Single-cell RNA-seq

SAFEclustering: SAFE (Single-cell Aggregated clustering From Ensemble): Cluster ensemble for single-cell RNA-seq data (GitHub, vignettes)

SAMEclustering: SAME (Single-cell RNA-seq Aggregated clustering via Mixture model Ensemble): Cluster ensemble for single-cell RNA-seq data (GitHub, vignettes)

SMNN: Batch Effect Correction for Single-cell RNA-seq data via Supervised Mutual Nearest Neighbor Detection (GitHub, vignettes)

iSMNN: Batch Effect Correction for Single-cell RNA-seq data via Iterative Supervised Mutual Nearest Neighbor Refinement (GitHub, vignettes)

ExpressHeart: Web Portal to Visualize Transcriptome Profiles of Non-cardiomyocyte Cells (http://shiny.bios.unc.edu/expressheart/)

Hi-C

MUNIn (Multiple tissue UNifying long-range chromatin Interaction detector): a statistical framework for identifying long-range chromatin interactions from multiple tissues/samples.(GitHub, vignettes)

FIREcaller: an R package for detecting frequently interacting re-gions from Hi-C data. (GitHub, vignettes)