Cell-free DNA Toolkit Documentation#
CFTK is a cfDNA analysis toolkit for bisulfite-sequencing processing and downstream analysis, designed to support biomarker discovery in large liquid-biopsy cohorts.
We provide a model power calculator to evaluate whether a proposed biomarker discovery cohort is likely to produce a useful and detectable internally cross-validated classifier.
Run the model-development power calculator locally to support cfDNA cohort study design. No public hosted deployment is currently advertised.
Run locally
The beginner workflow starts with cftk init and cftk run. CFTK validates
the schema-v2 project, runs core processing and QC with fail-fast stage
boundaries, and records exact commands, expected outputs, figures, tool
versions, and resume decisions. Advanced downstream analysis remains available
through explicit expert commands.
Please follow the guides below to explore more details about the CFTK package.
Install CFTK, set up the enviroment and dependiencies for running.
Create a project, prepare the default reference profile, and run the validated beginner workflow.
Inspect expected outputs and use expert workflows for processing, QC, and downstream analysis.
Explore all the available cftk commands and its function.
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