Repositories list

• H5_titers_vs_imprinting

  Public
  We ask if titers to H5 are more strongly associated with imprinting/year of birth than with age, in a collaboration led by the Hensey lab.

  R

  •0•0•0•0•Updated Oct 21, 2024Oct 21, 2024

• population_immunity_predicting_flu

  Public
  R

  •0•0•0•0•Updated Oct 2, 2024Oct 2, 2024

• lab_handbook

  Public
  TeX

  •

  Creative Commons Zero v1.0 Universal

  •2•1•0•2•Updated Jul 31, 2024Jul 31, 2024

• OAS-strain-replacement

  Public
  Code for reproducing results in "A speed limit on serial strain replacement from Original Antigenic Sin"

  Mathematica

  •

  MIT License

  •0•2•0•0•Updated May 29, 2024May 29, 2024

• FluVE_repeatvac_public

  Public
  HTML

  •0•3•0•0•Updated Apr 10, 2024Apr 10, 2024

• flu_strain_compare

  Public
  Visualizing mutations and PNGS changes between two strains

  ceirr-cmc

  Python

  •0•2•1•2•Updated Jan 18, 2024Jan 18, 2024

• hong_kong_publc_data_site

  Public
  Hong Kong flu data

  R

  •0•0•0•0•Updated Aug 16, 2023Aug 16, 2023

• v_gene_selection

  Public
  V gene usage in mice infected with flu.

  R

  •0•1•0•0•Updated Jul 5, 2023Jul 5, 2023

• Nextstrain-on-HPC

  Public
  How to install and run Nextstrain in HPC environments

  0•1•0•0•Updated Jan 10, 2023Jan 10, 2023

• digital-repeatability

  Public
  Materials for digital repeatability training

  0•0•0•0•Updated Dec 21, 2022Dec 21, 2022

• imprinting

  Public
  Code to reconstruct influenza imprinting probabilities from 1918 to present

  ceirr-cmc

  HTML

  •

  Other

  •0•0•0•0•Updated Dec 17, 2022Dec 17, 2022

• code-structure-training

  Public
  Materials for code structure training

  ceirr-cmc

  0•0•0•0•Updated Nov 18, 2022Nov 18, 2022

• version-control-training

  Public
  Materials for version control training

  ceirr-cmc

  Python

  •1•0•0•0•Updated Sep 30, 2022Sep 30, 2022

• antigenic-maps

  Public
  Code to infer antigenic maps from titer panel data

  R

  •0•1•0•0•Updated Sep 9, 2022Sep 9, 2022

• evolution_of_mutability

  Public
  Self-contained, publication-ready repository for the evolution of mutability project.

  Python

  •0•0•0•0•Updated Sep 9, 2022Sep 9, 2022

• imprinting_tutorial_bookdown

  Public
  Bookdown document with a lesson on calculating imprinting probabilities

  CSS

  •0•0•0•0•Updated Jul 13, 2022Jul 13, 2022

• Influenza-immune-dynamics

  Public
  Code to accompany the manuscript "Age-specific differences in the dynamics of protective immunity to influenza"

  R

  •3•7•0•0•Updated Jul 5, 2022Jul 5, 2022

• refit_antigenic_seniority

  Public
  Code to refit the models in Lessler et al. 2012, PLOS Pathogens

  HTML

  •0•0•0•0•Updated Jun 21, 2022Jun 21, 2022

• data-emporium

  Public
  A place to keep track of public or confidential datasets available to the Cobey Lab.

  1•1•0•0•Updated Apr 29, 2022Apr 29, 2022

• FluAImprinting

  Public
  Data and code for Arevalo et al., 2019

  Jupyter Notebook

  •

  Apache License 2.0

  •1•2•0•0•Updated Apr 5, 2022Apr 5, 2022

• psc_repertoire

  Public
  Analysis of B cell repertoires from patients with primary sclerosing cholangitis (PSC). Collaboration led by Dustin Shaw and Bana Jabri

  R

  •1•1•0•0•Updated Mar 25, 2022Mar 25, 2022

• vaccine-manuscript

  Public
  Java

  •0•1•0•0•Updated Aug 27, 2021Aug 27, 2021

• antigen-vaccine

  Public
  Java

  •1•1•0•0•Updated Aug 27, 2021Aug 27, 2021

• covid_IL

  Public
  R

  •

  Apache License 2.0

  •1•0•0•0•Updated Apr 8, 2021Apr 8, 2021

• egg_antibodies

  Public
  Analysis of non-templated insertions in glycan-binding antibodies of humans vaccinated with influenza

  R

  •0•0•0•0•Updated Jan 27, 2021Jan 27, 2021

• rough_rt

  Public
  Code for rough estimates from data

  R

  •0•1•0•0•Updated Jan 21, 2021Jan 21, 2021

• epidemic-deconvolution

  Public
  Example code for deconvolving epidemic time series

  R

  •2•5•0•0•Updated Dec 30, 2020Dec 30, 2020

• Rt_estimation

  Public
  Code to test Rt estimates against synthetic data

  R

  •15•16•1•0•Updated Nov 30, 2020Nov 30, 2020

• Flu-Middle-aged

  Public
  Data and analyses for Gouma et al

  Python

  •0•0•0•0•Updated Jul 22, 2020Jul 22, 2020

• covid19-forecast-hub

  Public
  Projections of COVID-19, in standardized format

  JavaScript

  •

  Other

  •327•0•0•0•Updated May 20, 2020May 20, 2020