EPPIcenter
A systems epidemiology approach to complex infectious disease dynamics: state-of-the-art data collection, molecular technologies, & computational analysis
United States of America
Pinned Repositories
dcifer
Distance for Complex Infections: Fast Estimation of Relatedness (R package)
flexfit
Flexible format standard curve fitting and data processing (R package)
liinc-Ab-dynamics
Source code and data for 'SARS-CoV-2 antibody magnitude and detectability are driven by disease severity, timing, and assay'
lumfit
Process raw Luminex files
mad4hatter
MicroSPAT
MicroSPAT- MicroSatellite Parameterized Analysis Tools A collection of tools for semi-automated analysis of raw capillary electrophoresis (CE) data output by the ABI 3730, and has been designed specifically for working with multi-allelic samples. Developed to improve reproducibility and consistency of microsatellite analysis between analysts.
moire
MOI and Allele Frequency Recovery from Noisy Polyallelic Genetics Data
sample_db
Application for managing a sample tracking DB
scale-it-2
THEREALMcCOIL
A Markov chain Monte Carlo method that estimates complexity of infection and population allele frequencies using SNP data obtained from Sequenom or similar types of SNP assays.
EPPIcenter's Repositories
EPPIcenter/moire
MOI and Allele Frequency Recovery from Noisy Polyallelic Genetics Data
EPPIcenter/dcifer
Distance for Complex Infections: Fast Estimation of Relatedness (R package)
EPPIcenter/mad4hatter
EPPIcenter/THEREALMcCOIL
A Markov chain Monte Carlo method that estimates complexity of infection and population allele frequencies using SNP data obtained from Sequenom or similar types of SNP assays.
EPPIcenter/sample_db
Application for managing a sample tracking DB
EPPIcenter/scale-it-2
EPPIcenter/eppicenter.r-universe.dev
The EPPIcenter R-Universe
EPPIcenter/flexfit
Flexible format standard curve fitting and data processing (R package)
EPPIcenter/lab-handbook
EPPIcenter Lab Handbook
EPPIcenter/lumfit
Process raw Luminex files
EPPIcenter/MicroSPAT
MicroSPAT- MicroSatellite Parameterized Analysis Tools A collection of tools for semi-automated analysis of raw capillary electrophoresis (CE) data output by the ABI 3730, and has been designed specifically for working with multi-allelic samples. Developed to improve reproducibility and consistency of microsatellite analysis between analysts.
EPPIcenter/ProteinArrays
comparison of GBL and Genepix
EPPIcenter/sampleDB-rpackage
EPPIcenter/bolinas-analysis
Source code for 'Universal PCR and antibody testing demonstrate little to no transmission of SARS-CoV-2 in a rural community'
EPPIcenter/liinc-Ab-dynamics
Source code and data for 'SARS-CoV-2 antibody magnitude and detectability are driven by disease severity, timing, and assay'
EPPIcenter/ClinEpiDB_transmission_data
Oocyst and bloodstage haplotype data from PRISM2
EPPIcenter/COVID_ITSA
Data and code for COVID ITSA
EPPIcenter/flexfitTemp
Temporary version of flexfit that allows for extrapolation (R package)
EPPIcenter/gblock-detection
Detect sequences in raw fastq files
EPPIcenter/geno_timelines
visualization of longitudinal qPCR or genotyping data
EPPIcenter/Kihihi_MS_genotyping
Within-household clustering of genetically related Plasmodium falciparum infections in a moderate transmission area of Uganda
EPPIcenter/MAGNETO
EPPIcenter/nf-wgs-dsl2
EPPIcenter/PBC_Covid_serology
Seroprevalence of Antibodies to SARS-CoV-2 in rural households in eastern Uganda, 2020-2022
EPPIcenter/scale-it
Source code for 'Citywide serosurveillance of the initial SARS-CoV-2 outbreak in San Francisco'
EPPIcenter/sex_based_differences
Sex-based differences in clearance of chronic Plasmodium falciparum infection