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    38 repositories

    • .github

      Public
      github profile README.md
      MIT License
      •0•0•0•0•Updated Dec 12, 2024Dec 12, 2024

    • bloom

      Public
      Templated Abstract Polymorphic (and opinionated) LIMS
      Python
      •
      Mozilla Public License 2.0
      •1•0•25•0•Updated Dec 11, 2024Dec 11, 2024

    • daylily

      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.
      awsbioinformaticssnakemakescalableec2ngsslurmbudgetingbioinformatics-pipelineinformatics
      WDL
      •
      GNU General Public License v3.0
      •1•20•25•0•Updated Dec 5, 2024Dec 5, 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
      •561•0•0•0•Updated Nov 27, 2024Nov 27, 2024

    • rna-seq-star-deseq2

      Public
      RNA-seq workflow using STAR and DESeq2
      Python
      •
      MIT License
      •205•0•0•0•Updated Oct 24, 2024Oct 24, 2024

    • slim_goodie

      Public
      Minimal http server ( fastapi jinja2 supabase oauth2 )
      HTML
      •
      MIT License
      •0•0•0•0•Updated Oct 23, 2024Oct 23, 2024

    • 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.
      pluginawssnakemakesbatchslurmsnakemake-pluginpclusteraws-parallel-cluster
      Python
      •
      MIT License
      •0•0•0•0•Updated Oct 22, 2024Oct 22, 2024

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

      Public
      A Snakemake executor plugin for submitting jobs to a SLURM cluster
      pluginawssnakemakeslurmparallel-clustersnakemake-pluginpclusteraws-parallel-cluster
      Python
      •
      MIT License
      •20•1•0•0•Updated Oct 21, 2024Oct 21, 2024

    • aws-parallelcluster-cost-allocation-tags

      Public
      Shell
      •
      MIT No Attribution
      •7•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
      •13•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
      •728•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
      •138•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
      •20•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
      •18•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.
      pythonawsbioinformaticsbarcodebarcode-generatorsalesforcezplzebra-printerzebradiscovery-service
      Python
      •
      GNU General Public License v3.0
      •2•9•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
      shippingsimplepython3federatedfedexfedexapifedex-apipython
      Python
      •
      MIT License
      •0•2•0•0•Updated Nov 4, 2023Nov 4, 2023

    • yaml_config_day

      Public
      Slim Python yaml Config Manager
      configurationpython3yaml-configurationyaml-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
      •949•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

    • accept-a-payment

      Public
      Learn how to accept a payment from customers around the world with a variety of payment methods.
      JavaScript
      •
      MIT License
      •504•0•0•0•Updated Mar 30, 2023Mar 30, 2023

    • cronicle-edge

      Public
      Cronicle V2 (Orchestra) community prototype
      JavaScript
      •
      Other
      •26•0•0•0•Updated Feb 26, 2023Feb 26, 2023

    • HGTector

      Public
      HGTector2: Genome-wide prediction of horizontal gene transfer based on distribution of sequence homology patterns.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •35•0•0•0•Updated Jan 21, 2023Jan 21, 2023

    • sambamba

      Public
      Tools for working with SAM/BAM data
      D
      •
      GNU General Public License v2.0
      •106•0•0•0•Updated Jan 19, 2023Jan 19, 2023