aaronwolf1995

COMMOT

spacexr

Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial transcriptomics

starfysh

Spatial Transcriptomic Analysis using Reference-Free auxiliarY deep generative modeling and Shared Histology

istar

SCASL

single-cell clustering based on alternative splicing landscapes

cytospace

CytoSPACE: Optimal mapping of scRNA-seq data to spatial transcriptomics data

Cottrazm

Construct Tumor Transition Zone Microenvironment

COSGR

Accurate and fast cell marker gene identification with COSG

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.

MetaTiME

MetaTiME: Meta-components in Tumor immune MicroEnvironment

cellDancer

Predict RNA velocity through deep learning

mlr3proba

Probabilistic Learning for mlr3

BPCells

Scaling Single Cell Analysis to Millions of Cells

scriabin

Analysis of cell-cell communication at single-cell resolution

iMAP

A novel unsupervised batch removal framework, called iMAP, based on neural networks.

SCALEX

Online single-cell data integration through projecting heterogeneous datasets into a common cell-embedding space

PISCES

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

qupath

QuPath - Bioimage analysis & digital pathology

irGSEA

The integration of single cell rank-based gene set enrichment analysis

InteractiveComplexHeatmap

Make Interactive Complex Heatmaps

xSelectCells

A light weight shiny app tool to enable manually selection of cells from seurat object.

CellphoneDB

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

seurat

R toolkit for single cell genomics

shilts-et-al-2022-immunoreceptors

Supporting data files and code for the publication by Shilts et al.

single-cell-rcc-pipeline

Data files and code for analysis of single-cell ccRCC data for the manuscript "Tumor-Specific Cell Populations in Clear Cell Renal Carcinoma Associated with Clinical Outcome Identified Using Single-Cell Protein Activity Inference." Includes code for VIPER protein activity inference pipeline

IOBR

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

scMetabolism

Quantifying metabolism activity at the single-cell resolution

scRNA-seq-Analysis-of-Prostate-Cancer-Samples

Code for the manuscript "Single-cell analysis of human primary prostate cancer reveals the heterogeneity of tumor-associated epithelial cell states"

scCODE

The R package scCODE, a platform for data-specific DE gene detection for scRNA-seq data

job

job: free Your RStudio Console