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Starred repositories
DoWhy is a Python library for causal inference that supports explicit modeling and testing of causal assumptions. DoWhy is based on a unified language for causal inference, combining causal graphic…
OrthoFinder / OrthoFinder
Forked from davidemms/OrthoFinderPhylogenetic orthology inference for comparative genomics
Variational autoencoder for metagenomic binning
Toward High-Accuracy Open-Source Biomolecular Structure Prediction.
Multiple Protein Structure Alignment at Scale with FoldMason
The official pipeline for flexible and high-performance analysis of DNBelab C Serie single-cell data.
A reactive notebook for Python — run reproducible experiments, query with SQL, execute as a script, deploy as an app, and version with git. Stored as pure Python. All in a modern, AI-native editor.
Specification and documentation for Agent Skills
Algorithm for ultra-scale multiple sequence alignments (3M protein sequences in 5 minutes and 24 GB of RAM)
RNA velocity inference for single cell and spatial data
Infer Copy Number Alterations and Clonality in (Single-Cell) RNA-Seq Data
Haplotype-aware CNV analysis from single-cell RNA-seq, ATAC-seq, and multiome
Democratizing AI scientists with ToolUniverse
A GTF-native ORF annotation tool for transcriptomes
A tool for exploring large trees in the browser
A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.
scikit-bio: a community-driven Python library for bioinformatics, providing versatile data structures, algorithms and educational resources.
The Book of Statistical Proofs
An extremely fast Python package and project manager, written in Rust.
R bindings to libarchive, supporting a large variety of archive formats
Scalable annotated de Bruijn graphs for DNA indexing, alignment, and assembly
Using Deep Learning to predict gene annotations
This repository contains the source code of the R package for EvoGeneX, a software to infer the mode of evolution from the gene expression data.