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2023_talat_india-hww

Data, code, and analyses for Talat & Blake et al. (2023). Microbiology Spectrum. PMID: 36786639.

amriwa

Data analysis for the HWW metagenomes from Benin, Burkina Faso and Finland (AMRIWA project)

angelynlao.github.io

attack_amr

Source code for analysis of hospital wastewater metagenomic data

bacteriophagehostprediction

Code and database related to our manuscript "Predicting bacteriophage hosts based on receptor-binding proteins"

bayesimpute

a Bayesian imputation method for single-cell RNA-seq data

bert

TensorFlow code and pre-trained models for BERT

biobakery_workflows

bioBakery workflows is a collection of workflows and tasks for executing common microbial community analyses using standardized, validated tools and parameters.

bioinfo-combio

The rendered book can be found at https://liulab-dfci.github.io/bioinfo-combio/

bioinfodlsu.github.io

Website of the Bioinformatics Lab at DLSU Manila

candida-amr

comparison_of_da_microbiome_methods

comprehensive-adipocyte

The code related to the manuscript titled "A comprehensive mechanistic model of adipocyte signaling with layers of confidence"

cuimc-nyp_covid_autopsy_lung

db-benchmarks-2020

Database benchmarks using RESCRIPt

edmendoza.github.io

epi-impute

Epi-Impute: single-cell RNA-seq imputation via integration with single-cell ATAC-seq data

esviritu

Read mapping pipeline for detection and measurement of virus pathogens from metagenomic or clinical data

f1000_workflow

faraway

R package, scripts and documentation supporting R books by Julian Faraway

food-dbs

Repository used for creating/maintaining FoodSeq reference databases. Forked from Brianna Petrone's original repository.

gaussian-process-regression-tutorial

An Intuitive Tutorial to Gaussian Processes Regression

inphared

Providing up-to-date phage genome databases, metrics and useful input files for a number of bioinformatic pipelines.

jmodeltest2

Automatically exported from code.google.com/p/jmodeltest2

learn-wdl

Educational materials for learning WDL

mb-pipeline

Code for analyzing metabarcoding datasets

mice8992-2016

Code used in MiCE 8992 Spring 2016

phage-host-prediction

Our work shows that the use of embeddings of receptor-binding proteins presents improvements over handcrafted genomic and protein sequence features for phage-host interaction prediction, with the highest performance obtained using the transformer-based autoencoder protein language model ProtT5

phyloseq_sankey

A function that makes it easy to make interactive Sankey plots from phyloseq objects. Based on the hiervis package which is based on d3-hierarchy and d3-hiervis.

plant-richness

Code accompanying the manuscript "Diversity of plant DNA in stool is linked to dietary quality, age, and household income"