lzj1769

seqspec

machine-readable file format for genomic library sequence and structure

SCENT

Single-Cell ENhancer Target gene mapping using multimodal data with ATAC + RNA

Banksy

BANKSY: spatial clustering

daft

Render probabilistic graphical models using matplotlib

cSplotch

hdWGCNA

High dimensional weighted gene co-expression network analysis

PyComplexHeatmap

PyComplexHeatmap: A Python package to plot complex heatmap (clustermap)

cytospace

CytoSPACE: Optimal mapping of scRNA-seq data to spatial transcriptomics data

single-cell-best-practices

https://www.sc-best-practices.org

reg-gen

Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.

openproblems-v2

Formalizing and benchmarking open problems in single-cell genomics

gget

🧬 gget enables efficient querying of genomic reference databases

footprint-tools

A toolset to analyze genomic footprinting data

pysamstats

A fast Python and command-line utility for extracting simple statistics against genome positions based on sequence alignments from a SAM or BAM file.

pyranges

Performant Pythonic GenomicRanges

GLUE

Graph-linked unified embedding for single-cell multi-omics data integration

BI-BE-CS-183-2023

Introduction to Computational Biology and Bioinformatics Course at Caltech, 2023

PyTorch-BigGraph

Generate embeddings from large-scale graph-structured data.

tomotopy

Python package of Tomoto, the Topic Modeling Tool

gensim

Topic Modelling for Humans

scDesign3

scDesign3 generates realistic in silico data for multimodal single-cell and spatial omics

pypop

PyPop7: A Pure-Python Library for POPulation-based Black-Box Optimization (BBO), especially their *Large-Scale* versions/variants. https://pypop.rtfd.io/

SVGP-VAE

Tensorflow implementation for the SVGP-VAE model.

spatial-VAE

Source code for "Explicitly disentangling image content from translation and rotation with spatial-VAE" - NeurIPS 2019

dictys

Context specific and dynamic gene regulatory network reconstruction and analysis

GPPVAE

Gaussian Process Prior Variational Autoencoder

DIALOGUE

DIALOGUE is a dimensionality reduction method that uses cross-cell-type associations to identify multicellular programs (MCPs) and map the cell transcriptome as a function of its environment.

pyliger

Python package for integrating and analyzing multiple single-cell datasets (A Python version of LIGER)

MI-Zero

Visual Language Pretrained Multiple Instance Zero-Shot Transfer for Histopathology Images - CVPR 2023

anndataR

AnnData interoperability in R