Algorithms for the modeling and processing of CRISPR screens:

  • MAGeCK*: Model-based analysis of CRISPR/Cas9 knockout screens. [Genome Bio. 2014][code]
  • MAGeCK-VISPR*: Quality control, modeling and visualization of CRISPR screens. [Genome Bio. 2015][code]
  • MAGeCKFlute*: Integrative analysis of pooled CRISPR genetic screens. [Nature Protocols 2019][code]
  • CRISP-View*: A Comprehensive Database of CRISPR Screen Data. [website]

Guide-RNA design algorithms:

Algorithms for modeling single-cell CRISPR screens:

  • scMAGeCK*: Linking genotypes with multiple phenotypes in single-cell RNA-seq based CRISPR screens. [Genome Biology 2020][code]

Algorithms for RNA-seq:

  • IsoLasso*: A lasso regression approach to RNA-seq based transcriptome assembly. [RECOMB & JCB 2011][code]
  • CEM*: Transcriptome Assembly and Isoform Expression Level Estimation from Biased RNA-Seq Reads. [Bioinformatics 2011][code]
  • ISP*: Accurate inference of isoforms from multiple sample RNA-Seq data. [APBC & BMC genomics 2015][code]
  • IsoInfer: Inference of isoforms from short sequence reads using combinatorial optimization. [RECOMB & JCB 2010]
  • RNAseqMut: A light-weight, fast mutation calling tool from RNA-seq (and other types of sequencing) data. [code]

*  Softwares where we are the major contributors.