Repositories list

• carnation

  Public
  Interactive shiny app for deeply exploring bulk RNA-Seq data

  R

  •

  Other

  •1•2•0•1•Updated Mar 20, 2026Mar 20, 2026

• aksenova-2025

  Public
  R

  •0•0•0•0•Updated Mar 20, 2026Mar 20, 2026

• cascadeR

  Public
  Interactive shiny dashboard for comprehensive single-cell data exploration

  R

  •

  Other

  •0•0•0•1•Updated Mar 18, 2026Mar 18, 2026

• lee-2026

  Public
  Workflows and code to reproduce results from Lee 2026

  Python

  •

  MIT License

  •0•0•0•0•Updated Jan 21, 2026Jan 21, 2026

• AnalyzeOlink

  Public
  R package, RMarkdown files, and Snakemake workflow for analyzing Olink proximal extension assay data

  R

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Dec 18, 2025Dec 18, 2025

• trip-wire-test-data

  Public
  Test data for the trip-wire workflow

  Python

  •

  MIT License

  •0•0•0•0•Updated Dec 11, 2025Dec 11, 2025

• training

  Public
  Source code of https://nichd-bspc.github.io/training

  CSS

  •2•0•0•0•Updated Jul 4, 2025Jul 4, 2025

• bacteria-dash

  Public
  Python

  •0•0•0•0•Updated Jun 25, 2025Jun 25, 2025

• intro-rnaseq-hpc

  Public
  HTML

  •0•0•5•0•Updated May 19, 2025May 19, 2025

• branched-docs-demo

  Public
  Example of building HTML docs hosted on github.io with subdirectories for selected branches

  MIT License

  •1•0•0•1•Updated Apr 16, 2025Apr 16, 2025

• termseq-peaks

  Public
  Peak-calling for term-seq data in bacteria

  Python

  •

  MIT License

  •0•6•0•0•Updated Apr 10, 2025Apr 10, 2025

• multiome-wf

  Public
  Python

  •0•0•0•0•Updated Mar 28, 2025Mar 28, 2025

• thongdee-2025

  Public
  Source code for Thongdee et al 2025, "Modulation of protein activity by small RNA base pairing internal to coding sequences"

  Python

  •

  MIT License

  •0•0•0•0•Updated Mar 27, 2025Mar 27, 2025

• docker-pilot

  Public
  Testing integration with GH Actions & quay.io

  Dockerfile

  •0•0•0•0•Updated Mar 13, 2025Mar 13, 2025

• snakemake_profile

  Public
  Minimal snakemake profile for biowulf cluster

  Python

  •3•0•0•0•Updated Jan 21, 2025Jan 21, 2025

• chrom-name-mappings

  Public
  Automated workflow for matching chromosome names between genome assemblies.

  Python

  •

  MIT License

  •0•0•0•0•Updated Sep 25, 2024Sep 25, 2024

• effort-log

  Public
  Dockerized Flask web app for lightweight project tracking

  Python

  •

  MIT License

  •0•3•0•1•Updated Nov 25, 2023Nov 25, 2023

• r-setup

  Public
  Documentation and config files for setting up R

  Vim Script

  •0•3•0•0•Updated Apr 10, 2023Apr 10, 2023

• trip-wire-data

  Public
  MIT License

  •0•0•0•0•Updated Sep 27, 2022Sep 27, 2022

• documentation-template

  Public
  Repository demonstrating how to deploy Sphinx documentation to GitHub Pages

  Python

  •

  MIT License

  •0•3•0•0•Updated Sep 24, 2022Sep 24, 2022

• spatial_clustering

  Public
  Assess the spatial clustering of variants within cDNA with permutation testing

  Python

  •

  MIT License

  •0•0•0•0•Updated Jan 27, 2022Jan 27, 2022

• chooseR

  Public
  An R framework for choosing clustering parameters

  R

  •

  GNU General Public License v3.0

  •10•0•0•0•Updated Sep 29, 2021Sep 29, 2021

• olink

  Public
  Tools for analyzing data from Olink assays

  Shell

  •

  MIT License

  •0•0•9•0•Updated Mar 22, 2021Mar 22, 2021

• httools

  Public
  Tool to map and quantify retroelements integrations

  Python

  •

  MIT License

  •0•0•1•0•Updated Feb 22, 2021Feb 22, 2021

• geo_prepper

  Public
  Tool to help prepare data for GEO submission

  Python

  •

  GNU General Public License v3.0

  •1•3•0•0•Updated Dec 22, 2020Dec 22, 2020

• rhoterm-peaks

  Public
  Call peaks at Rho termination regions

  Python

  •

  MIT License

  •0•0•0•0•Updated Nov 21, 2020Nov 21, 2020