cody-mar10
PhD student in @AnantharamanLab interested in developing bioinformatic tools for viral metagenomics
Pinned Repositories
async-kegg
BIOL647_Digital_Biology_2021
BMI775_scripts
Disruptin_Fig5
Holt et al. 2021 J Bacteriol, https://doi.org/10.1128/JB.00214-21
esm_embed
Generate ESM-2 embeddings
genslm_embed
hyena-dna-embed
lightning-crossval
Cross validation with Lightning Fabric
pyapply
map variable input arguments to command line scripts/executables
pydantic-argparse
Typed Argument Parsing with Pydantic
cody-mar10's Repositories
cody-mar10/lightning-crossval
Cross validation with Lightning Fabric
cody-mar10/protein_set_transformer
Protein Set Transformer (PST) framework for training protein-language-model-based genome language models. Inference is possible for viral genomes using our pretrained viral foundation model.
cody-mar10/pyapply
map variable input arguments to command line scripts/executables
cody-mar10/pydantic-argparse
Typed Argument Parsing with Pydantic
cody-mar10/async-kegg
cody-mar10/BIOL647_Digital_Biology_2021
cody-mar10/BMI775_scripts
cody-mar10/Disruptin_Fig5
Holt et al. 2021 J Bacteriol, https://doi.org/10.1128/JB.00214-21
cody-mar10/esm_embed
Generate ESM-2 embeddings
cody-mar10/genslm_embed
cody-mar10/hyena-dna-embed
cody-mar10/intro_R
Brief intro to using R and ggplot
cody-mar10/lysis_curves
Plotting lysis curves with computational software, including how to format data from wide to long format
cody-mar10/jsonargparse
Implement minimal boilerplate CLIs derived from type hints and parse from command line, config files and environment variables
cody-mar10/mapping
cody-mar10/metapyrodigal
Using pyrodigal for orf prediction for large volumes of metagenomic sequences efficiently
cody-mar10/operon_finder
cody-mar10/optuna
A hyperparameter optimization framework
cody-mar10/phage_taxonomy_tool
cody-mar10/plate_reader
Process infinite200 pro plate reader tecan i-control 1.7.1.12 software plate reader files
cody-mar10/PST_host_prediction
cody-mar10/pyfastatools
cody-mar10/pyhmmsearch
Custom hmm search cli using pyhmmer
cody-mar10/skani-vMAG
cody-mar10/stacked_batch_chamfer_distance
All-against-all chamfer distance with graphs/point sets
cody-mar10/VIBRANT
Virus Identification By iteRative ANnoTation
cody-mar10/ViWrap
A wrapper to identify, bin, classify, and predict host-viral relationship for viruses