compbio

Bioconductor cheat sheet

Platform for running comp bio applications on distributed compute and storage infrastructure

Methods for summarizing and visualizing multi-biosample functional genomic annotations

GWAS summary statistics files QC tool

Toolbox for single-cell data analysis on sample level

CAMUS (Constrained Algorithm Maximizing qUartetS) is a dynamic programming algorithm for inferring level-1 phylogenetic networks from quartets and a constraint tree.

Low level bindings and wrapper for slow5lib, an alternative for ONT Nanopore sequencing FAST5 output

The one-stop-shop for Morphological Profiling and JUMP Cell-Painting

Simulate phenotypic effects on a GRG

CompBio app server to host Python and R Shiny web apps

Julia package for the inference of semi-directed phylogenetic networks under pseudolikelihood model

Set up a computer for Computational Biology

Python implementation of SR-Dyna from Russek, Momennejad et al 2017

Standalone Python audit suite that evaluates the agentic bioinformatics tools suite ClawBio for safety, security, and correctness.

Small-molecule 3D conformers generation from SMILES on GPU — one CUDA warp per molecule — 100,000+ conformers/s on 8x GPUs

r-readstore is the R client (SDK) for the ReadStore API

CTCeek is a user-friendly, no-code web application designed for the rapid and automated identification of Circulating Tumor Cells (CTCs) in single-cell RNA sequencing (scRNA-seq) data.

Sourcecode for the official website of the CompBio@Berkeley Student Organization

A Python bioinformatics tool for genomic pseudo-alignment, variant calling (SNPs), and coverage analysis.

Transformers for Longer Sequences