yupaulk

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)

ancientDNA

angelynlao.github.io

attack_amr

Source code for analysis of hospital wastewater metagenomic data

AuditingBiologicalML

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

GuidedSparseKmeans

yupaulk.github.io

yupaulk/2023_Talat_India-HWW

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

yupaulk/AMRIWA

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

yupaulk/AuditingBiologicalML

yupaulk/BacteriophageHostPrediction

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

yupaulk/bert

TensorFlow code and pre-trained models for BERT

yupaulk/bioinfo-combio

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

yupaulk/BOOST-GP

Bayesian mOdeling Of Spatial Transcriptomics via Gaussian Process

yupaulk/Comparison_of_DA_microbiome_methods

yupaulk/comprehensive-adipocyte

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

yupaulk/CUIMC-NYP_COVID_autopsy_lung

yupaulk/db-benchmarks-2020

Database benchmarks using RESCRIPt

yupaulk/driver

Utility Functions from Justin Silverman

yupaulk/inphared

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

yupaulk/jmodeltest2

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

yupaulk/learn-wdl

Educational materials for learning WDL

yupaulk/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

yupaulk/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.

yupaulk/plant-richness

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

yupaulk/protein-localization

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

yupaulk/R-t2d-deseq2-phyloseq

Analysis of metatranscriptome data from human microbiomes using phyloseq and deseq2

yupaulk/samar

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

yupaulk/sanbomics_scripts

scripts and notebooks from sanbomics

yupaulk/scGAE

single-cell graph autoencoder

yupaulk/scImpute

Accurate and robust imputation of scRNA-seq data

yupaulk/splatter

Simple simulation of single-cell RNA sequencing data

yupaulk/splatter-paper

Data and analysis for the Splatter paper

yupaulk/stat_rethinking_2023

Statistical Rethinking Course for Jan-Mar 2023

yupaulk/transformers

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

yupaulk/trnL-pipeline

trnL metabarcoding protocols and bioinformatic pipeline

yupaulk/Urban-MAGs