MalariaGEN parasite-data-explorer

Current Demo for Pf8 Streamlit App

A Streamlit replication of the MalariaGEN Pf8 web app.

Pages

Page	Description
Home	Overview, metrics, samples-per-year chart, section cards
Countries	Choropleth world map + country summary table
Studies	Filterable by country/year, charts, study table
Samples	Full filter panel, charts, map, download CSV
Publications	Citation and link to MalariaGEN publications
People	Full Pf8 contributor list with search

Quick start

# 1. Create virtual environment
python3 -m venv .venv
source .venv/bin/activate

# 2. Install dependencies
pip install -r requirements.txt

# 3. Run
streamlit run Home.py

Data files

Place your data files in the data/ directory:

File	Description
Pf8_samples.txt	Tab-separated, one row per sample
Pf8_inferred_resistance_status_classification.tsv	Tab-separated resistance calls

Expected columns in Pf8_samples.txt

Column	Notes
Sample	Unique sample ID
Study	Study identifier
Country	Country name
Admin level 1	Region / province
Country latitude	Country centroid latitude
Country longitude	Country centroid longitude
Admin level 1 latitude	Region centroid latitude
Admin level 1 longitude	Region centroid longitude
Year	Collection year
ENA	ENA accession
Population	Population code
% callable	Genome callability
QC pass	True / False
Exclusion reason	Reason if QC fail
Sample type	gDNA / sWGA
Sample was in Pf7	True / False

Expected columns in resistance TSV

Column	Values
Sample	Joins to samples file
Artemisinin	Resistant / Sensitive / Undetermined
Chloroquine	Resistant / Sensitive / Undetermined
Mefloquine	Resistant / Sensitive / Undetermined
Piperaquine	Resistant / Sensitive / Undetermined
Pyrimethamine	Resistant / Sensitive / Undetermined
Sulfadoxine	Resistant / Sensitive / Undetermined