gcyuan

diHMM

SCUBA

diHMM-cpp

Improved implementation of diHMM in C++

ECLAIR

Robust and scalable inference of cell lineages via consensus clustering. Features novel algorithms for the comparison of weighted graphs and unrooted trees.

PySCUBA

Python for Single-cell Clustering Using Bifurcation Analysis

GiniClust

GiniClust: Detecting Rare Cell Types from Single-Cell Gene Expression Data with Gini Index

CRISPResso

Software pipeline for the analysis of CRISPR-Cas9 genome editing outcomes from sequencing data

CUT-RUNTools-2.0

DWLS

Gene expression deconvolution using dampened weighted least squares

GiniClust2

Giotto

Single-cell spatial analysis toolbox

ONTraC

Ordered Niche Trajectory Construction

GiniClust3

Rare cell identification tool for single cell datasets

Giotto_ReadtheDocs

haystack_bio

Haystack: Epigenetic Variability and Transcription Factor Motifs Analysis Pipeline

HubPredictor

HubPredictor is the R function to run Bayesian Additive Regression Trees (BART) model for predicting chromatin interaction hubs using histone marks information.

mim

Motif Independent Metric

rescue

Bootstrap imputation for scRNAseq data

STREAM

STREAM: Single-cell Trajectories Reconstruction, Exploration And Mapping of single-cell data