PHATE (Potential of Heat-diffusion for Affinity-based Transition Embedding) is a tool for visualizing high dimensional data.
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Updated
Feb 20, 2024 - Python
PHATE (Potential of Heat-diffusion for Affinity-based Transition Embedding) is a tool for visualizing high dimensional data.
pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.
Graph-linked unified embedding for single-cell multi-omics data integration
DANCE: a deep learning library and benchmark platform for single-cell analysis
Single cell perturbation prediction
A tool for semi-automatic cell type classification
RNA velocity estimation in Python
Deep neural networks for predicting CpG methylation
Python package to perform enrichment analysis from omics data.
scGNN (single cell graph neural networks) for single cell clustering and imputation using graph neural networks
Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy.
LIANA+: an all-in-one framework for cell-cell communication
Convert between AnnData and SingleCellExperiment
mgatk: mitochondrial genome analysis toolkit
Multi-omic single-cell optimal transport tools
Cell-type Annotation for Single-cell Transcriptomics using Deep Learning with a Weighted Graph Neural Network
Rapids_singlecell: A GPU-accelerated tool for scRNA analysis. Offers seamless scverse compatibility for efficient single-cell data processing and analysis.
Systematically learn and evaluate manifolds from high-dimensional data
Perturbation Analysis in the scverse ecosystem.
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