Single-cell best practices
Saturday sandbox
Single-cell best practices (Heumos et al., theislab) — sc-best-practices.org, introduction and quality-control chapters
In: LABLOOP-W19 Notebook
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MIT 6.874 single-cell lecture
Saturday sandbox · after Single-cell best practices
MIT 6.874 single-cell lecture (Kellis, YouTube)
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In: LABLOOP-W19 Notebook
Cumming (2014), "The new statistics: why and how"
Saturday sandbox · after MIT 6.874 single-cell lecture
Cumming (2014), "The new statistics: why and how", Psychological Science 25(1):7-29 — the case for estimation and intervals over p-values
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In: LABLOOP-W19 Notebook
Chip Huyen, ML Interviews Book
Saturday sandbox · after Cumming (2014), "The new statistics: why and how"
Chip Huyen, ML Interviews Book — huyenchip.com/ml-interviews-book (free) — chapters on the interview process, for the applications you send this week
In: LABLOOP-W19 Notebook
StatQuest "PCA main ideas", "t-SNE, Clearly Explained" and "UMAP Dimension Reduction, Main Ideas…
StatQuest "PCA main ideas", "t-SNE, Clearly Explained" and "UMAP Dimension Reduction, Main Ideas!!!" (YouTube, 30 min) — the three plots every single-cell talk shows
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In: LABLOOP-W19 Notebook
scverse/scanpy
PBMC 3k tutorial notebook (in the docs; scverse/scanpy-tutorials is archived, ★ 242) in Colab
In: LABLOOP-W19 Notebook
theislab/single-cell-best-practices
Run the quality-control notebook on the same data; compare cell counts after filtering
In: LABLOOP-W19 Notebook
scipy/scipy
scipy.stats.bootstrap on your key metrics; replace every naked number in both papers
In: LABLOOP-W19 Notebook