• Giotto: A comprehensive toolbox for spatial multi-omic data analysis. 

[ Link to Giotto Page ]

• DWLS: Cell-type deconvolution by using single-cell RNA-sequencing data.

[ Link to CRAN ]

• CUT&RUNTools: Analyzing CUT&RUN and CUT&Tag data. 

[ Version 1 (bulk analysis); Version 2 (single-cell analysis) ]

• GiniClust: Detection of rare cell-types from single-cell RNAseq data. 

[ Version 1; Version 2; Version 3 ]

• diHMM: Multi-scale chromatin state annotation from ChIPseq data.

[Link to GitHub].

• CRISPResso: Analyzing deep-sequencing CRISPR-Cas9 genome editing outcome data

[Link to GitHub]

• SCUBA: Trajectory and bifurcation analysis of single-cell RNAseq data

[Link to GitHub]

• STREAM: Pseudotime and trajectory analysis from single-cell RNAseq or ATACseq data.

[ Link to Website ]

• RESCUE: Imputing dropouts in single-cell RNA-sequencing data.

[ Link to GitHub ]

• Haystack: Quantifying chromatin state variability and prediction of driving transcription factors

[ Link to Github ]

• PANDA: Constructing gene regulatory network from RNA, TF motif, and PPI data 

[Link to Website]

• MAnorm: a robust model for quantitative comparison of ChIP-seq datasets

[Link to Website]