influenza

There are 2 repositories under influenza topic.

• nextstrain / nextclade

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

  cladecladescoronaviruscovidcovid-19dnancovneherlabnextstrainresearchrnasars-cov-2sciencesequencessequencingstrainviruscovid19next-generation-sequencinginfluenza
  Language:Rust 215

• reichlab / flusight

  Influenza forecasts visualizer

  forecastingepidemiologystatisticspredictionvisualizerinfluenza
  Language:JavaScript 41

• ericmjl / flu-sequence-predictor

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

  fluflu-forecasterprotein-sequencesinfluenzainfluenza-protein-sequencespymcvaccineflaskbokehdeep-learningvariational-autoencodersgaussian-processes
  Language:Jupyter Notebook 37
• cotect

  cotect / cotect

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

  coronaviruscovidcovid-19dockerfirebasefluinfluenzaneo4jreact-native
  Language:JavaScript 14

• kmcconeghy / flumodelr

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

  rinfluenzamodelingserflingarima
  Language:R 12

• lozalojo / mem

  The Moving Epidemic Method R Package

  influenzamem
  Language:R 12

• 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.

  earthechartswebglweb-glecharts4covid-19covid-datafluinfluenzacovidgoogle-earthecharts-glwuhanglobeincidentglobalwardoomsday
  Language:HTML 11

• LogIN- / fluprint

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

  vaccineinfluenzaimmune-systemdatasetdataset-generationmolecular-underpinningscytometryphospho-flow
  Language:PHP 11

• HopkinsIDD / flepiMoP

  The Flexible Epidemic Modeling Pipeline

  compartmental-modelscovid-19dynamical-modelinginfectious-disease-modelsinfluenza
  Language:HTML 9

• 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-)

  dna-sequencesegfrgene-sequencinginfluenzaprimer-designsars-cov-2
  Language:Jupyter Notebook 7

• blab / flu-forecasting

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

  predictioninfluenzamodeling
  Language:Jupyter Notebook 5

• USDA-VS / vSNP3

  vSNP -- validate SNPs

  bam-filessnpsanalysis-pipelinebrucellafreebayesgenomicshigh-throughput-sequencinginfluenzamycobacterium-tuberculosis-complexphylogeneticspipelinesars-cov-2tuberculosisvcf-fileswgswhole-genome-sequencingmycobacterium-bovismycobacterium-bovis-af2122bwa-mem
  Language:Python 5

• emmecola / influbot

  A Python script that sends Italian flu updates to Mastodon

  botinfluenzainfluenza-datamastodonmastodon-bot
  Language:Python 4

• 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.

  influenzaevolutionngs-analysis
  Language:Jupyter Notebook 4

• ecoronado92 / Model_Influeza_Seasonal_Dynamics

  stochastic modeling | HMM

  hmmbaum-welchviterbinfluenzastochastic-processes
  Language:HTML 3

• Emergent-Epidemics / US_influenza_data_1998_09-2019

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

  cdc-dataepidemiologyinfluenzarusa
  Language:R 3

• FluSightNetwork / FSN-Model-Comparison

  Shiny app for FSN model comparison

  influenzabiostatisticsshinyplotlytimeseries-forecastinginteractive-visualizationsreichlabflusightnetworkggplot2r
  Language:R 3

• fluTN / influenza-wikipedia-dataset

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

  influenzawikipediapageviewspagecounts
  3

• 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)

  rrstatsdelphi-epidatailinetcdcinfluenza
  Language:R 3

• lozalojo / memapp

  The Moving Epidemic Method Shiny Web Application

  influenzamem
  Language:R 3

• nextstrain / flu_frequencies

  Flu clade and mutation frequencies

  cladesfluinfluenzamutations
  Language:TypeScript 3

• raghavagps / FluSPred

  Prediction infectious strains of Influenza A virus for human

  genomeinfectious-diseasesinfluenzaprediction-modelproteinstrainsvirus
  Language:Python 3

• wuaipinglab / RECDS

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

  antigenic-siteinfluenzamachine-learning
  Language:Python 3

• 4ment / aiv-migratory-flyways

  datainfluenza
  Language:Python 2

• Abdo-Lab / auir

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

  influenzapipelinewhole-genome-sequencing
  Language:Python 2

• AdrianLimaG / Influenza_Pipeline

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

  bioinformatics-pipelineinfluenzakansasminionirmanextclade
  Language:Perl 2

• CDPHE-bioinformatics / CDPHE-influenza

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

  bioinformaticsinfluenzawdl
  Language:WDL 2

• colbyford / Influenza_H5-Antibody_Predictions

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

  antibodybioinformaticscomputational-biologyinfluenzaprotein-modelingvirology
  Language:Jupyter Notebook 2

• IRI-UW-Bioinformatics / flu-ngs

  NGS pipeline for influenza virus libraries

  fluinfluenzangsngs-analysisngs-pipelinepipelinesnakemakesnakemake-workflow
  Language:Python 2

• jimmyliu1326 / InfluenzaNanopore

  Influenza A Full-Length Consensus Calling for Nanopore Sequencing Data

  bioinformaticsconsensus-callinginfluenzananopore-sequencing
  Language:Shell 2

• sociovirology / human_influenza_LMGSeq

  Linked Multilocus Genotype by Sequencing (LMGSeq) applied to high-throughput quantification of genetic exchange among diverse human Influenza A virus strains

  influenzareassortmentviral-genomics
  Language:R 2

• IAmJuniorB / Covid-Analysis

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

  covidcovid-19covid-datacovid19covid19-datainfluenzapandemicpandemic-analysispneumoniapythonpython-analysispython3united-states
  Language:Python 1

• Kai-Ref / DeepAR_InfluenzaForecast

  DeepAR implementation for seasonal influenza cases in German districts

  deeparepidemiologyinfluenzajupyter-notebookpythonrepidemic-modellingepidemiological-predictionsgluontsprobabilistic-forecastingray-tunesurveillancehhh4
  Language:Jupyter Notebook 1

• treangenlab / InfA-amplicon

  Amplicon sequencing of influenza A

  amplicon-sequencinginfluenza
  1

• tyg3rr / Kent-County-ILI

  MPH Capstone Data Management & Analysis

  biostatisticscommunicable-diseasedata-sciencedisease-predictionepidemiologyinfluenzainformaticsmphpreparednessrespiratory-diseaserespiratory-virus-responsethesis-projectdata-modernizationlocal-public-health
  Language:Python 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

  chinadiseasesepidemiologyinfectious-disease-modelsinfectious-diseasesinfluenzajupyter-notebookmodeling-and-simulationpopulation-dynamicspythondisease-controldisease-modeling
  Language:Jupyter Notebook 1