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CCBR / CHAMPAGNE

CHromAtin iMmuno PrecipitAtion sequencinG aNalysis pipEline
https://ccbr.github.io/CHAMPAGNE/
MIT License
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Reproduce differential analysis with a published dataset #162

Closed kelly-sovacool closed 1 week ago

kelly-sovacool commented 6 months ago

Find a simple dataset from ENCODE with e.g. the same cells in 2 different conditions. See if we can reproduce the differential peak analysis results.

Potential paper to use:

Eder, T., Grebien, F. Comprehensive assessment of differential ChIP-seq tools guides optimal algorithm selection. Genome Biol 23, 119 (2022). https://doi.org/10.1186/s13059-022-02686-y

kelly-sovacool commented 6 months ago

Instead of the DCSsim/DCSsub datasets, let's use #165

kelly-sovacool commented 6 months ago

Question: how did the DCS authors run diffbind, since it can use either EdgeR and DESeq2? https://github.com/Edert/DCS_predictions/blob/main/run_pd_diffbind.sh

kelly-sovacool commented 1 week ago

superseded by https://github.com/CCBR/CHAMPAGNE/issues/165