Repositories list

• daylily-omics-analysis

  Public
  Breaking out the omics analysis bits from the AWS infra bits

  Python

  •

  GNU General Public License v3.0

  •1•2•0•0•Updated Jul 28, 2025Jul 28, 2025

• daylily-ephemeral-cluster

  Public
  A NGS analysis framework for WGS data, which automates the entire process of spinning up AWS EC2 spot instances and processing FASTQ to snvVCF in <60m, for dollars a sample and achieving Fscores of 0.998.

  awsbioinformaticsscalable+ 16ec2ngsslurmbudgetingbioinformatics-pipelineinformaticsscaling+ 9

  Shell

  •

  GNU General Public License v3.0

  •3•23•28•0•Updated Jul 28, 2025Jul 28, 2025

• bloom

  Public
  Templated Abstract Polymorphic (and opinionated) LIMS

  Python

  •

  Mozilla Public License 2.0

  •1•1•26•3•Updated Jul 5, 2025Jul 5, 2025

• daylily-ephemeral-cluster-tmp

  Public archive
  Breaking out the AWS Parallel Cluster infra from the analysis pipelines

  Shell

  •

  GNU General Public License v3.0

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

• rna-seq-star-deseq2

  Public
  RNA-seq workflow using STAR and DESeq2

  Python

  •

  MIT License

  •209•1•0•0•Updated Jun 26, 2025Jun 26, 2025

• .github

  Public
  github profile README.md

  MIT License

  •0•0•0•0•Updated May 29, 2025May 29, 2025

• snakemake-executor-plugin-pcluster-slurm

  Public
  slurm executor for use by snakemake when running on the slurm flavor which is unique to aws parallel cluster slrum pcluster.

  pluginawssnakemake+ 5sbatchslurmsnakemake-pluginpclusteraws-parallel-cluster

  Python

  •

  MIT License

  •0•1•0•0•Updated May 29, 2025May 29, 2025

• deepvariant-avx512

  Public
  DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •758•0•0•0•Updated May 20, 2025May 20, 2025

• daylily_giab_analyses

  Public
  HTML

  •

  MIT License

  •0•0•0•0•Updated Mar 20, 2025Mar 20, 2025

• slim_goodie

  Public
  Minimal http server ( fastapi jinja2 supabase oauth2 )

  Python

  •

  MIT License

  •0•0•0•0•Updated Dec 30, 2024Dec 30, 2024

• github_markdown_text_colorizer

  Public
  Service to return images of text where the input text can have font, font size and color set

  Python

  •

  MIT License

  •0•1•0•0•Updated Dec 2, 2024Dec 2, 2024

• snakemake

  Public
  This is the development home of the workflow management system Snakemake. For general information, see

  HTML

  •

  MIT License

  •601•0•0•0•Updated Nov 27, 2024Nov 27, 2024

• snakemake-executor-plugin-pcluster-slurm-ref

  Public archive
  A Snakemake executor plugin for submitting jobs to a SLURM cluster

  pluginawssnakemake+ 5slurmparallel-clustersnakemake-pluginpclusteraws-parallel-cluster

  Python

  •

  MIT License

  •34•1•0•0•Updated Oct 21, 2024Oct 21, 2024

• aws-parallelcluster-cost-allocation-tags

  Public
  Shell

  •

  MIT No Attribution

  •8•0•0•0•Updated Oct 19, 2024Oct 19, 2024

• transXpress

  Public
  transXpress: a Snakemake pipeline for streamlined de novo transcriptome assembly and annotation

  Python

  •

  GNU General Public License v3.0

  •14•0•0•0•Updated Oct 9, 2024Oct 9, 2024

• metapub_peep

  Public
  Slim fastapi / jinja2 web application to expose metapub command line functionality.

  Python

  •

  MIT License

  •0•0•0•0•Updated Sep 15, 2024Sep 15, 2024

• deepvariant

  Public
  DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •758•0•0•0•Updated Sep 2, 2024Sep 2, 2024

• Atlas

  Public
  ATLAS is an open source software tool for researchers to conduct scientific analyses on standardized observational data

  JavaScript

  •

  Apache License 2.0

  •145•0•0•0•Updated Aug 30, 2024Aug 30, 2024

• metapub

  Public
  Python toolkit for NCBI metadata (via eutils) and pubmed article text mining -- official primary repo.

  Python

  •

  Apache License 2.0

  •26•0•0•0•Updated Aug 16, 2024Aug 16, 2024

• xcures_day

  Public
  python wrapper for the xcures REST api

  Python

  •

  MIT License

  •0•0•0•0•Updated Jun 25, 2024Jun 25, 2024

• smk-simple-slurm

  Public
  A simple Snakemake profile for Slurm without --cluster-config

  Shell

  •

  Creative Commons Zero v1.0 Universal

  •19•0•0•0•Updated Jun 20, 2024Jun 20, 2024

• zebra_day

  Public
  Zebra Label Printing library & API (for network connected printers). Manage 100s of printers and ZPL label templates in one place.

  pythonawsbioinformatics+ 16barcodebarcode-generatorsalesforcezplzebra-printerzebradiscovery-service+ 9

  Python

  •

  GNU General Public License v3.0

  •2•10•2•1•Updated May 9, 2024May 9, 2024

• jinja2_fmt_day

  Public
  Simple tool to standardize the indentation of jinja2 files.

  Python

  •0•0•0•0•Updated Dec 22, 2023Dec 22, 2023

• img_stitcher_day

  Public
  Playing around with merging images taken of the outside of a tube.

  Python

  •

  MIT License

  •0•1•0•0•Updated Nov 24, 2023Nov 24, 2023

• fedex_tracking_day

  Public
  Python Module Interfacing w/The FedEx Tracking API

  shippingsimplepython3+ 5federatedfedexfedexapifedex-apipython

  Python

  •

  MIT License

  •0•4•0•0•Updated Nov 4, 2023Nov 4, 2023

• yaml_config_day

  Public
  Slim Python yaml Config Manager

  configurationpython3yaml-configuration+ 5yaml-configsyaml-configyaml-configurationspythonyaml

  Python

  •

  MIT License

  •0•0•0•0•Updated Nov 1, 2023Nov 1, 2023

• tmhmm.py

  Public
  A transmembrane helix finder in Python 3.

  Python

  •

  MIT License

  •12•0•0•0•Updated Oct 4, 2023Oct 4, 2023

• bulk_sms

  Public
  MIT License

  •0•0•0•0•Updated Jun 18, 2023Jun 18, 2023

• gspread

  Public
  Google Sheets Python API

  Python

  •

  MIT License

  •967•0•0•0•Updated May 16, 2023May 16, 2023

• bwa-mem-scale

  Public
  C++

  •

  Other

  •2•0•0•0•Updated Apr 30, 2023Apr 30, 2023