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antartic

Pipeline for lineage assignment and other analyses post artic

arete

AMR/VF LGT focused bacterial genomics analysis workflow

bi-be-cs-183-2023

Introduction to Computational Biology and Bioinformatics Course at Caltech, 2023

bioinfotraining

copi

Pipeline for detecting coinfection of SARS-CoV-2 variants.

dengue-ngs

denguetemp

dev_runningtbprofiler

dev_srasubmission

digester-multisequencing

Repository for scripts and resources used for metagenomics with Nanopore, PacBio and Illumina sequencing

dnabert_s

DNABERT_S: Learning Species-Aware DNA Embedding with Genome Foundation Models

dockerimages

Docker files being maintained

epitomas

antimicrobial resistance

evo

DNA foundation modeling from molecular to genome scale

figaro

Pipeline for analyzing HIVDR samples sequenced using Oxford Nanopore Technologies (ONT).

geco-run

Running ncov2019-artic-nf in RITM-MBL compute

geojsonph

GeoJSON Repository of Philippine Maps

gisaid-scrapper

Scrapping tool for GISAID data regarding SARS-CoV-2

gwa_tutorial

A comprehensive tutorial about GWAS and PRS

handson-ml3

A series of Jupyter notebooks that walk you through the fundamentals of Machine Learning and Deep Learning in Python using Scikit-Learn, Keras and TensorFlow 2.

hyphy_tohoku

Positive selection analysis using Hyphy

karumata

HIV pipeline

kubidcoverage

maskbammix

massiveqc

The MassiveQC is a python-based tool for quality control of massive RNA-seq data.

melonmask

Masking regions flagged to be mix sites and regions with reads in the negative control

microbial_amr_ml

Code repository for machine learning and computational analysis of large-scale microbial genomics data (https://rdcu.be/9rHj)

mlstphylogeny

Phylogeny using MLST genes

monkeypox-nf

A monkeypox virus (MPXV) assembly pipeline using Nextflow for host-removal, reference-based assembly, and generation of sequence quality metrics for Illumina paired-end data using a shotgun metagenomic sequencing approach.

nano_recall

Oxford Nanopore HIV resistance analysis