influenza | Topic | Ecosyste.ms: Repos

Topic: "influenza"

nextstrain/nextclade

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

Language: Rust - Size: 61.9 MB - Last synced at: 1 day ago - Pushed at: 14 days ago - Stars: 240 - Forks: 64

reichlab/flusight

Influenza forecasts visualizer

Language: JavaScript - Size: 24.9 MB - Last synced at: 1 day ago - Pushed at: over 2 years ago - Stars: 41 - Forks: 11

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 at: 3 months ago - Pushed at: almost 2 years ago - Stars: 37 - Forks: 12

CDCgov/MIRA

Language: Python - Size: 192 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 18 - Forks: 6

lozalojo/mem

The Moving Epidemic Method R Package

Language: R - Size: 873 KB - Last synced at: about 1 month ago - Pushed at: 2 months ago - Stars: 15 - Forks: 4

cotect/cotect

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

Language: JavaScript - Size: 6.72 MB - Last synced at: almost 2 years ago - Pushed at: over 2 years ago - Stars: 14 - Forks: 4

robert-koch-institut/GrippeWeb_Daten_des_Wochenberichts

GrippeWeb ist ein Online-Portal des Robert Koch-Instituts (RKI). Es wurde im Jahr 2011 gegründet und ist das erste Webportal, das die Aktivität akuter Atemwegserkrankungen (ARE) in Deutschland beobachtet, und dabei Informationen direkt aus der Bevölkerung verwendet. Es ist ein robustes und zeitnahes System der partizipativen syndromischen Survei...

Size: 9.14 MB - Last synced at: 14 days ago - Pushed at: 14 days ago - Stars: 13 - Forks: 3

USDA-VS/vSNP3

vSNP -- validate SNPs

Language: Python - Size: 5.93 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 12 - Forks: 2

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 at: 4 months ago - Pushed at: over 5 years ago - Stars: 11 - Forks: 0

kmcconeghy/flumodelr

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

Language: R - Size: 19.4 MB - Last synced at: over 1 year ago - Pushed at: about 6 years ago - Stars: 11 - Forks: 0

LogIN-/fluprint

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

Language: PHP - Size: 96.7 KB - Last synced at: 8 months ago - Pushed at: about 6 years ago - Stars: 11 - Forks: 3

HopkinsIDD/flepiMoP

The Flexible Epidemic Modeling Pipeline

Language: HTML - Size: 144 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 9 - Forks: 4

CDCgov/MIRA-NF

Language: Nextflow - Size: 12.4 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 9 - Forks: 6

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 at: about 1 year ago - Pushed at: about 1 year ago - Stars: 7 - Forks: 0

nextstrain/flu_frequencies

Flu clade and mutation frequencies

Language: TypeScript - Size: 132 MB - Last synced at: about 2 months ago - Pushed at: 5 months ago - Stars: 5 - Forks: 4

CDCgov/influenza-generation_time-us

Estimating the generation time for influenza transmission using household data in the United States

Language: R - Size: 209 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 4 - Forks: 2

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 at: about 1 year ago - Pushed at: over 1 year ago - Stars: 4 - Forks: 1

emmecola/influbot

A Python script that sends Italian flu updates to Mastodon

Language: Python - Size: 38.1 KB - Last synced at: 7 days ago - Pushed at: over 2 years ago - Stars: 4 - Forks: 1

colbyford/Influenza_H5-Antibody_Predictions

Large-Scale Computational Modeling of H5 Influenza Variants Against HA1-Neutralizing Antibodies

Language: Jupyter Notebook - Size: 2.77 GB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 3 - Forks: 1

lozalojo/memapp

The Moving Epidemic Method Shiny Web Application

Language: R - Size: 12.7 MB - Last synced at: 2 months ago - Pushed at: 5 months ago - Stars: 3 - Forks: 4

raghavagps/FluSPred

Prediction infectious strains of Influenza A virus for human

Language: Python - Size: 28.2 MB - Last synced at: 13 days ago - Pushed at: almost 2 years ago - Stars: 3 - Forks: 1

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 at: over 2 years ago - Pushed at: over 3 years ago - Stars: 3 - Forks: 2

wuaipinglab/RECDS

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

Language: Python - Size: 40.2 MB - Last synced at: about 1 year ago - Pushed at: almost 5 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 at: over 2 years ago - Pushed at: about 5 years ago - Stars: 3 - Forks: 0

ecoronado92/Model_Influeza_Seasonal_Dynamics

stochastic modeling | HMM

Language: HTML - Size: 2.39 MB - Last synced at: 4 months ago - Pushed at: over 5 years ago - Stars: 3 - Forks: 1

FluSightNetwork/FSN-Model-Comparison

Shiny app for FSN model comparison

Language: R - Size: 42.6 MB - Last synced at: almost 2 years ago - Pushed at: about 7 years ago - Stars: 3 - Forks: 2

CDPHE-bioinformatics/CDPHE-influenza

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

Language: WDL - Size: 1010 KB - Last synced at: 9 days ago - Pushed at: 10 days ago - Stars: 2 - Forks: 1

IRI-UW-Bioinformatics/flu-ngs

NGS pipeline for influenza virus libraries

Language: Python - Size: 135 KB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 2 - Forks: 0

wzbillings/dissertation-proposal 📦

Code, text, figures, etc. for reproducing my dissertation proposal, "Impact of Host and Vaccine Characteristics on Immune Responses following Influenza Vaccination".

Language: TeX - Size: 138 MB - Last synced at: 3 days ago - Pushed at: 11 months ago - Stars: 2 - Forks: 0

jimmyliu1326/InfluenzaNanopore

Influenza A Full-Length Consensus Calling for Nanopore Sequencing Data

Language: Shell - Size: 3.66 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 2 - Forks: 0

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 at: about 2 years ago - Pushed at: over 5 years ago - Stars: 2 - 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 at: about 1 month ago - Pushed at: about 6 years ago - Stars: 2 - Forks: 1

Abdo-Lab/auir

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

Language: Python - Size: 43.3 MB - Last synced at: over 2 years ago - Pushed at: over 7 years ago - Stars: 2 - Forks: 0

4ment/aiv-migratory-flyways

Language: Python - Size: 3.58 MB - Last synced at: 2 months ago - Pushed at: about 8 years ago - Stars: 2 - Forks: 0

giffordlabcvr/Flu-GLUE

A GLUE project for influenzaviruses

Language: JavaScript - Size: 90.9 MB - Last synced at: 21 days ago - Pushed at: 21 days ago - Stars: 1 - Forks: 0

robert-koch-institut/Influenzafaelle_in_Deutschland

Im Datensatz "Laborbestätigte Influenzafälle in Deutschland" werden die wöchentlichen Fallzahlen und Inzidenzen (Fälle pro 100.000 Personen) der nach den Vorgaben des Infektionsschutzgesetzes (IfSG) von den Gesundheitsämtern in Deutschland an die zuständigen Landesbehördne und das Robert Koch-Institut (RKI) übermittelten laborbestätigt...

Size: 6.76 MB - Last synced at: 21 days ago - Pushed at: 21 days ago - Stars: 1 - Forks: 1

william-swl/gisflu

Access the GISAID Flu database using Python

Language: Python - Size: 2.04 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 1 - Forks: 1

ctkqiang/Influenza-ML

本项目开发了一个基于机器学习的禽流感病毒(H5N1)预测系统，旨在通过分析历史数据和实时社交媒体信息，对禽流感疫情进行预测和风险评估。该系统采用决策树算法结合 SMOTE 过采样技术，实现了对不平衡数据的有效处理和高精度预测。

Language: Python - Size: 0 Bytes - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 1 - Forks: 0

Kai-Ref/DeepAR_InfluenzaForecast

DeepAR implementation for seasonal influenza cases in German districts

Language: Jupyter Notebook - Size: 207 MB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 1 - Forks: 0

mytechnotalent/chicago-influenza-binary-classification

Data Analysis & Machine Learning w/ Chicago Inpatient, Emergency Department, and Outpatient Visits for Respiratory Illnesses

Language: Jupyter Notebook - Size: 22.8 MB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 1 - Forks: 0

treangenlab/InfA-amplicon

Amplicon sequencing of influenza A

Size: 8.26 MB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 1 - Forks: 0

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 at: about 1 year ago - Pushed at: about 1 year ago - Stars: 1 - Forks: 0

tyg3rr/Kent-County-ILI

MPH Capstone Data Management & Analysis

Language: Python - Size: 3.99 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 1

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 at: 5 months ago - Pushed at: almost 2 years ago - Stars: 1 - Forks: 0

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 at: over 1 year ago - Pushed at: over 2 years ago - Stars: 1 - Forks: 1

GaryWang7/COVID19_Cross_Reference

TCR analysis for COVID and Influenza A M1 epitope

Language: Jupyter Notebook - Size: 17.2 MB - Last synced at: over 1 year ago - Pushed at: almost 3 years ago - Stars: 1 - Forks: 0

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 at: almost 2 years ago - Pushed at: about 3 years 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 at: over 1 year ago - Pushed at: over 5 years ago - Stars: 1 - Forks: 0

jon-mah/influenzaMarkov

A Discrete-time Markov Process for Predicting Influenza Evolution.

Language: TeX - Size: 9.4 MB - Last synced at: about 2 years ago - Pushed at: almost 7 years ago - Stars: 1 - Forks: 0

satoshikawato/flasc

inFLuenza Amino acid Substitution Caller

Language: Python - Size: 29.3 KB - Last synced at: 11 days ago - Pushed at: 11 days ago - Stars: 0 - Forks: 0

satoshikawato/ganflu

Genome ANnotator for inFLUenza viruses

Language: Python - Size: 32.2 KB - Last synced at: 11 days ago - Pushed at: 11 days ago - Stars: 0 - Forks: 0

CDPHE-bioinformatics/CDPHE-H5-influenza

Workflows and scripts for the assembly and analysis of H5 influenza

Language: Jupyter Notebook - Size: 231 KB - Last synced at: 16 days ago - Pushed at: 16 days ago - Stars: 0 - Forks: 0

robert-koch-institut/Abwassersurveillance_AMELAG_-_Wochenbericht

Im Rahmen des Vorhabens „Abwassermonitoring für die epidemiologische Lagebewertung“ (AMELAG) wird in Deutschland das Abwasser von ausgewählten Kläranlagen auf verschiedene Krankheitserreger untersucht. Der folgende Bericht präsentiert die vergangenen und aktuellen Ergebnisse und Entwicklungen dieser Untersuchungen.

Language: HTML - Size: 20.9 MB - Last synced at: 20 days ago - Pushed at: 20 days ago - Stars: 0 - Forks: 0

ahgroup/billings-comp-agdist-public

Code and data associated with Billings et al., "Different antigenic distance metrics generate similar predictions of influenza vaccine response breadth despite low correlation", in preparation.

Language: TeX - Size: 98.1 MB - Last synced at: 3 days ago - Pushed at: 22 days ago - Stars: 0 - Forks: 0

ahgroup/billings-high-dose-heterologous-public 📦

Code and data associated with Billings et al., "High dose inactivated influenza vaccine inconsistently improves heterologous antibody responses in an elderly human cohort", JID 2025.

Language: TeX - Size: 2.37 GB - Last synced at: 3 days ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0

jeremyButtler/fluDI

Find complete diRNA and vRNA influenza reads ids in long reads. Use something like fqGetIds or seqkit to extract reads by read ids.

Language: C - Size: 1.22 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 0 - Forks: 0

rki-mf1/VirusWarn-Flu

A mutation-based alert system to prioritize concerning Influenza variants from sequencing data.

Language: HTML - Size: 3.58 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 0 - Forks: 0

Luhter1/MultiAgentModel

Мультиагентная модель гриппа работающая с популяциями соответствующими стандартам RTI International

Language: C - Size: 800 KB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 0 - Forks: 0

HopkinsIDD/flepiMoP_site Fork of mmistakes/minimal-mistakes

Website for the Flexible Epidemic Modeling Pipeline

Language: JavaScript - Size: 102 MB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 0 - Forks: 0

Pragya-Ghosh/VIS-Analysis-of-Influenza

This project analyzes the weekly data on Influenza Type A and Type B cases in the US for the period 2023-24.

Language: Python - Size: 45.9 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - 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 at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

tom-sapletta-com/linfluencer

linfluencer degrees

Size: 8.79 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

florez-alberto/TDP-43

TDP-43 motifs in the GISAID Database

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

ahgroup/billings-patient-reported-symptom-data-public 📦

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 at: 3 days ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

e3bo/epidatr 📦

Language: R - Size: 42 KB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 0

dataguy2020/Influenza

Data set for Flu cases in Maryland, United States

Size: 40 KB - Last synced at: over 2 years ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

rrosebrook/InfluenzaPostCOVID

COVID's Influence on Influenza

Language: R - Size: 962 KB - Last synced at: over 2 years ago - Pushed at: almost 3 years ago - Stars: 0 - 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 at: over 2 years ago - Pushed at: over 3 years ago - Stars: 0 - 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 at: about 2 years ago - Pushed at: almost 4 years ago - Stars: 0 - Forks: 0

yrodriguezmd/Flu

Competition entry: DataDriven_Flu

Size: 8.79 KB - Last synced at: about 2 years ago - Pushed at: about 4 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 at: over 2 years ago - Pushed at: about 4 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 at: over 1 year ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 0

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 at: almost 2 years ago - Pushed at: 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 at: about 2 years ago - Pushed at: about 5 years ago - Stars: 0 - 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 at: over 1 year ago - Pushed at: over 5 years ago - Stars: 0 - Forks: 0