Current release

Under development! 🎊

Please also check (probably side branches of):

Old release

Repo organization

schemas, yaml sample and configs, includes samples.schema.yaml and config.schema.yaml
runs, data getters, config files and accessors for specific runs, e.g. encode, glios, simulations, test
snakefiles, snakefiles for different runs

Current runs

glios, explores entropies from https://www.ebi.ac.uk/ega/datasets/EGAD00001004074, for which clinical data are available
encode, explores the association between entropies and HMM segmentations using data from ENCODE
test, uses the methtuple bismark bam testfiles

To do

Implementation

Tests
Config yaml for multisample handling

Metric

Scores: explore alternatives to methylation-standardized entropy
Strand specificity, skipped currently

Simulations

Simulations based en epiallele diversity
Simulations based in DNA meth
Simulations based in sequencing depth
Simulations based in read length

Use cases

Test dataset provided by methtuple
HMM cell-line specificity, e.g. enhancer detection
RRBS-derived outcome prediction (glioblastomas)

Use cases challenges

Confounding with purity/deconvolution of purity
ASM
CNV

Further capabilities?

Differential entropy?
Regional differential entropy?

Benchmark

Feinberg's matlab
Guo et al 2017
?

Global

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