scLT-kit: a versatile toolkit for automated processing and analysis of single-cell lineage tracing data

Graphical abstract

References

[1] Wagner D E, Klein A M . Lineage tracing meets single-cell omics: opportunities and challenges. Nature Reviews Genetics, 2020, 21( 7): 410–427

[2] Weinreb C, Rodriguez-Fraticelli A, Camargo F D, Klein A M . Lineage tracing on transcriptional landscapes links state to fate during differentiation. Science, 2020, 367( 6479): eaaw3381

[3] Packer J S, Zhu Q, Huynh C, Sivaramakrishnan P, Preston E, Dueck H, Stefanik D, Tan K, Trapnell C, Kim J, Waterston R H, Murray J I . A lineage-resolved molecular atlas of C. elegans embryogenesis at single-cell resolution. Science, 2019, 365( 6459): eaax1971

[4] Biddy B A, Kong W, Kamimoto K, Guo C, Waye S E, Sun T, Morris S A . Single-cell mapping of lineage and identity in direct reprogramming. Nature, 2018, 564( 7735): 219–224

[5] Oren Y, Tsabar M, Cuoco M S, Amir-Zilberstein L, Cabanos H F, Hütter J C, Hu B, Thakore P I, Tabaka M, Fulco C P, Colgan W, Cuevas B M, Hurvitz S A, Slamon D J, Deik A, Pierce K A, Clish C, Hata A N, Zaganjor E, Lahav G, Politi K, Brugge J S, Regev A . Cycling cancer persister cells arise from lineages with distinct programs. Nature, 2021, 596( 7873): 576–582

[6] Chang M T, Shanahan F, Nguyen T T T, Staben S T, Gazzard L, Yamazoe S, Wertz I E, Piskol R, Yang Y A, Modrusan Z, Haley B, Evangelista M, Malek S, Foster S A, Ye X . Identifying transcriptional programs underlying cancer drug response with TraCe-seq. Nature Biotechnology, 2022, 40( 1): 86–93

[7] Wolf F A, Angerer P, Theis F J . SCANPY: large-scale single-cell gene expression data analysis. Genome Biology, 2018, 19( 1): 15

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