We have created a Docker container that contains everything needed for the workshop (in case the internet is wonky). Please download and install Docker and the container prior to your arrival in case the internet is unreliable.
Follow the instructions on Docker's website to install Docker on your machine.
| # Load libraries | |
| library(data.table) | |
| library(ggplot2) | |
| library(lubridate) # for month() | |
| # https://reporter.nih.gov/search/43gg1_mEQUWulgAiysCfEg/projects?shared=true | |
| # Load data | |
| data <- fread('SearchResult_Export_06Jul2025_102053.csv') | |
| data <- data[!duplicated(`Serial Number`)] | |
| # Convert 'Award Notice Date' to Date |
| # Start with Ubuntu base image | |
| FROM ubuntu:22.04 | |
| # Set environment variables to prevent prompts during package installation | |
| ENV DEBIAN_FRONTEND=noninteractive | |
| # Update and install dependencies | |
| RUN apt-get update && apt-get install -y \ | |
| software-properties-common \ | |
| build-essential \ |
| selected_dir<- system('osascript -l JavaScript -e \'a=Application.currentApplication();a.includeStandardAdditions=true;a.chooseFolder({withPrompt:"Please select a file to process:"}).toString()\'', intern = TRUE, ignore.stderr = T) |
| import pandas as pd | |
| from shiny import App, Inputs, Outputs, Session, reactive, render, ui | |
| from shiny.types import FileInfo | |
| app_ui = ui.page_fluid( | |
| ui.input_file("file1", "Choose CSV File", accept=[".csv"], multiple=False), | |
| ui.input_checkbox_group( | |
| "stats", | |
| "Summary Stats", |
| library(IDBacApp) | |
| library(dplyr) | |
| library(DBI) | |
| library(pool) | |
| library(coop) | |
| # Change this to be the full file path to your sqlite file | |
| sqlite_filepath <- "/home/chase/Downloads/NK_Library_Full_Up_To_2023-10-02-Copy.sqlite" |
| def parse_fasta(filepath: str) -> Generator[str, str]: | |
| seq_id = "" | |
| with open(filepath, "r") as h: | |
| seq_id = "" | |
| seq = "" | |
| for i in h: | |
| if i[0] == ">": | |
| if seq_id: | |
| yield (seq_id, seq) | |
| seq_id = i[1:].strip() |
| #!/usr/bin/python3 | |
| # MIT License | |
| # Copyright (c) Chase M. Clark | |
| # Permission is hereby granted, free of charge, to any person obtaining a copy | |
| # of this software and associated documentation files (the "Software"), to deal | |
| # in the Software without restriction, including without limitation the rights | |
| # to use, copy, modify, merge, publish, distribute, sublicense, and/or sell |
| https://docs.google.com/presentation/d/1NqwMVOYB2o_sqkOjoPH_AK1zKxrYyYcaUv8ZuAmU8og/edit?usp=sharing |