• 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]