Software
A non-exhaustive list of coding and analysis projects
Software Packages
esgaliant
Building Synthetic data to anchor large scale foundations models and understand that actual biology of large scale data sets.
Work In Progress
python package
Vesalius
Dissecting Tissue Anatomy From Spatial Transcriptomics data and Mapping heterogenous Spatial data.
Stable
R Package
Bombadillo
Spatial Omics simulator including cell-cell interactions.
Work In Progress
Julia Package
Kuresi
Assessing Cancer Competivity through ELO style DEG tournaments.
Work In Progress
R package
ChIPanalyser
Bioconductor package to predict Transcription Factor Binding to DNA using a statistical thermodynamic framework and evolutionary optimization.
Stable
R package
lighteR
The lighteR packages enables the analysis of Non-Photochemical quenching data as given by FluorImage. The analysis pipeline will go from loading data, cleaning data, filtering low quality disks, fitting models, plotting, extracting parameters and exporting results.
Stale
R package
Analysis
Vesalius Analysis
Analysis repository for Vesalius 2.0.0. (Nature Communications).
SPIX Analysis
Nextflow pipeline with containers (Docker and Apptainer) with all the analysis related to the Super Pixel (SPIX) project.
Development enviroment handled with Nix.
esgaliant-an
Nextflow pipeline with containers (Docker and Apptainer) with all the analysis related to the esgliant project.
Development enviroment handled with Nix.
GAND
Nextflow pipeline with conda environments with all the analysis related to the GAND Neuro-degenerative diseases project.
Conda will replaced with containers at publication time.