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Similarity/Homology Assessment by Relating K-mers

PICNIC (Proteins Involved in CoNdensates In Cells) is machine learning-based model that predicts proteins involved in biomolecular condensates.

Completly reimplmented Lipidxplorer, with adaptation layer to read lipidxplorer1 files

Repository containing the scripts used in Iglesias-Artola et al 2024. Quantitative imaging of species-specific lipid transport in mammalian cells

Backend APIs (Flask) exposing data from database in RESTful format

Sequencing analysis pipeline for our paper "Human liver cholangiocyte organoids capture the heterogeneity of in vivo liver ductal epithelium"

Web frontend (VueJs) and CMS (Strapi)

openfpm_pdata

Library implementing TIGHT-CUT heuristic for solving FASP (Feedback Arc Set Problem)

Pinc: a simple probabilistic AlphaFold interaction score

Python Scripts to generate data in MongoDB after aggregation from source databases; update/modify data for the web app as well as the predictor; manipulate data for "Condensate Proteome Predictor"

A collection of tools to process and manipulate high-throughput sequencing data

Documentations for CD-CODE project

Implementation of 2D unet. Use as base for user projects.

PDE inference from limited spatio-temporal data

Geometric computation benchmarks with classic numerical schemes for comparison with Global Polynomial Level Set method.

Complementary information to the image analysis script described in the paper "Salamander Eci: an optical clearing protocol for the three-dimensional exploration of regeneration".

Library for producing and processing on the Adaptive Particle Representation (APR)

Repository of Code used in the Bachelor Thesis "Guanine crystal segmentation and classification imaged in the eye of zebrafish embryos"