An R interface to open-access malaria data, hosted by the Malaria Atlas Project.

Analysis code for malaria

An R interface for dEploid. dEploid is designed for deconvoluting mixed genomes with unknown proportions. Traditional ‘phasing’ programs are limited to diploid organisms. Our method modifies Li and Stephen’s algorithm with Markov chain Monte Carlo (MCMC) approaches, and builds a generic framework that allows haloptype searches in a multiple infe…

Companion repository for: "Comparative transcriptomics reveal differential gene expression among Plasmodium vivax geographical isolates and implications on erythrocyte invasion mechanisms" by Kepple, et al.

Cleaning and preliminary analysis of mosquito/blood data

Data analysis for my PhD

Analysis code for the manuscript "Hematological profiles in patients infected with malaria in an endemic area of ​​Peru"

Simulating the impact of strata-specific intervention mixes in Mainland Tanzania (2018)

This repository includes the R code and data used in the analysis for the main manuscript of the paper. The cleaned data file consists of the data for only the 104 incident infections used. The ped.RDS file is an R data file for the piece-wise exponential data formulation of the survival data for the competing risks analysis. The descriptives fi…

Preliminary tabulation of real-time PCR data for malarial mosquitoes

This is a repository of the files created to analyse single-cell RNA seq of P. vivax.

Evaluation of different deployment strategies for larviciding to control malaria: a simulation study

Population Genomics Analysis for Plasmodium falciparum

Detection of inversions in P. falciparum from long read assemblies.