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André F. Rendeiro afrendeiro

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@afrendeiro
afrendeiro / README.md
Last active June 2, 2026 09:06
Tmux setup on CachyOS (fish + alacritty)

tmux Setup Guide for Fish + Alacritty

This guide documents a complete tmux configuration optimized for Fish shell and Alacritty terminal on Linux systems.

Installation

Prerequisites

Ensure you have the following installed:

  • tmux
@afrendeiro
afrendeiro / spatial_classifier_demo.py
Last active September 9, 2025 18:47
A quick demo of cell type classification from graphs
#!/usr/bin/env uv --script
# /// script
# dependencies = [
# "numpy",
# "squidpy>=1.6.5",
# "scikit-network",
# ]
# python_version = ">=3.12"
# ///
@afrendeiro
afrendeiro / convert_to_pptx.sh
Created June 25, 2025 15:29
Guaranteed flawless odp to pptx convertion
#!/bin/bash
set -e
INPUT="$1"
EXT="${INPUT##*.}"
BASENAME=$(basename "$INPUT" ."$EXT")
INPUT_DIR=$(dirname "$(realpath "$INPUT")")
TMPDIR=$(mktemp -d)
@afrendeiro
afrendeiro / modeling_compositional_data.py
Last active February 19, 2025 08:23
Testing out ILR transformation and compositional data testing
# /// script
# dependencies = [
# "numpy",
# "pandas",
# "statsmodels",
# "scikit-learn",
# "scikit-bio",
# "matplotlib",
# ]
# ///
@afrendeiro
afrendeiro / _template_fig.svg
Created April 3, 2024 17:02
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@afrendeiro
afrendeiro / transcribe.py
Created March 20, 2024 19:58
#! python3.7
import argparse
import os
import numpy as np
import speech_recognition as sr
import whisper
import torch
from datetime import datetime, timedelta
@afrendeiro
afrendeiro / rendeiro_Nature_2021_covid19_paper.geomx_diff_expression.py
Last active March 19, 2024 10:02
Re-analyze GeoMx data from Rendeiro et al. 2021 doi:s41586-021-03475-6
"""
Re-analyze GeoMx data from Rendeiro et al. 2021 doi:s41586-021-03475-6
Requirements (Python 3.10+):
pip install \
"anndata" \
"matplotlib>=3.8.3" \
"numpy>=1.26.4" \
"pandas>=2.1.0" \
"scanpy" \
@afrendeiro
afrendeiro / gdrive_download.py
Last active February 20, 2024 09:45
Download file given Google Drive URL
"""
Download file from Google Drive URL
"""
import os
import time
import click
from selenium import webdriver
from selenium.webdriver.common.by import By
from selenium.webdriver.firefox.options import Options as FirefoxOptions
@afrendeiro
afrendeiro / oils.csv
Created December 24, 2023 18:15
oil saturated polyunsaturated (omega 3 & 6) monounsaturated trans fat other fat omega 3 omega 6 yield, litres per hectare smoke point flavour cooking conditions
almond 0.08 0.17 0.7 0.0 0.05 0.0 0.17 1380 230 2 >230 °C (Deep-frying)
beef tallow 0.5 0.04 0.42 0.0 0.04 0.01 0.03 - 220 1 200-229 °C (Stir-frying)
flaxseed 0.09 0.66 0.2 0.0 0.05 0.59 0.13 506 107 2 <150 °C (Dressings)
apricot kernel 0.06 0.29 0.6 0.0 0.05 0.0 0.29 680 257 0 >230 °C (Deep-frying)
argan 0.18 0.37 0.43 0.0 0.02 0.02 0.35 0.06 218 2 200-229 °C (Stir-frying)
avocado 0.12 0.14 0.71 0.0 0.03 0.01 0.13 2638 269 1 >230 °C (Deep-frying)
brazil nut 0.25 0.36 0.39 0.0 0.0 0.0 0.36 2392 195 2 150-199 °C (Light saute)
butter 0.51 0.03 0.21 0.033 0.25 0.0 0.03 - 167 2 150-199 °C (Light saute)
butter, clarified (ghee) 0.65 0.03 0.32 0.0 0.0 0.0 0.03 - 235 2 >230 °C (Deep-frying)
@afrendeiro
afrendeiro / test_nuclei_dataloaders.py
Last active November 21, 2023 17:46
Use torch dataloaders with nuclei coordinates for training.
"""
Use dataloaders with nuclei coordinates for training.
"""
from functools import partial
import requests
import h5py
from tqdm import tqdm
import numpy as np