yupaulk

yupaulk.github.io

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.

bioinfodlsu.github.io

Website of the Bioinformatics Lab at DLSU Manila

candida-amr

comprehensive-adipocyte

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

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

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.

inphared

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

mb-pipeline

Code for analyzing metabarcoding datasets

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

plant-richness

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

protein-localization

Using Transformer protein embeddings with a linear attention mechanism to make SOTA de-novo predictions for the subcellular location of proteins :microscope:

ProtTrans

ProtTrans is providing state of the art pretrained language models for proteins. ProtTrans was trained on thousands of GPUs from Summit and hundreds of Google TPUs using Transformers Models.

reference_database_creator

creating reference databases for amplicon sequencing

RESCRIPt

REference Sequence annotation and CuRatIon Pipeline

samar

Samar is a pipeline for speedy, assembly-free differential gene expression analysis in non-model organisms.

sanbomics_scripts

scripts and notebooks from sanbomics

splatter

Simple simulation of single-cell RNA sequencing data

stat_rethinking_2023

Statistical Rethinking Course for Jan-Mar 2023

transformers

🤗 Transformers: State-of-the-art Machine Learning for Pytorch, TensorFlow, and JAX.

trnL-pipeline

trnL metabarcoding protocols and bioinformatic pipeline