cellxgene

Pegasus is a Python package for analyzing and visualizing large-scale single-cell and single-nucleus RNA-seq data, developed by the Broad Institute's Li Lab. Performs QC filtering, normalization, PCA,

1 shared topic • 2 shared operations

scanpy-plots — visualization layer of the Scanpy single-cell RNA-seq analysis suite (scanpy.pl module). Generates UMAP, t-SNE, PCA embeddings, violin plots, dot plots, heatmaps, matrix plots, stacked

1 shared topic • 2 shared operations

scvi-tools — probabilistic deep learning framework for single-cell omics analysis built on PyTorch and AnnData. Provides variational autoencoders for dimensionality reduction and batch integration (sc

1 shared topic • 2 shared operations

CellTypist — automated cell type annotation for scRNA-seq using logistic regression with pre-trained immune models, majority voting refinement, multi-label classification, custom model training, cross

1 shared topic • 1 shared operation

Seurat — comprehensive R toolkit for single-cell genomics enabling QC, normalization (LogNormalize, SCTransform), feature selection, dimensionality reduction (PCA, UMAP, t-SNE), graph-based clustering

1 shared topic • 1 shared operation