Repository Index

Official git repository for Biopython (originally converted from CVS)

• python
• bioinformatics
• genomics
• biopython

Deep probabilistic analysis of single-cell and spatial omics data

• scrna-seq
• variational-bayes
• variational-autoencoder
• cite-seq

Notebooks for financial economics. Keywords: Jupyter notebook pandas Federal Reserve FRED Ferbus GDP CPI PCE inflation unemployment wage income debt Case-Shiller housing asset portfolio equities SPX bonds TIPS rates currency FX euro EUR USD JPY yen XAU gold Brent WTI oil Holt-Winters time-series forecasting statistics econometrics

• jupyter-notebook
• pandas
• federal-reserve
• gdp

🦖 ClawBio - The first bioinformatics-native AI agent skill library. Local-first. Reproducible. Open. Free.

• ai-agents
• bioinformatics
• equity
• genomics

Cloud-native genomic dataframes and batch computing

• genetics
• vcf
• genomics
• gwas

ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark, and Apache Parquet. Apache 2 licensed.

• spark
• big-data
• bioinformatics
• genomics

Foundation Models for Genomics & Transcriptomics

• genomics
• deep-learning
• transformer
• dna

Official implementation for HyenaDNA, a long-range genomic foundation model built with Hyena

• foundation-models
• genomics
• language-models

C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings

• variant-calling
• genomics
• vcf-manipulation
• genotyping

Fast, sensitive and accurate integration of single-cell data with Harmony

• scrna-seq
• algorithm
• data-integration
• r

Spatial Single Cell Analysis in Python

• single-cell-rna-seq
• single-cell-genomics
• spatial-transcriptomics
• spatial-analysis

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

• bioinformatics
• deep-learning
• single-cell
• single-cell-multiomics

Tools for computational pathology

• machine-learning
• digital-pathology
• computational-pathology
• biomedical-image-processing

Multi-Omics Factor Analysis

• multi-omics
• factor-analysis
• mofa

Reference mapping for single-cell genomics

• single-cell
• deep-learning
• rna-seq-analysis
• data-integration

Genomic Pretrained Network - GPN, GPN-MSA, PhyloGPN, GPN-Star

• dna
• language-model
• variant-effect-prediction
• genomics

Native R and Python sample-deletion robustness for omics: candidate certificates, minimum deletion bounds, Bioconductor model refits and donor-level pseudobulk

• bioinformatics
• exact-optimization
• metabolomics
• paired-data

Pan-Cancer Integrative Histology-Genomic Analysis via Multimodal Deep Learning - Cancer Cell

• histology
• wsi-images
• pan-cancer-analysis
• genomics

Haplotype-aware CNV analysis from single-cell RNA-seq, ATAC-seq, and multiome

• cancer-genomics
• cnv-detection
• single-cell
• phylogeny

Genomic sequence storage, indexing and alignment inside PostgreSQL: https://bioseqdb.com/

• alignment
• bioinformatics
• biology
• database

A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.

PyTorch Connectomics: segmentation toolbox for EM connectomics

• computer-vision
• neuroscience
• connectomics
• pytorch

Cancer Imaging Phenomics Toolkit (CaPTk) is a software platform to perform image analysis and predictive modeling tasks. Documentation: https://cbica.github.io/CaPTk

• cancer-imaging-research
• radiomics
• radiomics-features
• machine-learning

Probabilistic cell segmentation for in situ spatial transcriptomics