Concepedia

Cicero Predicts cis-Regulatory DNA Interactions from Single-Cell Chromatin Accessibility Data

Hannah A. Pliner, Jonathan S. Packer, José L. McFaline‐Figueroa, Darren A. Cusanovich, Riza M. Daza, Delasa Aghamirzaie, Sanjay Srivatsan, Xiaojie Qiu, Dana L. Jackson, Anna Minkina,

Molecular Cell · 2018 · 912 citations · 59 references

DOIFull text

Open access

Concepts

References

59

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

Michael I. Love, Wolfgang Huber, Simon Anders · Genome biology · 2014 · 100.5K citations · Full text

, , +15

Trimmomatic: a flexible trimmer for Illumina sequence data

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

, , +13

The Sequence Alignment/Map format and SAMtools

Heng Li, Alec Wysoker, Tim Fennell et al. · Bioinformatics · 2009 · 67.5K citations · Full text

, , +17

Fast gapped-read alignment with Bowtie 2

Ben Langmead, Steven L. Salzberg · Nature Methods · 2012 · 61.1K citations

, , +11

BEDTools: a flexible suite of utilities for comparing genomic features

Aaron R. Quinlan, Ira M. Hall · Bioinformatics · 2010 · 30.4K citations · Full text

, , +14