Cunningham, Causal Inference: The Mixtape
Saturday sandbox
Cunningham, Causal Inference: The Mixtape — mixtape.scunning.com, ch. 3 (directed acyclic graphs)
In: LABLOOP-W22 Notebook
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Huntington-Klein, The Effect
Saturday sandbox · after Cunningham, Causal Inference: The Mixtape
Huntington-Klein, The Effect — theeffectbook.net, ch. 6-7 (causal diagrams), friendlier tone
In: LABLOOP-W22 Notebook
Coursera A Crash Course in Causality
Saturday sandbox · after Huntington-Klein, The Effect
Coursera A Crash Course in Causality (Penn), week 1
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In: LABLOOP-W22 Notebook
Steinegger & Söding (2017), "MMseqs2 enables sensitive protein sequence searching for the analys…
Saturday sandbox · after Coursera A Crash Course in Causality
Steinegger & Söding (2017), "MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets", Nature Biotechnology 35:1026-1028
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In: LABLOOP-W22 Notebook
StatQuest "Spearman's Rank Correlation" if needed
StatQuest "Spearman's Rank Correlation" if needed (search; verify) and "Bootstrapping Main Ideas" (carry over)
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In: LABLOOP-W22 Notebook
py-why/dowhy
Run the "getting started" notebook; draw a DAG for "organism growth temperature → sequence composition → Tm" to see where confounding lives
In: LABLOOP-W22 Notebook
scikit-learn/scikit-learn
GroupKFold / StratifiedGroupKFold with sequence-cluster IDs
In: LABLOOP-W22 Notebook
scikit-learn-contrib/MAPIE
Conformal intervals on the grouped folds; report coverage per fold
In: LABLOOP-W22 Notebook
soedinglab/MMseqs2
mmseqs easy-cluster on Meltome FASTA at 30% identity; save cluster TSV
In: LABLOOP-W22 Notebook