Differential expression analysis for single-cell RNA-seq data.

TensorDict is a pytorch dedicated tensor container.

The R package utilizes a statistical model to identify mitochondrial mutations.

Signature Analysis and Visualization for Single-Cell RNA-seq

Convert between AnnData and SingleCellExperiment

Python introduction for life scientists

Testing differences in cell type proportions from single-cell data.

Supervised Pathway DEConvolution of InTerpretable Gene ProgRAms

An alternative approach to capture the breadth of cellular functions by performing a functional analysis of existing biological networks.

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

Legend made easy for matplotlib

Implementation of Alphafold 3 in Pytorch

Declarative creation of composable visualization for Python (Complex heatmap, Upset plot, Oncoprint and more~)

Analyzing cellular niches in spatial transcriptomics data

Kolmogorov Arnold Networks

A library for efficient similarity search and clustering of dense vectors.

MinHash, LSH, LSH Forest, Weighted MinHash, HyperLogLog, HyperLogLog++, LSH Ensemble and HNSW

Approximate Nearest Neighbors in C++/Python optimized for memory usage and loading/saving to disk

A header-only C++ library for sketching in randomized linear algebra

Gene Set Scoring on the Nearest Neighbor Graph (gssnng) for Single Cell RNA-seq (scRNA-seq) using AnnData h5ad files.

A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.

A read extraction and realignment tool for next generation sequencing data

A Python toolkit for subcellular analysis of spatial transcriptomics data

K-nearest neighbor smoothing for high-throughput single-cell RNA-Seq data

MACS -- Model-based Analysis of ChIP-Seq

pycisTopic is a Python module to simultaneously identify cell states and cis-regulatory topics from single cell epigenomics data.

Unsupervised Instance Segmentation in Microscopy