparison between human and hamster SARS-CoV-2 neutralisation data, published by Rössler, Netzl et al.

roessler_netzl_et_al2024

Code repository for the non-human primate antigenic cartography manuscript by Rössler, Netzl, et al. 2024

seqdb-3

Set of tools to build and query sequence database v3

seqgen

Python code for generating sequences in FASTA format

signature-page

Programs to import phylogenetic tree and draw it on a tree or signature page