timedreamer / .gitgnore

Last active March 4, 2026 05:22

A general .gitignore file for python DS projects.

timedreamer / AGENTS.md

Last active May 6, 2026 19:38

For Python projects. Update 20260506.

Repository Guidelines

Tradeoff: These guidelines bias toward caution over speed. For trivial tasks, use judgment.

1. Think Before Coding

Don't assume. Don't hide confusion. Surface tradeoffs.

Before implementing:

timedreamer / microgpt.py

Created February 12, 2026 17:44 — forked from karpathy/microgpt.py

microgpt

	"""
	The most atomic way to train and inference 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

timedreamer / .lintr

Created March 23, 2024 00:04 — forked from strengejacke/.lintr

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))

timedreamer / example_bar_plot.R

Created February 28, 2023 19:22 — forked from raryskin/example_bar_plot.R

quick example of a (not ugly) ggplot bar graph with points for individual subjects and error bars

	# example of bar plot with individual subject points for Anya -04/24/2019
	# added error bars - 04/25/2019

	library(tidyverse) #will need to install this first (run: install.packages("tidyverse"))


	## fake data
	data = tibble( # creating a dataframe (aka "tibble") called data
	subject = rep(1:10,times = 2 ), # making a column/vector of subject numbers (1-10) x2
	condition = rep(c("hard", "easy"), each = 10), # making a column/vector of condition names

timedreamer / Plot_muli-plots_on_multi-page.R

Created January 13, 2023 01:24

It's useful to plot many gene expression plots on a pdf. Each page has 3x3 or 4x4 plots.

	# Thanks for the suggestion from Joseph Elsherbini.

	library(tidyverse)
	library(ggforce)

	n_pages(p) # use this to get the number of pages to print
	# then run a for loop to loop over pages

	pdf("test.pdf")
	for (i in 1:5) {

timedreamer / GO_anlaysis_using_topGO.R

Created December 14, 2022 19:56

Use topGO package for GO analysis in R.

	# 0. Prep -----------------------------------------------------------------

	library(tidyverse)
	library(here)

	# 1. Load and clean EggNOG output -----------------------------------------

	## The output was downloaded from the eggnog-mapper online run.
	eggnog_go <- read_tsv(here("data", "misc", "out.emapper.annotations.gz"),
	skip = 4) %>%

timedreamer / download _json_ffq.py

Created September 21, 2022 08:49

Download sequenncing file meta data using `ffq`

timedreamer / GENIE3_quick_test.R

Created January 6, 2022 19:11

Test using different Regulator or Targets in GENIE3, do I get the same output. It depends. Regulator-No; Target-Yes.

	# Test on GENIE3 whether
	# (Q1) if using more genes as regulator, for the same regulator-target edge
	# do I get the same order? No. The edge order will be different.

	# (Q2) if using more genes as targets, for the same regulator-target edges,
	# do I get the same order? Yes. The same edge will have the exact same weight.

	# Author: Ji Huang
	# Date: 2021-01-06

timedreamer / theme_jh.R

Last active March 17, 2021 14:34

The ggplot theme I updated based on theme_bw().

	library(ggplot2)
	theme_jh <- function (base_size = 11, base_family = "Arial",
	base_line_size = base_size/22,
	base_rect_size = base_size/22) {
	theme_grey(base_size = base_size, base_family = base_family,
	base_line_size = base_line_size,
	base_rect_size = base_rect_size) +
	theme(panel.background = element_rect(fill = "white", colour = NA),
	panel.border = element_rect(fill = NA, colour = "grey20"),
	panel.grid = element_line(colour = "grey92"),