Martin Kircher, BIH

cadd

CADD

Jesse Engreitz, Stanford

Predrag Radivojac, Northeastern

mutpred-lof

MutPred-LOF

Alan Boyle, UMich

surf and turf

SURF and TURF

remm

ReMM

Zhiping Weng, UMass

zmotif

ZMotif

Jason Ernst, UCLA

drem

DREM

Anshul Kundaje, Stanford

bpnet

BPNet

Soumya Raychaudhuri, Brigham and Women's Hospital

scent

SCENT

MutPred2 predicts pathogenicity and property scores of coding variants

mutpred2

chromhmm

ChromHMM

Hilary Finucane, Broad

pops

PoPS

Andrew Allen, Duke

qbic

Qbic

abc-max

ABC-Max

encode ccres

ENCODE cCREs

Collectively, the bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetics: that is, set theory on the genome. For example, bedtools allows one to intersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF/GTF, and VCF.

J. Michael Cherry, Stanford

bedtools

BEDTools

cnmf

cNMF

Xihong Lin, HSPH

favor

FAVOR

mutpred-indel

MutPred-Indel

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