Software¶
Web applications, pipelines, R packages and tutorials, from clinical mitochondrial genetics to scheduling and field-guide keys. Most are on GitHub.
Web Application
MITOMASTER
Web application that allows clinicians to quickly investigate mitochondrial mutations in sequenced or genotyped samples. Used worldwide for mitochondrial genetics research.
Django/Python
myBiC
Django application that manages user authentication and presentation of bioinformatics deliverables. Streamlines report delivery for core facilities.
Pipeline
InSiPiD
Integration Site Pipeline and Database - comprehensive toolset for managing viral integration site data processing, annotation, and analysis.
PHP · 2004
Alternative Splicing Gallery (ASG)
Searchable web gallery of splicing graphs for human genes, built from Ensembl, UniGene and EST alignments. Each graph shows every alternative transcript at once, colors cassette exons, intron retentions and competing splice sites, and lets you pick exons to assemble a transcript sequence.
Python · 2025
Rhylthyme Case study
A JSON-based markup language and toolchain for describing real-time programs that coordinate parallel tracks of work with resource constraints, timing dependencies, and flexible execution patterns. Includes a CLI runner, web visualizer, and MCP server for AI-assisted schedule generation.
R · 2020
dimoose
R package for dichotomous identification keys. Build a key from a plain spreadsheet with photos, draw it as a box diagram, or turn it into an offline web wizard for the field; also imports FishBase keys and generates keys from photos (CLIP/BioCLIP), sequence alignments and trait matrices. Includes an illustrated key to Montana's native broadleaf trees.
Python · 2017
awesome-reproducible-research
A curated list of reproducible research case studies, projects, tutorials, and media. Community-driven resource with 356+ stars.
R · 2011
berrylogo
A better seqLogo implementation for creating sequence logos in R. Enhanced visualization tool with 12+ stars.
HTML/R · 2016
opensnp
Validation of published GWAS studies using OpenSNP volunteered data. Binderized for reproducible analysis.
Python
clk
Command-line toolkit for bioinformatics workflows and data processing automation.
R/Snakemake · 2016
PAS_Premium
What do people pay to live in the Penn Alexander School catchment? A fully reproducible housing-price analysis of the West Philadelphia catchment, built with Snakemake, R, Conda and Docker.
More repositories¶
Tutorial · 2014
SandwichesWithSnakemake
Beginner's tutorial to Snakemake workflow management system. Popular educational resource with 70+ stars.
CSS/Snakemake · 2014
snakemake-example
RNA-Seq Snakemake example with Jekyll homepage creation. Complete workflow demonstration with 20+ stars.
Node.js · 2013
blast-wrapper
Node.js web-service wrapper for fetching pairwise BLAST alignments against a fixed reference.
R/Bioinformatics
placenta
Comprehensive analysis pipeline and resources for placental genomics research and developmental studies.
Genomics · 2022
ancestryinformativemarkers
Public Ancestry Informative Markers (AIMs) dataset and tools for population genetics analysis.
Python · 2020
ontopop
Analysis tool to measure popularity and usage of biological ontologies across scientific literature.
R/Bioinformatics
m6a
Analysis tools and workflows for N6-methyladenosine (m6A) RNA modification detection and quantification.
Documentation
metadata-in-rcr
Resources and examples for metadata standards in reproducible computational research. Supporting materials for academic publications.
JavaScript · 2018
fcs_api
Node API to the CytoVas flow cytometry database that serves queries and runs reports.
Python · 2018
fcs_lambda
AWS Lambda function that parses FCS files as they land in S3 and stores their metadata in DynamoDB.
HTML · 2018
fcs_upbrowse
CytoVas uploader and file browser for FCS files.
R · 2018
fcs_batch_titration
Container that processes one or more FCS files on AWS Batch or another runner and produces an HTML titration report.
Python · 2018
fcs_aws_tools
Day-to-day CytoVas tools for FCS files in S3 and the database.
R/Bioinformatics
mcmanus_ant1
Analysis pipeline for mitochondrial ANT1 gene studies and associated metabolic pathways.
Python
asciiruler
Command-line tool for generating ASCII rulers and measurement guides for sequence analysis.
Perl/Shell
standardized-velvet-assembly-report
Standardized reporting pipeline for Velvet genome assembly results and quality metrics.