Repositories list

• crc-survival

  Public
  Code for Tumor Microbiome is associated with survival in late stage colorectal cancer

  Jupyter Notebook

  •1•0•0•0•Updated Dec 12, 2024Dec 12, 2024

• ML_swemami

  Public
  Machine learning code used for SweMaMi study on miscarriage

  0•1•0•0•Updated Oct 1, 2024Oct 1, 2024

• valody

  Public
  A tool to assign VAginaL DYnamic categories to individuals based on their Valencia CST assignments

  Python

  •

  MIT License

  •1•2•0•0•Updated Sep 30, 2024Sep 30, 2024

• stag-mwc

  Public
  StaG Metagenomic Workflow Collaboration

  researchmetagenomicsmicrobiome+ 2metagenomic-analysissnakemake-workflows

  Python

  •

  MIT License

  •13•29•4•1•Updated Aug 20, 2024Aug 20, 2024

• rstudio_singularity

  Public
  Run Rstudio with Singularity

  Shell

  •

  MIT License

  •0•0•0•0•Updated May 6, 2024May 6, 2024

• ENA_submission_notebooks

  Public
  Notebooks in Jupyter that can be used for filling out meta data checklists required for uploading data to the ENA

  Jupyter Notebook

  •0•0•0•0•Updated Apr 12, 2024Apr 12, 2024

• 194_BOuru_shotgun_analysis

  Public
  0•0•0•0•Updated Nov 30, 2023Nov 30, 2023

• slurm-jobstats

  Public
  Compute job statistics for Slurm jobs

  Python

  •

  MIT License

  •0•2•0•0•Updated Nov 7, 2023Nov 7, 2023

• sm3

  Public
  Simple Snakemake example

  Python

  •

  MIT License

  •0•1•0•0•Updated May 2, 2023May 2, 2023

• ctmr-superset

  Public
  Custom Docker image for Apache Superset

  Shell

  •

  Apache License 2.0

  •0•0•0•0•Updated Apr 25, 2023Apr 25, 2023

• gitdemo

  Public
  0•0•0•0•Updated Apr 20, 2023Apr 20, 2023

• s3etag

  Public
  Compute ETag of local file and compare to file on S3

  Python

  •0•0•0•0•Updated Feb 2, 2023Feb 2, 2023

• bioinformatics_curriculum

  Public
  Some ideas on things to learn to get started with bioinformatics

  MIT License

  •7•17•1•0•Updated Dec 5, 2022Dec 5, 2022

• sourmash_sketch

  Public
  Compare samples based on kmers using Sourmash sketch

  Nextflow

  •

  MIT License

  •0•1•0•0•Updated Sep 13, 2022Sep 13, 2022

• claritylims

  Public
  Customizations for our GenoLogics BaseSpace Clarity LIMS

  lims

  Python

  •

  MIT License

  •2•2•17•2•Updated Jul 8, 2022Jul 8, 2022

• pseudomonas_boanensis_db1

  Public
  comparative genomic analysis for Pseudomonas boanensis DB1

  Jupyter Notebook

  •0•0•0•0•Updated Mar 14, 2022Mar 14, 2022

• run_in_parallel

  Public
  Run simple commands in parallel on Slurm

  Python

  •

  MIT License

  •0•0•4•0•Updated Feb 11, 2022Feb 11, 2022

• Salgae_c-di-GMP_analysis

  Public
  Minhash/pangenome analysis notebooks and associated files

  Jupyter Notebook

  •1•0•0•0•Updated Jan 5, 2022Jan 5, 2022

• ctmr_lab_interface

  Public
  Scripts used to facilitate the interface between bioinformatic and experimental microbiology

  Python

  •

  Creative Commons Zero v1.0 Universal

  •0•0•0•0•Updated Dec 17, 2021Dec 17, 2021

• optivag

  Public
  Database for annotating vaginal communities

  Python

  •

  MIT License

  •2•1•0•0•Updated Oct 8, 2021Oct 8, 2021

• print_ctmr_labels

  Public
  Print CTMR labels on Zebra printer

  Python

  •0•2•4•1•Updated May 21, 2021May 21, 2021

• estimate_seq_depth_notebooks

  Public
  Notebooks for the estimate_seq_depth project

  Jupyter Notebook

  •0•0•0•0•Updated May 20, 2021May 20, 2021

• SARS-CoV-2_Multi-PCR_v1.0

  Public
  SARS-CoV-2 analysis pipeline for multiplex-PCR MPS(Massive Parrallel Sequencing) data

  Perl

  •11•0•0•0•Updated May 18, 2021May 18, 2021

• BVAB-and-Lac-sequences

  Public
  The database contains a collection of sequences for BVAB (Bacterial vaginosis associated bacteria) and common vaginal Lactobacillus species.

  0•1•0•0•Updated Jul 5, 2020Jul 5, 2020

• Zebra_GK420t

  Public
  Script for printing labels on Zebra GK420t

  Python

  •

  MIT License

  •0•0•0•0•Updated Jun 11, 2020Jun 11, 2020

• mgi-ncov19-snakemake

  Public
  Python

  •1•1•0•0•Updated Apr 14, 2020Apr 14, 2020

• dockerfiles

  Public archive
  Dockerfiles used at CTMR

  Dockerfile

  •

  MIT License

  •0•0•2•1•Updated Mar 29, 2019Mar 29, 2019

• Amplicon_workflows

  Public
  Workflows and scripts for amplicon sequencing processing

  Python

  •1•1•0•0•Updated Jan 24, 2019Jan 24, 2019

• list_scanner

  Public
  List scanning application

  Python

  •

  MIT License

  •0•1•0•0•Updated Oct 24, 2018Oct 24, 2018

• estimate_seq_depth

  Public
  A small workflow that simulates metagenomes for use in estimating the required sequencing depth for different type of microbiome samples

  Groovy

  •

  MIT License

  •0•0•0•0•Updated Dec 28, 2017Dec 28, 2017