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Felix Raimundo Profile picture
Felix Raimundo
@gama_search
PhD student in computational biology, mostly single-cell, at Google Brain and Institut Curie (he/him)
Oct 4, 2022 • 7 tweets • 8 min read
"Best practices for single-cell histone modification analysis" w/ @VallotCeline @jeanphi_vert and @PPrompsy.

We identify how to analyze scCUT&Tag, from matrix construction, QC, #cells, up to dimension reduction.

paper: biorxiv.org/content/10.110…
code: github.com/vallotlab/benc… Image @VallotCeline @jeanphi_vert @PPrompsy We use multiomics assays to evaluate the quality of the representation in a completely unsupervised fashion, by using the kNN-AUC between the two modalities (see openproblems.bio/benchmarks/mul…)

We further look at the 5 most common histone marks on human PBMC and mouse brain data. Image