mjsteinbaugh’s gists

karpathy / microgpt.py

Last active March 17, 2026 05:41

microgpt

	"""
	The most atomic way to train and run inference for a GPT in pure, dependency-free Python.
	This file is the complete algorithm.
	Everything else is just efficiency.

	@karpathy
	"""

	import os # os.path.exists
	import math # math.log, math.exp

adlvdl / gemini_mmp.py

Created May 5, 2025 11:14

Results of Gemini prompt asking for a Python program to obtain MMPs

	# Import necessary libraries
	import pandas as pd
	from rdkit import Chem
	from rdkit.Chem import rdMMPA
	from collections import defaultdict
	import logging

	# Configure logging
	logging.basicConfig(level=logging.INFO, format='%(asctime)s - %(levelname)s - %(message)s')

stephenturner / reticulate-huggingface-pybigwig.R

Last active May 18, 2025 11:58

Demonstration using reticulate to access the Hugging Face transformers library and pyBigWig in R using uv

	# Demo 1: NLP -------------------------------------------------------------

	# Load reticulate, declare that we'll use pytorch and huggingface transformers
	library(reticulate)
	py_require("torch")
	py_require("transformers")

	# Use the transformers python, and use the sentiment analysis pipeline
	transformers <- import("transformers")
	analyzer <- transformers$pipeline("sentiment-analysis")

mikelove / deseq2_curves.R

Created June 15, 2023 06:17

Drawing DESeq2 fitted spline curves on top of scaled counts

	library(splines)
	library(DESeq2)

	# make some demo data
	dds <- makeExampleDESeqDataSet(n=100, m=40)
	dds$condition <- sort(runif(40))
	# make one gene where expression has a curve shape (just for demo)
	s_shape <- round(500 * sin(dds$condition2pi) + 1000 + rnorm(40,0,50))
	mode(s_shape) <- "integer"
	counts(dds)[1,] <- s_shape

JosiahParry / check_missing_value.R

Last active December 16, 2022 15:36

Checks if there are missing value tags in any man pages

	# Function to run to check if you have any missing `\value{}` tags
	check_missing_value <- function(pkg = ".") {
	pkg_root <- rprojroot::find_package_root_file(path = pkg)
	# find exported functions
	ns <- readLines(file.path(pkg_root, "NAMESPACE"))
	exports <- ns[which(grepl("export", ns))]
	# https://stackoverflow.com/questions/8613237/extract-info-inside-all-parenthesis-in-r
	exported_fxs <- stringr::str_extract(exports, "(?<=\$).+?(?=\$)")

	# parse all man pages

strengejacke / .lintr

Last active March 9, 2026 03:36

VS Code setup for R

	// save to windows-user directory

	linters: with_defaults(object_name_linter = NULL,
	object_length_linter(50),
	commented_code_linter = NULL,
	object_usage_linter = NULL,
	line_length_linter(120),
	cyclocomp_linter = cyclocomp_linter(50))

notheotherben / starship.toml

Created November 11, 2021 15:28

A Powerline configuration for Starship.rs

	format = """
	[\uE0B6](fg:#1C4961)[$directory](bg:#1C4961)[\uE0B0](fg:#1C4961 bg:#2F79A1)$git_branch[\uE0B0](fg:#2F79A1 bg:#3A95C7)$git_status[\uE0B0](#3A95C7 bg:#40A9E0)$time[\uE0B0](#40A9E0 bg:none) $all$character """

	add_newline = true

	[directory]
	style = "bg:#1C4961 fg:white"

	[git_branch]
	format = "[ $symbol$branch ]($style)"

obihill / Makefile-libbz2_dylib

Created April 20, 2021 12:46

Makefile to create shared library for libbz2 on MacOS


	# This Makefile builds a shared version of the library,
	# libbz2.dylib for MacOSX x86 (10.13.4 or higher),
	# with gcc-2.96 20000731 (Red Hat Linux 7.1 2.96-98).
	# It is a custom Makefile. Use at own risk.
	# Run in your MacOS terminal with the following command:
	# make -f Makefile-libbz2_dylib

	PKG_VERSION?=1.0.8
	PREFIX?=/usr/local

ATpoint / edgeR_TMM_vs_naive.R

Last active April 19, 2021 23:53

	library(recount)
	library(edgeR)

	#/ Get the counts from GTEx via recount as a SummarizedExperiment
	#/ => 1.3GB file
	options(timeout=600)
	download_study("SRP012682", type = "rse-gene")
	load(file.path("SRP012682", "rse_gene.Rdata"))

	#/ remove whitespaces in tissue names:

ATpoint / guides_angles.R

Last active September 24, 2021 10:35

No more messing with h/vjust when rotating labels

	library(ggplot2)
	library(reshape2)
	library(egg)

	# thanks to https://stackoverflow.com/questions/1330989/rotating-and-spacing-axis-labels-in-ggplot2/60650595#60650595

	dat<-reshape2::melt(data.frame(groupA=rnorm(20),
	groupB=rnorm(20),
	groupC=rnorm(20)))

Michael Steinbaugh mjsteinbaugh