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:

• DeepCas13*: deep learning approaches to optimize Cas13d guide fficiency. [Nature Communications 2023][web]
• CRISPR-FOCUS*: web-based tools to design focused CRISPR screens. [PLoS ONE 2017][web]
• MAGeCK-NEST*: improved design and analysis (using protein interactions) of CRISPR screens. [Bioinformatics 2018][web]
• SSC: Sequence determinants of improved CRISPR sgRNA design. [Genome Res. 2015][web]
• CRISPR-DO: genome-wide CRISPR design and optimization. [Bioinformatics 2016][web]

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.