tanlabcode

spatial-bonemarrow-atlas

This repository contains the code used to generate figures and perform analysis for the manuscript titled "Transcriptomic and Spatial Proteomic Profiling Reveals the Cellular Composition and Spatial Organization of the Human Bone Marrow Microenvironment"

CytoTalk

A novel computational method for inferring cell-type-specific signaling networks using single-cell transcriptomics data for better characterization of cell-cell communication.

CytoCommunity

The first computational tool that enables both unsupervised and supervised discovery of tissue spatial domains

scATAC-pro

A comprehensive tool for processing, analyzing and visulizing single cell chromatin accessibility sequencing data

GLUER

OptiCon

A general framework for systematic and de novo identification of synergistic key regulators.

SCRABBLE_PAPER

SCRABBLE

Single Cell RNA-Seq imputAtion constrained By BuLk RNAsEq data (SCRABBLE)

PIVOT

Platform for Interactive analysis and Visualization Of Transcriptomics data

arvin

A package that ranks the SNPs using genomic, epigenomic and network based features.

CelloType

CoSBI

CSI-ANN

FCOP

IM-PET

limacc

M-module

VisCello

Viscello for Visualization of Single Cell Data

CODEXImageProcessingPackage

KMT2Ar_Paper

MAPLE.1.0

An R package for predicting gene activity level for single cell DNA Methylation data

NBL_scMultiomics_Paper

Codes for preparing manuscript for studying high-risk NBL using longitudinal single-cell multiomics

PANGEA

rGMAP

scATAC-pro_paper

The data and scripts used for scATAC-pro manuscript

SINBAD

SINBAD

SINBAD.0.1

Single Cell DNA Methylation Pipeline