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A meta-repository to organize my public projects.
Python R Shell
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Type Name Latest commit message Commit time
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code Fix repo_count plot & ignore Limbo language manually Dec 7, 2019
config Save figures as png instead of svg Dec 7, 2019
.gitignore Ignore mac .DS_Store Nov 28, 2019
.pre-commit-config.yaml Install pre-commit for Black code formatting Oct 29, 2019 Save figures as png instead of svg Dec 7, 2019
Snakefile Save figures as png instead of svg Dec 7, 2019
meta-repo.Rproj Make plots with R Nov 10, 2019


A meta-repository to organize my public projects.



Repository Description Owner Language(s)
latex-cv My curriculum vitae in LaTeX + a Snakemake pipeline for compiling tex to pdf. kelly-sovacool TeX, Python, Shell
meta-repo A meta-repository to organize my public projects. kelly-sovacool Python, R, Shell The website for the Schloss Lab at the University of Michigan SchlossLab CSS, HTML, Ruby Website for the Data Analysis Networking Group at U-M. um-dang
2020-01-06-UMich-WISE Software Carpentry workshop for WISE at U-M UMSWC Python, HTML, CSS, R, Makefile, JavaScript, Shell, Ruby
tiger_salamander_project SNP pipeline using Snakemake for the Weisrock Lab's Tiger Salamander project. kelly-sovacool Python, Shell
CapstoneProject Capstone Project datasets & instructions. GWC-DCMB Jupyter Notebook
ClubCurriculum Curriculum for our weekly club for high school students. GWC-DCMB Jupyter Notebook, Shell
codeDemos Stand-alone Python coding demos. GWC-DCMB Jupyter Notebook, Python
strava Having fun plotting my activity data from Strava! kelly-sovacool R, Python, Shell
documenting-R Materials for a code review on documenting R code. SchlossLab R
exception-handling Materials for a code review on exception handling in R for lab meeting. SchlossLab R
snakemake_riffomonas_tutorial A snakemake tutorial for make users SchlossLab R, Python, Makefile, Shell UM Software and Data Carpentry Website UMSWC CSS, HTML, Python, Ruby My personal website, forked from the academicpages template. kelly-sovacool Shell
loops-apply-r Looping in R: for loops & the apply family um-dang
GWC-DCMB A meta-repository to help navigate the repos and resources of Girls Who Code at UM-DCMB. GWC-DCMB Python, Shell
SummerExperience Curriculum & materials for our week-long Data Science Summer Experience. GWC-DCMB Jupyter Notebook, Shell, Python
snakemake_hpc_mwe A minimal working example of using Snakemake on an HPC running PBS-torque or SLURM. kelly-sovacool Shell, Python
machine-learning-pipelines-r Machine Learning Pipelines in R: Predict colorectal cancer using microbiome data um-dang R
tcf-words TCF Overhead Words c-andy-martin
ozobotLessons Lesson plans for Ozobots. GWC-DCMB HTML
writing-functions-r Introduction to writing functions in R um-dang R
challengeQuestions Jupyter notebooks of challenge questions for learners. GWC-DCMB Jupyter Notebook, Python, Shell
FEMMES Resources for activities for U-M FEMMES. GWC-DCMB
Great_Lakes_SLURM Using the Great Lakes cluster and batch computing with SLURM SchlossLab
git_update Updating SWC git lessons with the puzzle analogy akhagan HTML, Python, CSS, R, Makefile, JavaScript, Ruby, Shell
stats-ref A reference for concepts & equations in statistics. kelly-sovacool Python, CSS


Repository Description Owner Language(s)
PyCon_2019 Repository for PyCon 2019 Education Summit Mini-Sprint: Workbooks that teach Python through scientific data exploration GabrielleRab Jupyter Notebook
advent-of-code-2018 My solutions to the Advent of Code 2018 puzzles. kelly-sovacool Jupyter Notebook, Python, Shell
useful-programs thesuperlab Python, Shell


Repository Description Owner Language(s)
undergrad-comp-sci A collection of code I wrote for assignments in computer science courses as an undergraduate student at the University of Kentucky (2014-2018). kelly-sovacool Python, C++, Ruby, PHP, JavaScript, Perl, R, HTML, CSS, Makefile
bioinf603-fall2019 Presentation for BIOINF 603: Journal Club kelly-sovacool
jupyter-ci-mwe A minimal working example of using continuous integration to convert jupyter notebooks to PDFs. kelly-sovacool Jupyter Notebook
planets-kelly Teaching git at Software Carpentry Workshop 2019-07-01 kelly-sovacool
lang-stats Collect & plot personal programming language statistics from GitHub repos kelly-sovacool Python
miRNA-diff-expr Differential expression analysis for miRNA sequence data kelly-sovacool R
dmrr-submission-prep Prepare miRNA metadata for submission to the exRNA Data Coordination Center kelly-sovacool Jupyter Notebook, Python
geo109-project Lexington collision maps for GEO109 kelly-sovacool Python


Notes on software performance analysis
Monte Carlo simulation to estimate the value of Pi
Lab Meeting Code Review 2019-09-30: Visualizing weights of model features
The first program I ever wrote! In 10th grade I was inspired by my biomedical science class. Saved here for posterity.
Keybase proof
My bio for the GWC-DCMB website
Test conda environments on HPC batch scheduler
Google Drive file I/O with Colab Jupyter notebooks
Implementation of binary numbers & arithmetic for education
Plotting the titanic data: task for the Schloss lab code review led by Begüm


The table above and plots below are generated by the snakemake workflow in the Snakefile.


  1. Clone this repo:

    git clone
  2. Change the URL to your own GitHub repo:

    git remote set-url origin
  3. Install dependencies:

    conda env create -n git-repos -f config/environment.yaml
    conda activate git-repos
  4. Generate an access token and paste it into a plain text file. Create a YAML file config/config.yml with the path to your token file:

    token_filename: path/to/token

    Don't share your token with anyone!

Run it

Run the whole workflow with:


It will collect information about repos you contribute to, write the data to csv, update the README projects table, & make plots.

Don't edit the README file directly. You can edit the head and tail to modify what appears before and after the projects table.

Alternate workflow

If you don't want to use snakemake, you can run the Python & R scripts in code/.

python code/ --token path_to_token

It will then collect the information from GitHub, write a csv file to data/, and generate the table in under the Projects subheading. Only repositories which you own or which you have contributed to are included.

Alternatively, you can supply your username. It will then prompt you for your password:

python code/ --username your_username

To update the plots, run the R script:

R -e "source('code/plot_language_stats.R')"

Plots of programming language statistics are written to figures/.

Private repos

By default, private repos are excluded from the table. However, they are always included in statistics for plots. If you wish to include them, use the flag --include_private:

python code/ --token path_to_token --include_private


python code/ --username your_username --include_private





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