jperkel

nature_bash

Example scripts demonstrating science at the command line.

computed_manuscript

A model executable manuscript

gb_read

An example GenBank file reader in Rust

example_notebook

A sample Jupyter notebook with Binder & Colab integration

covidlit

Growth of the COVID19 literature

mymanuscript

Demo manuscript using Manubot

cvd-graphic

jperkel.github.io

Mapping_tools_holepunch

cmdparseR

Simple command-line parser for R

parse_command_line

A simple command line parser for R

computed_quarto_manuscript

invoicing

A Bash invoice-tracking system for freelancers.

Julia_on_Nextjournal

GitHub backup of a Julia notebook created on Nextjournal

nature_code_survey

conda-env-tests

Scripts and environment files to test computational environments with conda.

MappingToolsBinder

A simple R Markdown notebook that can be executed in RStudio using Binder

Snakemake_example

A Snakemake 'Hello world!' workflow

awesome-single-cell

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

deep-review

A collaboratively written review paper on deep learning, genomics, and precision medicine

holepunch_test

iscb-diversity-manuscript

Analysis of ISCB Fellows and Keynotes Reveals Disparities

Mapping-tools-examples

Mapping in R

r-novice-inflammation

Repo creates a website for the Software Carpentry introduction to R for novices using inflammation data:

rootstock

Clone me to create your Manubot manuscript

rust_in_nature

sciwridiversity2020

Session notes from SciWri20 #SciWriDiversity breakout session, "Representation Matters: Better Writing Through Diversity"

tidytuesday

todo_list

try-manubot

A repository to practice contributing to a Manubot manuscript