Pinned Repositories
BACTpipe
BACTpipe: An assembly and annotation pipeline for bacterial genomics
bioinformatics_curriculum
Some ideas on things to learn to get started with bioinformatics
claritylims
Customizations for our GenoLogics BaseSpace Clarity LIMS
optivag
Database for annotating vaginal communities
print_ctmr_labels
Print CTMR labels on Zebra printer
run_in_parallel
Run simple commands in parallel on Slurm
slurm-jobstats
Compute job statistics for Slurm jobs
sm3
Simple Snakemake example
stag-mwc
StaG Metagenomic Workflow Collaboration
valody
A tool to assign VAginaL DYnamic categories to individuals based on their Valencia CST assignments
CTMR's Repositories
ctmrbio/stag-mwc
StaG Metagenomic Workflow Collaboration
ctmrbio/BACTpipe
BACTpipe: An assembly and annotation pipeline for bacterial genomics
ctmrbio/bioinformatics_curriculum
Some ideas on things to learn to get started with bioinformatics
ctmrbio/claritylims
Customizations for our GenoLogics BaseSpace Clarity LIMS
ctmrbio/print_ctmr_labels
Print CTMR labels on Zebra printer
ctmrbio/slurm-jobstats
Compute job statistics for Slurm jobs
ctmrbio/valody
A tool to assign VAginaL DYnamic categories to individuals based on their Valencia CST assignments
ctmrbio/Amplicon_workflows
Workflows and scripts for amplicon sequencing processing
ctmrbio/BVAB-and-Lac-sequences
The database contains a collection of sequences for BVAB (Bacterial vaginosis associated bacteria) and common vaginal Lactobacillus species.
ctmrbio/list_scanner
List scanning application
ctmrbio/mgi-ncov19-snakemake
ctmrbio/ML_swemami
Machine learning code used for SweMaMi study on miscarriage
ctmrbio/optivag
Database for annotating vaginal communities
ctmrbio/sm3
Simple Snakemake example
ctmrbio/sourmash_sketch
Compare samples based on kmers using Sourmash sketch
ctmrbio/dockerfiles
Dockerfiles used at CTMR
ctmrbio/run_in_parallel
Run simple commands in parallel on Slurm
ctmrbio/194_BOuru_shotgun_analysis
ctmrbio/crc-survival
Code for Tumor Microbiome is associated with survival in late stage colorectal cancer
ctmrbio/ctmr-superset
Custom Docker image for Apache Superset
ctmrbio/ctmr_lab_interface
Scripts used to facilitate the interface between bioinformatic and experimental microbiology
ctmrbio/ENA_submission_notebooks
Notebooks in Jupyter that can be used for filling out meta data checklists required for uploading data to the ENA
ctmrbio/estimate_seq_depth_notebooks
Notebooks for the estimate_seq_depth project
ctmrbio/gitdemo
ctmrbio/pseudomonas_boanensis_db1
comparative genomic analysis for Pseudomonas boanensis DB1
ctmrbio/rstudio_singularity
Run Rstudio with Singularity
ctmrbio/s3etag
Compute ETag of local file and compare to file on S3
ctmrbio/Salgae_c-di-GMP_analysis
Minhash/pangenome analysis notebooks and associated files
ctmrbio/SARS-CoV-2_Multi-PCR_v1.0
SARS-CoV-2 analysis pipeline for multiplex-PCR MPS(Massive Parrallel Sequencing) data
ctmrbio/Zebra_GK420t
Script for printing labels on Zebra GK420t