Bedford Lab (@blab)

Top repositories

1

nextflu

Real-time tracking of influenza evolution
JavaScript
88
star
2

sars-like-cov

This is a one-off Nextstrain build for SARS-like coronaviruses
Python
82
star
3

blotter

bedford lab research
HTML
67
star
4

rt-from-frequency-dynamics

Mathematica
46
star
5

beta-cov

One-off nextstrain build for betacoronavirus
Python
23
star
6

global-migration

Analysis of global migration patterns of seasonal influenza viruses
Mathematica
22
star
7

ncov-phylodynamics

Phylodynamic estimation of nCoV incidence and prevalence
Mathematica
19
star
8

zika-seq

Pipelines to do MinION sequencing of Zika virus
Python
15
star
9

ncov-wa-d614g

Mathematica
14
star
10

sarscov2-adaptive-evolution

Jupyter Notebook
9
star
11

ncov-omicron

Nextstrain build targeted to Omicron
Python
9
star
12

dengue-antigenic-dynamics

Dengue antigenic variation and evolutionary dynamics
Jupyter Notebook
9
star
13

seasonal-cov-adaptive-evolution

Nextstrain builds for seasonal coronavirus
Jupyter Notebook
7
star
14

mers-structure

MERS-CoV spillover at the camel-human interface
Jupyter Notebook
7
star
15

antigenic-clustering

Detailed antigenic dynamics of influenza virus revealed by Bayesian phylogenetic clustering
PostScript
6
star
16

size-genetic-clusters

Code and data for "Estimating the reproduction number and transmission heterogeneity from the size distribution of clusters of identical pathogen sequences"
R
6
star
17

siv-cst

Modern-day SIV viral diversity generated by extensive recombination and cross-species transmission
Jupyter Notebook
6
star
18

h5n1-cambodia

Within-host diversity in H5N1-infected humans and poultry in Cambodia
Jupyter Notebook
5
star
19

spatial-tumor-phylodynamics

Associated analyses for "State-dependent evolutionary models reveal modes of solid tumor growth"
R
5
star
20

flu-forecasting

Integrating genotypes and phenotypes improves long-term forecasts of seasonal influenza A/H3N2 evolution
Jupyter Notebook
5
star
21

cartography

Dimensionality reduction distills complex evolutionary relationships in seasonal influenza and SARS-CoV-2
HTML
5
star
22

veme-2022

Workshop for VEME 2022: Real-time tracking of pathogen evolution using Nextstrain
4
star
23

evofr

Tools for evolutionary forecasting
Jupyter Notebook
4
star
24

stability

Analysis of stabilizing and destabilizing mutations in influenza evolution
JavaScript
4
star
25

ncov-variant-rt

Analysis of state-by-variant Rt estimates
3
star
26

markov-intermediate

Calculation of state-distributions along Markov chain
Jupyter Notebook
3
star
27

adaptive-evolution

An atlas of continuous adaptive evolution in endemic human viruses
Jupyter Notebook
3
star
28

mumps-wa-phylodynamics

Repeated introductions and intensive community transmission fueled a mumps virus outbreak in Washington State
Jupyter Notebook
3
star
29

h3n2-reassortment

Evolution and rapid spread of a reassortant A(H3N2) virus that predominated the 2017-2018 influenza season
Jupyter Notebook
3
star
30

ncov-early-outbreak

Nextstrain build to examine early outbreak of SARS-CoV-2 in Wuhan
Python
2
star
31

ncov-variants

Nextstrain builds for particular variants of interest
Python
2
star
32

hcc-tumor-evol

Spatial and clonal dynamics of hepatocellular carcinoma
Jupyter Notebook
2
star
33

ncov-cryptic-transmission

Cryptic transmission of SARS-CoV-2 in Washington State
Mathematica
2
star
34

zika-usvi

Evolutionary analysis of USVI Zika epidemic
Jupyter Notebook
2
star
35

zika-colombia

Genetic analysis of the Zika epidemic in Colombia
Jupyter Notebook
2
star
36

genomic-horizon

Temporal horizons of genomic epidemiology
Jupyter Notebook
2
star
37

rsv_adaptive_evo

Jupyter Notebook
1
star
38

mumps-seq

Protocols for sequencing mumps viruses
1
star
39

ebola-narrative-ms

Jupyter Notebook
1
star
40

ebola-dates

Imputing sampling dates from sample IDs and sequences
Mathematica
1
star
41

unsampled

Estimating unsampled viral diversity
Jupyter Notebook
1
star
42

ncov-wa-phylodynamics

Viral genomes reveal patterns of the SARS-CoV-2 outbreak in Washington State
MATLAB
1
star
43

popcast

Long-term forecasts for pathogen populations
Python
1
star
44

coveme-2021

Materials relating to nextstrain tutorial presented at coVEME workshop 2021
1
star
45

roka

Evolutionary and epidemiological analysis of Roka HIV outbreak
Jupyter Notebook
1
star
46

fitness-dynamics

Comparing fitness dynamics across SARS-CoV-2, influenza H3 and influenza H1
Mathematica
1
star
47

ncov-usa-mig

R
1
star
48

norovirus

Nextstrain analysis of Norovirus
Python
1
star
49

ncov-wa-build

Augur build for Washington SARS-CoV-2 sequences.
Python
1
star
50

pathogen-embed

Create reduced dimension embeddings for pathogen sequences
Python
1
star
51

sars2-within-host-selection

Correlating within-host and between-host fitness in SARS-CoV-2
HTML
1
star
52

ncov-forecasting-fit

Assessing accuracy of fitness model forecasts
Jupyter Notebook
1
star
53

cholera

Jupyter Notebook
1
star
54

snakemake-stats

A timeline of your Snakemake run generated from the --stats output.
HTML
1
star
55

atlas-of-viral-adaptation

HTML
1
star