Stars
Permutect, an incredibly efficient deep learning architecture for somatic and germline variant calling
Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.
Generate R package documentation from inline R comments
Unified knowledge-driven network inference from omics data
NetworkCommons is a community-driven platform designed to simplify access to tools and resources for inferring context-specific protein interaction networks by integrating context-agnostic prior kn…
Formatting NCI60 data into cosmos ready inputs and generation of testable hypothesis connecting cell-line specific TF and metabolic deregulations.
COSMOS (Causal Oriented Search of Multi-Omic Space) is a method that integrates phosphoproteomics, transcriptomics, and metabolomics data sets.
Flexible, uncertainty-aware variant calling with parameter free filtration via FDR control.
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.
Episcanpy: Epigenomics Single Cell Analysis in Python
All code necessary for reconstructing Bonsai-trees on high-dimensional data and visualizing them in Bonsai-scout
A Python 3 library for generating Anki decks
Asynchronous HTTP/WebSocket graphics device for R with an interactive plot viewer
Work with trained factor models in Python
Python package to perform enrichment analysis from omics data.
A comprehensive cancer DNA/RNA analysis and reporting pipeline
Various algorithms for analysing genomics data
Ubuntu Installation with Btrfs and automatic snapshots
Querying cellular states and programs by learning representations of gene sets
A command-line and python toolkit for QC, counting, clustering and plotting of single-cell (epi)genomics data
Python Toolkit for Transcription Factor Activity Inference and Clustering of scRNA-seq Data