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    37 repositories

    • sampledb3

      Public
      TypeScript
      •0•0•0•0•Updated Apr 23, 2026Apr 23, 2026

    • wonderland-docs

      Public
      Documentation for mad4hatter pipeline and other tools
      0•1•0•1•Updated Apr 21, 2026Apr 21, 2026

    • imported-malaria-sw-uganda

      Public
      doi: 10.64898/2026.01.25.26344810
      Creative Commons Zero v1.0 Universal
      •1•0•0•1•Updated Apr 16, 2026Apr 16, 2026

    • copy-number-variation

      Public
      R
      •2•0•5•0•Updated Apr 13, 2026Apr 13, 2026

    • mad4hatter-tools

      Public
      R
      •1•0•0•0•Updated Apr 2, 2026Apr 2, 2026

    • mad4hatter

      Public
      Pipeline to process Plasmodium amplicon sequencing data
      R
      •29•9•9•2•Updated Apr 1, 2026Apr 1, 2026

    • Katairo_DR_UG_2023_2024

      Public
      Code for Katairo et al, Sustained High Prevalence of Multiple Antimalarial Drug Resistance Markers in Uganda in 2023-24
      Creative Commons Zero v1.0 Universal
      •0•0•0•0•Updated Mar 3, 2026Mar 3, 2026

    • ampseq-qc

      Public
      QC for targeted amplicon sequencing of Plasmodium.
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •2•3•7•1•Updated Mar 3, 2026Mar 3, 2026

    • dcifer

      Public
      Distance for Complex Infections: Fast Estimation of Relatedness (R package)
      C
      •
      Other
      •5•7•2•0•Updated Feb 25, 2026Feb 25, 2026

    • mad4hatter-wdl

      Public
      Repo for conversion of mad4hatter pipeline
      WDL
      •1•1•0•0•Updated Feb 18, 2026Feb 18, 2026

    • plasmotrack

      Public
      C++
      •
      MIT License
      •0•0•0•0•Updated Jan 9, 2026Jan 9, 2026

    • asterTES

      Public
      TES recurrence classification and failure rate estimation with Aster
      C
      •
      Other
      •1•0•0•0•Updated Nov 5, 2025Nov 5, 2025

    • moire

      Public
      MOI and Allele Frequency Recovery from Noisy Polyallelic Genetics Data
      rgenomicsr-package
      rgenomicsr-packagemalariamcmc
      C++
      •
      GNU General Public License v3.0
      •9•7•9•1•Updated Sep 16, 2025Sep 16, 2025

    • sampleDB-rpackage

      Public
      R
      •
      Other
      •3•1•20•2•Updated Sep 11, 2025Sep 11, 2025

    • nf-wgs-dsl2

      Public
      Nextflow
      •2•1•0•0•Updated Sep 2, 2025Sep 2, 2025

    • phipseqreadqaunt

      Public
      A nextflow pipeline for quantifying Phip-Seq sequenced libraries
      GNU General Public License v3.0
      •0•0•0•0•Updated Aug 25, 2025Aug 25, 2025

    • lab-handbook

      Public
      EPPIcenter Lab Handbook
      CSS
      •
      Creative Commons Zero v1.0 Universal
      •1•1•0•0•Updated Mar 12, 2025Mar 12, 2025

    • gblock-detection

      Public
      Detect sequences in raw fastq files
      HTML
      •0•0•0•0•Updated Jan 28, 2025Jan 28, 2025

    • eppicenter.r-universe.dev

      Public
      The EPPIcenter R-Universe
      0•1•0•0•Updated Jul 11, 2024Jul 11, 2024

    • geno_timelines

      Public
      visualization of longitudinal qPCR or genotyping data
      0•0•0•0•Updated Mar 19, 2024Mar 19, 2024

    • flexfit

      Public
      Flexible format standard curve fitting and data processing (R package)
      R
      •0•2•0•0•Updated Aug 2, 2023Aug 2, 2023

    • MicroSPAT

      Public archive
      MicroSPAT- MicroSatellite Parameterized Analysis Tools A collection of tools for semi-automated analysis of raw capillary electrophoresis (CE) data output by t…
      TypeScript
      •
      GNU Affero General Public License v3.0
      •0•2•0•1•Updated May 31, 2023May 31, 2023

    • sample_db

      Public archive
      Application for managing a sample tracking DB
      TypeScript
      •2•3•13•19•Updated May 31, 2023May 31, 2023

    • PBC_Covid_serology

      Public
      Seroprevalence of Antibodies to SARS-CoV-2 in rural households in eastern Uganda, 2020-2022
      0•0•0•0•Updated Mar 2, 2023Mar 2, 2023

    • scale-it-2

      Public
      R
      •0•2•0•0•Updated Mar 15, 2022Mar 15, 2022

    • liinc-Ab-dynamics

      Public
      Source code and data for 'SARS-CoV-2 antibody magnitude and detectability are driven by disease severity, timing, and assay'
      R
      •0•0•0•0•Updated Feb 24, 2022Feb 24, 2022

    • COVID_ITSA

      Public
      Data and code for COVID ITSA
      Creative Commons Zero v1.0 Universal
      •0•0•0•0•Updated Aug 6, 2021Aug 6, 2021

    • scale-it

      Public
      Source code for 'Citywide serosurveillance of the initial SARS-CoV-2 outbreak in San Francisco'
      R
      •0•0•0•0•Updated Apr 15, 2021Apr 15, 2021

    • ClinEpiDB_transmission_data

      Public
      Oocyst and bloodstage haplotype data from PRISM2
      GNU General Public License v3.0
      •0•0•0•0•Updated Feb 12, 2021Feb 12, 2021

    • Kihihi_MS_genotyping

      Public
      Within-household clustering of genetically related Plasmodium falciparum infections in a moderate transmission area of Uganda
      Creative Commons Zero v1.0 Universal
      •0•0•0•0•Updated Nov 13, 2020Nov 13, 2020
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