André F. Rendeiro afrendeiro

## modeling_compositional_data.py
# /// script
# dependencies = [
#   "numpy",
#   "pandas",
#   "statsmodels",
#   "scikit-learn",
#   "scikit-bio",
#   "matplotlib",
# ]
# ///

## jupyter_notebooks.md

      
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              February 17, 2025 01:55
            
              
                A list of jupyter notebooks in bioinformatics
              
          
    Introduction to linux command line/ipython/git/R for bioinformatics:


https://github.com/biom262/biom262-2016
https://github.com/ricket-sjtu/bi028
https://github.com/YeoLab/single-cell-bioinformatics/
https://github.com/YeoLab/single-cell-bioinformatics/tree/master/notebooks
https://github.com/ltminty/Bioinformatics-and-R/blob/master/Rbioinformatics.ipynb

RNA-seq:


https://github.com/Caroldm/RNA-Seq-Tutorial---Jupyter-notebook/blob/master/RNAseq%20tutorial.ipynb


## ubuntu_fresh_install.sh
# New users
sudo adduser username

# Grant the new user sudo privileges
sudo visudo
# username ALL=(ALL:ALL) ALL
# add this line ^^

# change to that user
su - username

## series_matrix2csv.py
#!/usr/bin/env python

"""
Get a GEO series matrix file describing an experiment and
parse it into project level and sample level data.
"""

import os
from typing import Tuple, Union
import tempfile

## flac+cue2mp3.sh
#!/bin/sh

# Flacon-style convert to mp3 and split tracks from flac+cue files
# Made by André Rendeiro (afrendeiro@gmail.com)

# Rename
{
find . -name '* *' | while read file; do target=`echo "$file" | sed 's/ /_/g'`; mv "$file" "$target"; done
find . -name '* *' | while read file; do target=`echo "$file" | sed 's/ /_/g'`; mv "$file" "$target"; done
find . -name '* *' | while read file; do target=`echo "$file" | sed 's/ /_/g'`; mv "$file" "$target"; done

## _template_fig.svg

      
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## transcribe.py
#! python3.7

import argparse
import os
import numpy as np
import speech_recognition as sr
import whisper
import torch

from datetime import datetime, timedelta

## rasterize_pdf.sh
#!/bin/bash

# Terminate on first error
set -e

# Check if input file is provided
if [ -z "$1" ]; then
  echo "Usage: $0 <input_file.pdf>"
  exit 1
fi

## rendeiro_Nature_2021_covid19_paper.geomx_diff_expression.py
"""
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" \

## get_gene_set_libraries.py
from pathlib import Path

import parmap
import requests


def update(gsll):
    return [g for g in gsll if not (output_dir / (g + ".gmt")).exists()]
	# /// script
	# dependencies = [
	# "numpy",
	# "pandas",
	# "statsmodels",
	# "scikit-learn",
	# "scikit-bio",
	# "matplotlib",
	# ]
	# ///
	# New users
	sudo adduser username

	# Grant the new user sudo privileges
	sudo visudo
	# username ALL=(ALL:ALL) ALL
	# add this line ^^

	# change to that user
	su - username
	#!/usr/bin/env python

	"""
	Get a GEO series matrix file describing an experiment and
	parse it into project level and sample level data.
	"""

	import os
	from typing import Tuple, Union
	import tempfile
	#!/bin/sh

	# Flacon-style convert to mp3 and split tracks from flac+cue files
	# Made by André Rendeiro (afrendeiro@gmail.com)

	# Rename
	{
	find . -name '* *' \| while read file; do target=`echo "$file" \| sed 's/ /_/g'`; mv "$file" "$target"; done
	find . -name '* *' \| while read file; do target=`echo "$file" \| sed 's/ /_/g'`; mv "$file" "$target"; done
	find . -name '* *' \| while read file; do target=`echo "$file" \| sed 's/ /_/g'`; mv "$file" "$target"; done
	#! python3.7

	import argparse
	import os
	import numpy as np
	import speech_recognition as sr
	import whisper
	import torch

	from datetime import datetime, timedelta
	#!/bin/bash

	# Terminate on first error
	set -e

	# Check if input file is provided
	if [ -z "$1" ]; then
	echo "Usage: $0 <input_file.pdf>"
	exit 1
	fi
	"""
	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" \
	from pathlib import Path

	import parmap
	import requests


	def update(gsll):
	return [g for g in gsll if not (output_dir / (g + ".gmt")).exists()]