xiangyupan

cellcall

inferring cell-cell communication from scRNA-seq of ligand-receptor

AddVelocyto

Merge Velocyto Loom into one

Axolotl_AER_2023

GSVA

Gene set variation analysis

GEARS

GEARS is a geometric deep learning model that predicts outcomes of novel multi-gene perturbations

trRosetta2

Repository for publicly available deep learning models developed in Rosetta community

SoloTE

LandSCENT

Landscape Single Cell Entropy

cpplot

Visualize the results of cell-cell communication analysis

progeny

R package for Pathway RespOnsive GENe activity inference

seurat

R toolkit for single cell genomics

scFEA

single cell Flux Estimation Analysis (scFEA) Try the below web server!

irGSEA

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

myTAI

Evolutionary Transcriptomics with R

HCRProbeMakerCL

insitu_probe_generator

Generate HCR-style Probe Pairs for mRNA visualization

probegenerator

Generate and validate probes for multiplexed RNA-FISH

sc-compReg

R package for single-cell comparative regulatory analysis

human_single_cell

Single cell transcriptome profiling of the human developing spinal cord reveals a conserved genetic programme with human specific features

MouseSpinalCordAtlas

Single-cell RNA-seq analysis from "Single cell transcriptomics reveals spatial and temporal dynamics of gene expression in the developing mouse spinal cord" (2019)

naughty_monkey

Some useful gadgets

RabbitGastrulation2022

SAMap

SAMap: Mapping single-cell RNA sequencing datasets from evolutionarily distant organisms.

published_phylomaps

A Collection of Published Phylostratigraphic Maps and Divergence Maps

stagewiseNN

Constructing developmental tree from scRNA-seq data

LampreyBrainAtlas

A comprehensive single-cell atlas of the sea-lamprey brain.

create_cisTarget_databases

Create cisTarget databases

SCENICprotocol

A scalable SCENIC workflow for single-cell gene regulatory network analysis

Phylostratigraphy

Pipeline for Phylostratigraphy

irescue

Uncertainty-aware quantification of Transposable Elements expression in scRNA-seq