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Single-cell analysis of experience-dependent transcriptomic states in the mouse visual cortex

Siniša Hrvatin, Daniel R. Hochbaum, M. Aurel Nagy, Marcelo Cicconet, Keiramarie Robertson, Lucas Cheadle, Rapolas Žilionis, Alex Ratner, Rebeca Borges-Monroy, Allon M. Klein,

Nature Neuroscience · 2017 · 555 citations · 61 references

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61

Trimmomatic: a flexible trimmer for Illumina sequence data

Anthony Bolger, Marc Lohse, Björn Usadel · Bioinformatics · 2014 · 69.7K citations · Full text

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<tt>edgeR</tt> : a Bioconductor package for differential expression analysis of digital gene expression data

Mark D. Robinson, Davis J. McCarthy, Gordon K. Smyth · Bioinformatics · 2009 · 44.5K citations · Full text

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limma powers differential expression analyses for RNA-sequencing and microarray studies

Matthew E. Ritchie, Belinda Phipson, Di Wu et al. · Nucleic Acids Research · 2015 · 43K citations · Full text

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Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

Da Wei Huang, Brad T. Sherman, Richard A. Lempicki · Nature Protocols · 2008 · 37.4K citations

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Visualizing Data using t-SNE

Laurens van der Maaten, Geoffrey E. Hinton · Journal of Machine Learning Research · 2008 · 35.7K citations

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