chooliu

conos

R package for the joint analysis of multiple single-cell RNA-seq datasets

systemsgenetics

Generic Java genotype reader / writer, QTL mapping software, Strand alignment tool

SEACells

SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data

plyranges

A grammar of genomic data transformation

dictys

Context specific and dynamic gene regulatory network reconstruction and analysis

STITCH

STITCH - Sequencing To Imputation Through Constructing Haplotypes

Monopogen

SNV calling from single cell sequencing

scDesign3

scDesign3 generates realistic in silico data for multimodal single-cell and spatial omics

MARVEL

SnapHiC

SnapHiC: Single Nucleus Analysis Pipeline for Hi-C Data

SCARlink

scrna-parameter-estimation

Direct estimation of mean and covariance from single cell RNA seq experiments

Genes2Genes

Aligning gene expression trajectories of single-cell reference and query systems

Fast-Higashi

single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, tensor decomposition

AMARETTO

Regulatory network inference and driver gene evaluation using integrative multi-omics analysis and penalized regression

apex

Toolkit for QTL mapping and meta-analysis.

ASElux

BetaVAEImputation

MetacellAnalysisToolkit

Toolkit for metacell analysis

DAESC

CLIMB

Composite LIkelihood eMpirical Bayes

vmrseq

An R package for detecting cell-to-cell variably methylated regions (VMRs) from single-cell bisulfite sequencing leveraging probabilistic models.

LeafletSC

Leaflet is a probabilistic model that identifies latent cell states defined by splicing changes.

ballcools

tools for binary file format of DNA methylation data

sciMETv2

LogBTF

LogBTFs: A method of inferring gene regulatory network from single-cell gene expression data using Boolean threshold network model.

mixqtl

Total and allele specific read based cis-QTL, fine-mapping, and prediction

CTMM

robustlink

A python package that links enhancers to genes using single-cell transcriptomes and epigenomes

VscRNAseq