nextstrain/nextclade

Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement

Language: Rust - Size: 58 MB - Last synced: about 8 hours ago - Pushed: about 9 hours ago - Stars: 202 - Forks: 58

USDA-VS/vSNP3

vSNP -- validate SNPs

Language: Python - Size: 5.34 MB - Last synced: 4 days ago - Pushed: 4 days ago - Stars: 3 - Forks: 1

ZEROXMU/Flu_vac_model_mc_2024

The mathematical modeling of the optimal strategy for influenza vaccination was studied using a transmission dynamics model that considered population movement, province, and age group

Language: Jupyter Notebook - Size: 2.47 MB - Last synced: 5 days ago - Pushed: 6 days ago - Stars: 1 - Forks: 0

HopkinsIDD/flepiMoP_site Fork of mmistakes/minimal-mistakes

Website for the Flexible Epidemic Modeling Pipeline

Language: JavaScript - Size: 88.2 MB - Last synced: 7 days ago - Pushed: 7 days ago - Stars: 0 - Forks: 0

HopkinsIDD/flepiMoP

The Flexible Epidemic Modeling Pipeline

Language: HTML - Size: 93.2 MB - Last synced: 20 days ago - Pushed: 20 days ago - Stars: 6 - Forks: 2

Owaiskhan9654/Gene-Sequence-Primer-

Gene and Primer Sequence Analysis for SARS-CoV-2, EGFR(Non Small Lung Cancer Cell), Influenza DNAs ### How can I check my Oligo primers to ensure there are no significant primer design issues? - The difference between melting temperatures (Tm) of the primers should be less than 5°C. - The GC content should be between 35-80% or equivalent to the product being amplified. - The Delta G value of any self-dimers, hairpins, and heterodimers should be weaker (more positive) than -9.0 kcal/mole. Positive numbers indicate that the actual secondary structure shown will not form at all. - Avoid 3' complementarity between the two primers to prevent primer dimers. The IDT OligoAnalyzer APIs can be used to assess these different criteria for a proposed oligo. #### [Reference](https://sg.idtdna.com/pages/support/faqs/how-can-i-check-my-pcr-primers-using-the-oligoanalyzer-program-to-ensure-there-are-no-significant-primer-design-issues-)

Language: Jupyter Notebook - Size: 4.78 MB - Last synced: 12 days ago - Pushed: 12 days ago - Stars: 7 - Forks: 0

InstitutoTodosPelaSaude/respat_snakemake

Pipeline for analyses of multiple pathogens, like SARS-CoV-2 with positivity rate analyses

Language: Python - Size: 36.7 MB - Last synced: 12 days ago - Pushed: about 1 month ago - Stars: 0 - Forks: 0

socket-var/CDC-R-Shiny

Learning R by trying to replicate the charts available at https://www.cdc.gov/flu/weekly/ . Visualization available at

Language: Jupyter Notebook - Size: 3.74 MB - Last synced: 14 days ago - Pushed: over 5 years ago - Stars: 0 - Forks: 0

IRI-UW-Bioinformatics/flu-ngs

NGS pipeline for influenza virus libraries

Language: Python - Size: 103 KB - Last synced: 23 days ago - Pushed: 24 days ago - Stars: 2 - Forks: 0

nextstrain/flu_frequencies

Flu clade and mutation frequencies

Language: TypeScript - Size: 117 MB - Last synced: 26 days ago - Pushed: 27 days ago - Stars: 3 - Forks: 3

CDPHE-bioinformatics/CDPHE-influenza

Workflows and scripts for the assembly and analysis of influenza whole genome amplicon sequencing.

Language: WDL - Size: 714 KB - Last synced: 3 days ago - Pushed: 3 days ago - Stars: 2 - Forks: 1

YogiOnBioinformatics/Molecular-Phylogenomics-Using-Mega-X

Examples of Molecular Phylogenomics figures created from self-taught usage of MEGA-X software.

Size: 119 KB - Last synced: about 1 month ago - Pushed: over 5 years ago - Stars: 0 - Forks: 0

tom-sapletta-com/linfluencer

linfluencer degrees

Size: 8.79 KB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 0 - Forks: 0

reichlab/flusight

Influenza forecasts visualizer

Language: JavaScript - Size: 24.9 MB - Last synced: 2 months ago - Pushed: over 1 year ago - Stars: 40 - Forks: 10

tyg3rr/Kent-County-ILI

MPH Capstone Data Management & Analysis

Language: Python - Size: 3.99 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 1 - Forks: 1

florez-alberto/TDP-43

TDP-43 motifs in the GISAID Database

Language: Python - Size: 40 KB - Last synced: 3 months ago - Pushed: 4 months ago - Stars: 0 - Forks: 0

mminici/Influenza-Like-Illness-prediction

Influenza-like illness prediction model

Language: Jupyter Notebook - Size: 760 KB - Last synced: 5 months ago - Pushed: almost 5 years ago - Stars: 0 - Forks: 1

AdrianLimaG/Infulenza_Pipeline

KDHE Influenza A pipeline, built to take MinIon fastq files and produce clade analysis

Language: Perl - Size: 32.3 MB - Last synced: 6 months ago - Pushed: over 1 year ago - Stars: 1 - Forks: 1

ericmjl/flu-sequence-predictor

An experimental deep learning & genotype network-based system for predicting new influenza protein sequences.

Language: Jupyter Notebook - Size: 120 MB - Last synced: about 1 month ago - Pushed: 10 months ago - Stars: 36 - Forks: 12

wzbillings/Patient-vs-Clinician-Symptom-Reports

Code to accompany "Use of Patient-Reported Symptom Data in Clinical Decision Rules for Predicting Influenza in a Telemedicine Setting" by Billings et al, JABFM 2023

Language: R - Size: 21.6 MB - Last synced: 7 months ago - Pushed: 7 months ago - Stars: 0 - Forks: 0

blab/flu-forecasting

Integrating genotypes and phenotypes improves long-term forecasts of seasonal influenza A/H3N2 evolution

Language: Jupyter Notebook - Size: 461 MB - Last synced: about 1 month ago - Pushed: 3 months ago - Stars: 4 - Forks: 1

LogIN-/fluprint

Import script needed to build FluPRINT database from source :computer:

Language: PHP - Size: 96.7 KB - Last synced: about 1 month ago - Pushed: about 5 years ago - Stars: 11 - Forks: 3

e3bo/epidatr 📦

Language: R - Size: 42 KB - Last synced: 8 months ago - Pushed: 8 months ago - Stars: 0 - Forks: 0

kmcconeghy/flumodelr

A R statistical software package for estimating attributable influenza morbidity & mortality

Language: R - Size: 19.4 MB - Last synced: 4 months ago - Pushed: about 5 years ago - Stars: 11 - Forks: 0

jimmyliu1326/InfluenzaNanopore

Influenza A Full-Length Consensus Calling for Nanopore Sequencing Data

Language: Shell - Size: 3.66 MB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 2 - Forks: 0

raghavagps/FluSPred

Prediction infectious strains of Influenza A virus for human

Language: Python - Size: 28.2 MB - Last synced: about 1 month ago - Pushed: 10 months ago - Stars: 3 - Forks: 1

GabrielMenescal/BII-Work

Work done while at interning at the Bioinformatics Institute

Language: JavaScript - Size: 55.7 KB - Last synced: 10 months ago - Pushed: almost 7 years ago - Stars: 0 - Forks: 0

FluSightNetwork/FSN-Model-Comparison

Shiny app for FSN model comparison

Language: R - Size: 42.6 MB - Last synced: 10 months ago - Pushed: almost 6 years ago - Stars: 3 - Forks: 2

maevadevs/Project-CovFlu

Shiny App: Project CovFlu - A Comparative Exploration of Covid-19 and Influenza Demographics in the U.S.

Language: R - Size: 40.8 MB - Last synced: 11 months ago - Pushed: over 3 years ago - Stars: 0 - Forks: 0

IAmJuniorB/Covid-Analysis

Heatmap showing the number of deaths month to month since the beginning of the pandemic.

Language: Python - Size: 1.89 MB - Last synced: 11 months ago - Pushed: 11 months ago - Stars: 1 - Forks: 0

Lakdawala-Lab/Parallel-Evolution-Of-Influenza-Viral-RNA

Source code and data files accompanying "Parallel evolution between genomic segments of seasonal human influenza viruses reveals RNA-RNA relationships" by Jones et al eLife 2021.

Language: R - Size: 12.4 MB - Last synced: 11 months ago - Pushed: almost 3 years ago - Stars: 0 - Forks: 0

Kai-Ref/DeepAR_InfluenzaForecast

DeepAR implementation for seasonal influenza cases in German districts

Language: Jupyter Notebook - Size: 207 MB - Last synced: 26 days ago - Pushed: 4 months ago - Stars: 1 - Forks: 0

nirbhayph/Geographic-Information-Sciences-and-Technologies-RIT

Contains Weekly Activites for the (ISTE 740) Geographic Information Sciences and Technologies Course @ RIT

Language: HTML - Size: 21.5 MB - Last synced: 4 months ago - Pushed: over 4 years ago - Stars: 1 - Forks: 0

lozalojo/mem

The Moving Epidemic Method R Package

Language: R - Size: 716 KB - Last synced: 7 months ago - Pushed: 12 months ago - Stars: 10 - Forks: 4

emmecola/influbot

A Python script that sends Italian flu updates to Mastodon

Language: Python - Size: 38.1 KB - Last synced: about 2 months ago - Pushed: over 1 year ago - Stars: 3 - Forks: 1

Emergent-Epidemics/US_influenza_data_1998_09-2019

Data on US ILI, influenza pos lab tests, and total influenza cases from 1998-2019

Language: R - Size: 1.1 MB - Last synced: about 1 year ago - Pushed: over 4 years ago - Stars: 2 - Forks: 0

hugetiny/endofworld

🌏Record the last days of this earth. Don't they know this's the end of the world. It ended when you say good-bye.

Language: HTML - Size: 6.8 MB - Last synced: over 1 year ago - Pushed: about 4 years ago - Stars: 10 - Forks: 0

Abdo-Lab/auir

AUIR: A high-throughput analysis pipeline for influenza sequence data

Language: Python - Size: 43.3 MB - Last synced: over 1 year ago - Pushed: over 6 years ago - Stars: 2 - Forks: 0

Wangyiquan95/NA_EPI

We apply combinatorial mutagenesis and next-generation sequencing to characterize the local fitness landscape in an antigenic region of NA in six different human H3N2 strains that were isolated around 10 years apart. This pipeline is used to analyze data and plotting.

Language: Jupyter Notebook - Size: 40.3 MB - Last synced: over 1 year ago - Pushed: over 2 years ago - Stars: 3 - Forks: 2

dataguy2020/Influenza

Data set for Flu cases in Maryland, United States

Size: 40 KB - Last synced: over 1 year ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

rrosebrook/InfluenzaPostCOVID

COVID's Influence on Influenza

Language: R - Size: 962 KB - Last synced: over 1 year ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

GaryWang7/COVID19_Cross_Reference

TCR analysis for COVID and Influenza A M1 epitope

Language: Jupyter Notebook - Size: 17.2 MB - Last synced: 8 months ago - Pushed: almost 2 years ago - Stars: 1 - Forks: 0

cotect/cotect

🛡Crowd-sourced COVID-19 reporting and assessment system.

Language: JavaScript - Size: 6.72 MB - Last synced: 8 months ago - Pushed: over 1 year ago - Stars: 14 - Forks: 4

lozalojo/memapp

The Moving Epidemic Method Shiny Web Application

Language: R - Size: 11.4 MB - Last synced: 10 days ago - Pushed: 10 days ago - Stars: 3 - Forks: 4

bansallab/spatialaggregation

Accompanies the manuscript "Spatial aggregation choice in the era of digital and administrative surveillance data"

Language: R - Size: 3.15 MB - Last synced: 10 months ago - Pushed: almost 2 years ago - Stars: 1 - Forks: 0

4ment/aiv-migratory-flyways

Language: Python - Size: 3.58 MB - Last synced: over 1 year ago - Pushed: about 7 years ago - Stars: 2 - Forks: 0

radonahue/MedicareFluShotsAnalysis

Analysis project looking at Medicare flushot vaccination rates from 2013-2019, with attempts to infer how this population would respond to required seasonal covid boosters. All relevant code is in the R Markdown file, overall analysis and conclusions are in the pdf file. All data used is publicly available from CMS and the Census Bureau.

Size: 90.5 MB - Last synced: over 1 year ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

yrodriguezmd/Flu

Competition entry: DataDriven_Flu

Size: 8.79 KB - Last synced: about 1 year ago - Pushed: almost 3 years ago - Stars: 0 - Forks: 0

ahenoch/Masterthesis

Results of the thesis for the M.Sc. Bioinformatics program at the Friedrich Schiller University Jena.

Language: Jupyter Notebook - Size: 865 MB - Last synced: over 1 year ago - Pushed: almost 3 years ago - Stars: 0 - Forks: 0

kmiller222/bi382_remodeling_project

SIRV disease model of the impacts of vaccination on a hypothetical influenza outbreak, based on a recreation of the paper, Impact of influenza vaccine-modified infectivity on attack rate, case fatality ratio, and mortality (Nah et al. 2020)

Language: HTML - Size: 11.9 MB - Last synced: 4 months ago - Pushed: about 3 years ago - Stars: 0 - Forks: 0

wuaipinglab/RECDS

RECDS identifies cluster-transition determining sites underlying the antigenic evolution of seasonal influenza viruses

Language: Python - Size: 40.2 MB - Last synced: over 1 year ago - Pushed: almost 4 years ago - Stars: 3 - Forks: 1

fluTN/influenza-wikipedia-dataset

Dataset of Influenza Incidence and Wikipedia Pagecounts (and Pageviews).

Size: 10.3 MB - Last synced: about 1 year ago - Pushed: about 4 years ago - Stars: 3 - Forks: 0

ggrrll/aerosol Fork of digitalepidemiologylab/aerosol

Code and data for the paper "Assessing the Dynamics and Control of Droplet- and Aerosol-Transmitted Influenza Using an Indoor Positioning System" Edit Add topics

Language: HTML - Size: 51.9 MB - Last synced: 4 months ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0

Emergent-Epidemics/influenza_surveillance_bias_texas

Code and data for, "Socioeconomic bias in influenza surveillance"

Size: 21.5 KB - Last synced: about 1 year ago - Pushed: almost 4 years ago - Stars: 0 - Forks: 0

hrbrmstr/delphiepidata

Query the 'CMU' 'DELPHI' Epidemiological Data 'API' (package wrapper https://github.com/cmu-delphi/delphi-epidata/blob/master/src/client/delphi_epidata.R)

Language: R - Size: 16.6 KB - Last synced: about 1 year ago - Pushed: about 5 years ago - Stars: 2 - Forks: 1

jon-mah/influenzaMarkov

A Discrete-time Markov Process for Predicting Influenza Evolution.

Language: TeX - Size: 9.4 MB - Last synced: about 1 year ago - Pushed: almost 6 years ago - Stars: 1 - Forks: 0

ldeecke/two-cell-influenza

Stochastic integration of influenza dynamics.

Language: C++ - Size: 139 KB - Last synced: over 1 year ago - Pushed: about 5 years ago - Stars: 0 - Forks: 0

geektoni/bachelor-thesis

Bachelor's Thesis on forecasting influenza season in Italy by looking at Wikipedia usage.

Language: TeX - Size: 7.06 MB - Last synced: over 1 year ago - Pushed: over 6 years ago - Stars: 0 - Forks: 0

4ment/aiv-rate-heterogeneity

Avian influenza virus data sets

Size: 815 KB - Last synced: over 1 year ago - Pushed: over 8 years ago - Stars: 0 - Forks: 0