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awesome-single-cell

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

bulk2space

a spatial deconvolution method based on deep learning frameworks, which converts bulk transcriptomes into spatially resolved single-cell expression profiles

ccl-cgps

A clinical genomics-guided prioritizing strategy enables accurately selecting proper cancer cell lines for biomedical research

celltalkdb

A manually curated database of literature-supported ligand-receptor interactions in human and mouse

kano

Code and data for the Nature Machine Intelligence paper "Knowledge graph-enhanced molecular contrastive learning with functional prompt".

perturbmerge

perturbmeta

perturbscore

samba

sccatch

Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data

sccatch_performance_comparison

The source code and results of performance comparison on the detail of the process among scCATCH, CellAssign, Garnett, SingleR, scMap and CHETAH, and CellMatch database

sccrosstalk

sccube

an SRT simulator for simulating multiple spatial variability in spatial resolved transcriptomics and generating unbiased simulated SRT data

scdeepsort

Cell-type Annotation for Single-cell Transcriptomics using Deep Learning with a Weighted Graph Neural Network

scdeepsort_performance_comparison

The source code and results for different methods on annotating external testing datsets of human and mouse.

scdeeptalk

Infer cell-cell communications based on feed-forward neural network

scdisprocema

scotch

SCOTCH is a Single-Cell multi-modal integration method leveraging the Optimal Transport algorithm and a cell matCHing strategy

scrank

A computational method to rank and infer drug-responsive cell population towards in-silico drug perturbation using a target-perturbed gene regulatory network (tpGRN) for single-cell transcriptomic data

scspace

an integrative algorithm to distinguish spatially variable cell subclusters by reconstructing cells onto a pseudo space with spatial transcriptome references

sctitans

Identifying key genes and cell subclusters for time-series single cell sequencing data

simo

spatalk

Knowledge-graph-based cell-cell communication inference for spatially resolved transcriptomic data

spatrio