Computational Tools

Category	Tool Type	Tool	Purpose	References
CRISPR Screens	design	CRISPRi Tiling Design	Design gRNA pools for CRISPRi tiling screens (including selecting elements/promoters, scoring and selecting gRNAs, adding ctrl gRNAs)
	design	TAPseq (R package)	Design TAP-seq primers for a set of target genes for targeted scRNA-seq
	design	CRISPR-SURF	Design and analyses of tiling screens	30504875
	design	CRISPResso2	Quantification of genome editing from targeted or WGS sequencing data	30809026
	processing	CRISPRme	Enumeration of potential off-target sites taking into account genetic variant
	analysis	CRISPRiScreen	Map enhancer-gene connections from TAP-seq/Perturb-seq experiments differential expression testing
Reporter Assays (MPRA/ STARR-seq)	processing	MPRAflow MPRAsnakeflow	Process, manipulate, filter MPRA data (assignment+counts) to create count tables and statistics	32641802
	analysis	MPRAanalyze	Analysis framework designed for data generated from MPRA
	analysis	SHARPR	Systematic High-resolution Activation and Repression Profiling with Reporter-tiling (SHARPR). High resolution inference of activing and repressive bases from MPRA tiling designs	27701403
	analysis	BIRD	Estimate variant effects from STARR-seq/MPRA data	31368479
	analysis	mpra (Bioconductor)	Differential analysis and visualization
Single Cell Multiome (RNA-seq / ATAC-seq)	analysis	snapATAC2	scATAC analysis + clustering
	analysis	SIMBA	MultiOme integration
	analysis	CellSpace	scATAC batch integration + analysis
	analysis	ArchR	Robust and scaleable analysis of single-cell chromatin accessibility data
	analysis	FastGxC	Fast and powerful cell-type specific xQTL mapping from single-cell RNA-Seq, ATAC-Seq etc data	BioRXiv
	analysis	CONTENT	Fast and powerful TWAS in single-cell RNA-Seq experiments	36171194
	analysis	sclinker / GSSG	GWAS analysis identifying tissue-level processes and cell types and cellular process for complex diseases and traits	34845454