127 citations · 143 across the 3 of their papers we have counts for
4 papers
dotears: Scalable, consistent DAG estimation using observational and interventional data
Albert Xue, Jingyou Rao, Sriram Sankararaman +1
New biological assays like Perturb-seq link highly parallel CRISPR interventions to a high-dimensional transcriptomic readout, providing insight into gene regulatory networks. Caus…
Pseudoalignment for metagenomic read assignment
Lorian Schaeffer, Harold Pimentel, Nicolas Bray +2
We explore connections between metagenomic read assignment and the quantification of transcripts from RNA-Seq data. In particular, we show that the recent idea of pseudoalignment i…
Keep Me Around: Intron Retention Detection and Analysis
Harold Pimentel, John G. Conboy, Lior Pachter
We present a tool, keep me around (kma), a suite of python scripts and an R package that finds retained introns in RNA-Seq experiments and incorporates biological replicates to red…
Near-optimal RNA-Seq quantification
Nicolas Bray, Harold Pimentel, Páll Melsted +1
We present a novel approach to RNA-Seq quantification that is near optimal in speed and accuracy. Software implementing the approach, called kallisto, can be used to analyze 30 mil…