afrendeiro

toolkit

A toolkit for NGS analysis with Python

afrendeiro.github.io

Personal website

pipelines

[deprecated] Pipelines for ngs

_project_template

A template for my projects

combat

python / numpy / pandas / patsy version of ComBat for removing batch effects - pip installable

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.

_package_template

anndata

Annotated data.

astir

astir | Automated cell identity from single-cell multiplexed imaging and proteomics 🖥🔬✨

boxcomtools

clif

clip-retrieval

Easily compute clip embeddings and build a clip retrieval system with them

CytoSpill

divideAndSlurm

Map-reduce style submission of jobs to a Slurm cluster.

dotfiles

fastcups

git2labnotebook

Make your git commits into your lab notebook

HPC_schedulers

Which schedulers do public facing HPC systems use?

nanodl

A Jax-based library for designing and training transformer models from scratch.

page-enrichment

Parametric Analysis of Gene Set Enrichment (PAGE) - Python implementation

presentations

PubChemPy

Python wrapper for the PubChem PUG REST API.

pyaging

A Python-based compendium of GPU-optimized aging clocks.

pybedtools

Python wrapper -- and more -- for Aaron Quinlan's BEDTools (bioinformatics tools)

quantify_me

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

seaborn

Statistical data visualization using matplotlib

tensorflow_cookbook

Code for Tensorflow Machine Learning Cookbook