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adult_foetal_epicardial_comparison_2022

awesome-single-cell

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

banovichlab

Public code repository for the Banovich Lab at the Translational Genomics Research Institute (TGen).

basiss

Code for the "Spatial genomics maps the structure, character and evolution of cancer clones" paper

celltypist

A tool for semi-automatic cell type annotation

chicken_heart

Spatiotemporal single-cell RNA sequencing of developing hearts reveals interplay between cellular differentiation and morphogenesis

dandelion

dandelion - A single cell BCR/TCR V(D)J-seq analysis package for 10X Chromium 5' data

fastintegration

FastIntegrate integrates thousands of scRNA-seq datasets and outputs batch-corrected values for downstream analysis

fg-lab

gtex-single-nucleus-reference

Code repository for the snRNA-seq cross-tissue atlas project

human_keloid_scrnaseq

single RNA-seq analysis of human keloid samples

humanpdac

single cell analysis of treatment naive and treated human PDAC

hurley2022scrna

Code for prostate cancer paper

ibex

BCR

immuneresistance

This resource provides the code developed in the study of Jerby-Arnon _et al. "Single-cell RNA-seq of melanoma ecosystems reveals sources of T cell exclusion linked to immunotherapy clinical outcomes".

ktplotspy

Python library for plotting Cellphonedb results. Ported from ktplots R package.

mouse_brain_borders_natureprotocols

ncem_benchmarks

neoantigen-specific-t-cells-nsclc

nichenetr

NicheNet: predict active ligand-target links between interacting cells

notebooks

Cellular Genetics Informatics Notebooks

panmyeloid

pathml

Tools for computational pathology

pdac

plot1cell

prostateimmuneatlas

single-cell RNAseq analysis notebooks accompanying Tuong et al.

redsea

scp

Single Cell Pipeline

scplc

Codes for the scPLC project

sctoolkit