aaronwolf1995

IOBR

IOBR is an R package to perform comprehensive analysis of tumor microenvironment and signatures for immuno-oncology.

ArchR

ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)

BPCells

Scaling Single Cell Analysis to Millions of Cells

CellphoneDB

CellPhoneDB can be used to search for a particular ligand/receptor, or interrogate your own HUMAN single-cell transcriptomics data.

dataviz

A book covering the fundamentals of data visualization

GTEx-Networks

Tissue specific network for GTEx tissue data (TPM normalized).

Kassandra

Bostongene cell deconvolution algorithm from RNAseq

liger

R package for integrating and analyzing multiple single-cell datasets

LoomXpy

Python package (compatible with SCope) to create .loom files and extend them with other data e.g.: SCENIC regulons

MetaTiME

MetaTiME: Meta-components in Tumor immune MicroEnvironment

NaRnEA

NaRnEA (Nonparametric analytical Rank-based Enrichment Analysis)

NetBID

Data-driven Network-based Bayesian Inference of Drivers

PISCES

R package for Protein activity analysis of single-cell RNAseq.

pycistarget

pycistarget is a python module to perform motif enrichment analysis in sets of regions with different tools and identify high confidence TF cistromes.

R_study

rstudio_cloud

My Rstudio cloud project.

scRNA-seq_notes

A list of scRNA-seq analysis tools

pycisTopic

pycisTopic is a Python module to simultaneously identify cell states and cis-regulatory topics from single cell epigenomics data.

pySCENIC

pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.

rstudio-server-conda

Run Rstudio Server in a conda environment

scDART

scenicplus

SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) and single-cell chromatin accessibility (scATAC-seq) data.

scriabin

Analysis of cell-cell communication at single-cell resolution

seurat

R toolkit for single cell genomics

seurat-data

Dataset distribution for Seurat

SJARACNe

Scalable Tool for Gene Network Reverse Engineering