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crispresso

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

cut-runtools-2.0

dihmm

dihmm-cpp

Improved implementation of diHMM in C++

dwls

Gene expression deconvolution using dampened weighted least squares

eclair

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

giniclust

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

giniclust2

giniclust3

Rare cell identification tool for single cell datasets

giotto

Single-cell spatial analysis toolbox

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

pyscuba

Python for Single-cell Clustering Using Bifurcation Analysis

rescue

Bootstrap imputation for scRNAseq data

scuba

stream

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