PAGA - partition-based graph abstraction

Mapping out the coarse-grained connectivity structures of complex manifolds (Genome Biology, 2019).

PAGA is available within Scanpy through: tl.paga | pl.paga | pl.paga_path | pl.paga_compare.

Below you find links to all central example notebooks, which also allow reproducing all main figures of the paper. If you start working with PAGA, go through blood/paul15.

notebook | system | details | reference | figure ---------------| ---------------| ---------| ----------| ------ blood/simulated | hematopoiesis | simulated | Krumsiek et al., Plos One (2011) | 2a blood/paul15 | murine hematopoiesis | 2,730 cells, MARS-seq | Paul et al., Cell (2015) | 2b blood/nestorowa16 | murine hematopoiesis | 1,654 cells, Smart-seq2 | Nestorowa et al., Blood (2016) | 2c blood/dahlin18 | murine hematopoiesis | 44,802 cells, 10x Genomics | Dahlin et al., Blood (2018) | 2d planaria | planaria | 21,612 cells | Plass et al., Science (2018) | 3 zebrafish | zebrafish embryo | 53,181 cells | Wagner et al., Science (2018) | 4 1M_neurons | neurons | 1.3 million cells, 10x Genomics | 10x Genomics (2017) | S12 deep_learning | cycling Jurkat cells | 30,000 single-cell images | Eulenberg et al., Nat. Commun. (2017) | S14

All supplemental figures of the paper can be reproduced based on the following table.

notebook | description | figure ---------------| ----------| ------ connectivity_measure | connectivity measure | S1, S2, S3 robustness | robustness and multi-resolution capacity | S4, S5 comparisons/simulated_data | comparisons for simulated data | S6, S7 comparisons/paul15_monocle2 | comparison Monocle 2 for Paul et al. (2015) | S8 comparisons/nestorowa16_monocle2 | comparison Monocle 2 for Nestorowa et al. (2016) | S9 embedding_quality | quantifying embedding quality | S10 simulation | simulating hematopoiesis | S11 1M_neurons | neurons, 1.3 million cells, 10x Genomics, 10x Genomics (2017) | S12 blood/paul15 | annotation of louvain clusters using PAGA | S13 deep_learning | cycling Jurkat cells, 30,000 single-cell images, Eulenberg et al., Nat. Commun. (2017) | S14