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Image correction software for chromatic shifts in fluorescence microscopic images
A snakemake workflow for de novo genome assembly. It produces chromosome-scale primary/phased assemblies complete with organelles (mitochondrion and/or chloroplast). It automatically assesses the q…
Detection of remote homology by comparison of protein language model representations
How to build a simple alignment laser for typical optical alignment tasks.
AlphaFold-initiated replica exchange protein docking
Tool for plotting sequencing data along genomic coordinates.
Collection of custom elements that appear hand drawn. Great for wireframes or a fun look.
Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
Custom code (Matlab functions/scripts) associated with publication: White, M.A. et al. (2023). Crossover Interference Mediates Multiscale Patterning Along Meiotic Chromosomes. bioRxiv. https://doi.…
Code for the ProteinMPNN paper
A Python GUI-based framework for segmentation, tracking and cell cycle annotations of microscopy data
LinguaCafe is a self-hosted software that helps language learners read foreign languages.
A Python implementation of the MRC2014 file format
napari: a fast, interactive, multi-dimensional image viewer for python
QC and assemble reads from different sequencing technologies into a genome obtained from a single organism
Intel lab's open sourced data science framework for accelerating digital biology
Deep Learning tool trained on protein sequence embeddings from protein language models to accurately detect remote homologues for CATH superfamilies
ProtFlash: A lightweight protein language model
ProtTrans is providing state of the art pretrained language models for proteins. ProtTrans was trained on thousands of GPUs from Summit and hundreds of Google TPUs using Transformers Models.
Correct and scaffold assemblies using long reads
ZELDA: a 3D Image Segmentation and Parent to Child relation plugin for microscopy image analysis in napari
Foldseek enables fast and sensitive comparisons of large structure sets.
Making Protein folding accessible to all!