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Robust single-cell discovery of RNA targets of RNA-binding proteins and ribosomes

Kristopher W. Brannan, Isaac A. Chaim, Ryan J. Marina, Brian A. Yee, Eric Kofman, Daniel A. Lorenz, Pratibha Jagannatha, Kevin Dong, Assael A. Madrigal, Jason G. Underwood,

Nature Methods · 2021 · 176 citations · 53 references

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53

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

Michael I. Love, Wolfgang Huber, Simon Anders · Genome biology · 2014 · 94.7K citations · Full text

Minimap2: pairwise alignment for nucleotide sequences

Heng Li · Bioinformatics · 2018 · 15.5K citations · Full text

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

Sven Heinz, Christopher Benner, Nathanael J. Spann et al. · Molecular Cell · 2010 · 14K citations · Full text

, , +9

SCANPY: large-scale single-cell gene expression data analysis

F. Alexander Wolf, Philipp Angerer, Fabian J. Theis · Genome biology · 2018 · 8.6K citations · Full text

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

Jason D. Buenrostro, Paul G. Giresi, Lisa C. Zaba et al. · Nature Methods · 2013 · 6.8K citations · Full text

, , +15