afrendeiro
Principal Investigator at CeMM - Research Center for Molecular Medicine, Vienna Austria; Leading @rendeirolab; he/him
CeMM - Research Center for Molecular MedicineVienna, Austria
Pinned Repositories
afrendeiro.github.io
Personal website
cv
My cv
env
My work environment: dockerfiles, dotfiles, ipython configs and ways to get static files
seaborn_extensions
My collection of general ploting functions that I build on top of seaborn.
toolkit
A toolkit for NGS analysis with Python
university-of-aveiro-LaTeX-thesis-template
Latex thesis template of the University of Aveiro
imc
A package for the analysis of Imaging Mass Cytometry data
afrendeiro's Repositories
afrendeiro/toolkit
A toolkit for NGS analysis with Python
afrendeiro/afrendeiro.github.io
Personal website
afrendeiro/pipelines
[deprecated] Pipelines for ngs
afrendeiro/_project_template
A template for my projects
afrendeiro/combat
python / numpy / pandas / patsy version of ComBat for removing batch effects - pip installable
afrendeiro/cv
My cv
afrendeiro/env
My work environment: dockerfiles, dotfiles, ipython configs and ways to get static files
afrendeiro/seaborn_extensions
My collection of general ploting functions that I build on top of seaborn.
afrendeiro/_package_template
afrendeiro/anndata
Annotated data.
afrendeiro/astir
astir | Automated cell identity from single-cell multiplexed imaging and proteomics 🖥🔬✨
afrendeiro/boxcomtools
afrendeiro/clif
afrendeiro/clip-retrieval
Easily compute clip embeddings and build a clip retrieval system with them
afrendeiro/CytoSpill
afrendeiro/divideAndSlurm
Map-reduce style submission of jobs to a Slurm cluster.
afrendeiro/dotfiles
afrendeiro/fastcups
afrendeiro/figuremaker
afrendeiro/git2labnotebook
Make your git commits into your lab notebook
afrendeiro/HPC_schedulers
Which schedulers do public facing HPC systems use?
afrendeiro/nanodl
A Jax-based library for designing and training transformer models from scratch.
afrendeiro/page-enrichment
Parametric Analysis of Gene Set Enrichment (PAGE) - Python implementation
afrendeiro/presentations
afrendeiro/PubChemPy
Python wrapper for the PubChem PUG REST API.
afrendeiro/pyaging
A Python-based compendium of GPU-optimized aging clocks.
afrendeiro/pybedtools
Python wrapper -- and more -- for Aaron Quinlan's BEDTools (bioinformatics tools)
afrendeiro/quantify_me
afrendeiro/sc_MTOP
sc-MTOP is an analysis framework based on deep learning and computational pathology. This framework aims to characterize the tumor ecosystem diversity at the single-cell level. This code provide 1) Hover-Net-based nuclear segmentation and classification; 2) Nuclear morphological and texture feature extraction; 3) Multi-level pairwise nuclear graph
afrendeiro/seaborn
Statistical data visualization using matplotlib