Nagarajan Lab

lofreq

LoFreq Star: Sensitive variant calling from sequencing data

OPERA-MS

OPERA-MS - Hybrid Metagenomic Assembler

CaDRReS

Cancer Drug Response prediction using a Recommender System

GERMS_16S_pipeline

Pipeline for Illumina shotgun sequencing of 16S rRNA amplicon sequences

INC-Seq

INC-Seq: Accurate single molecule reads using nanopore sequencing

CaDRReS-Sc

CaDRReS-Sc is a framework for analyzing drug response heterogeneity based on single-cell RNA-seq data

hospital_microbiome

shotgun-metagenomics-pipeline

A pipeline for primary analysis of shotgun metagenomic sequencing data

BEEM

BEEM: Estimating Lotka-Volterra models from time-course microbiome sequencing data

BEEM-static

BEEM-Static: An R package for inferring microbial interactions based on generalized Lotka-Volterra models

OncoIMPACT

Cancer-omics Data Integration

TUGDA

TUGDA is a novel multi-task unsupervised domain adaptation method that leverages transfer learning from tasks/domains in a unified framework.

hospital_microbiome_explorer

splash

Scripts to analyze data from the SPLASH protocol for generating in vivo RNA interactome maps

driver_evaluation

MetageNN

MetageNN is a proof of concept neural network used to obtain a memory-efficient taxonomic classifier robust to sequencing errors and missing genomes

Recovery_Determinants_Study

Data and scripts of Antibiotic Recovery Study

shotgunmetagenomics-nf

SPMP

Singapore Platinum Metagenomes Project

decont

Decontaminate FastQ files

EDDA

Power Your Design

GiRaF

Robust, Computational Identification of Influenza Reassortments via Graph Mining

Candida_auris_CladeVI

WGS analysis for Candida auris

csb5.github.io

github pages for csb5

PLoT-ME

Clustering of Genomic databases (RefSeq) for high memory reduction of taxonomic classifiers (Kraken2, Centrifuge). Designed to pre-processing long DNA reads (Nanopore/PacBio) into these clusters for further classification

AD-caregiver-manuscript

Files and scripts to generate figures for the manuscript titled "Shared signatures and divergence in skin microbiomes of children with atopic dermatitis and their adult caregivers"

CPE-microbiome

drug_response_consistency

Preliminary study of consistency among public cancer drug response datasets

food_centre_microbiome

City-wide metagenomic surveillance of food centres reveals location-specific microbial signatures and enrichment of antibiotic resistance genes

SG90