Pinned Repositories
BEEM
BEEM: Estimating Lotka-Volterra models from time-course microbiome sequencing data
CaDRReS
Cancer Drug Response prediction using a Recommender System
CaDRReS-Sc
CaDRReS-Sc is a framework for analyzing drug response heterogeneity based on single-cell RNA-seq data
GERMS_16S_pipeline
Pipeline for Illumina shotgun sequencing of 16S rRNA amplicon sequences
hospital_microbiome
INC-Seq
INC-Seq: Accurate single molecule reads using nanopore sequencing
lofreq
LoFreq Star: Sensitive variant calling from sequencing data
OncoIMPACT
Cancer-omics Data Integration
OPERA-MS
OPERA-MS - Hybrid Metagenomic Assembler
shotgun-metagenomics-pipeline
A pipeline for primary analysis of shotgun metagenomic sequencing data
Nagarajan Lab's Repositories
CSB5/lofreq
LoFreq Star: Sensitive variant calling from sequencing data
CSB5/OPERA-MS
OPERA-MS - Hybrid Metagenomic Assembler
CSB5/CaDRReS
Cancer Drug Response prediction using a Recommender System
CSB5/CaDRReS-Sc
CaDRReS-Sc is a framework for analyzing drug response heterogeneity based on single-cell RNA-seq data
CSB5/INC-Seq
INC-Seq: Accurate single molecule reads using nanopore sequencing
CSB5/shotgun-metagenomics-pipeline
A pipeline for primary analysis of shotgun metagenomic sequencing data
CSB5/hospital_microbiome
CSB5/BEEM
BEEM: Estimating Lotka-Volterra models from time-course microbiome sequencing data
CSB5/BEEM-static
BEEM-Static: An R package for inferring microbial interactions based on generalized Lotka-Volterra models
CSB5/OncoIMPACT
Cancer-omics Data Integration
CSB5/Recovery_Determinants_Study
Data and scripts of Antibiotic Recovery Study
CSB5/splash
Scripts to analyze data from the SPLASH protocol for generating in vivo RNA interactome maps
CSB5/hospital_microbiome_explorer
CSB5/MetageNN
MetageNN is a proof of concept neural network used to obtain a memory-efficient taxonomic classifier robust to sequencing errors and missing genomes
CSB5/TUGDA
TUGDA is a novel multi-task unsupervised domain adaptation method that leverages transfer learning from tasks/domains in a unified framework.
CSB5/driver_evaluation
CSB5/shotgunmetagenomics-nf
CSB5/SPMP
Singapore Platinum Metagenomes Project
CSB5/Candida_auris_CladeVI
WGS analysis for Candida auris
CSB5/decont
Decontaminate FastQ files
CSB5/EDDA
Power Your Design
CSB5/XNA_Basecaller
Code for paper: "Direct high-throughput deconvolution of unnatural bases via nanopore sequencing and bootstrapped learning"
CSB5/csb5.github.io
github pages for csb5
CSB5/food_centre_microbiome
City-wide metagenomic surveillance of food centres reveals location-specific microbial signatures and enrichment of antibiotic resistance genes
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
CSB5/SG90
CSB5/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"
CSB5/CPE-microbiome
CSB5/drug_response_consistency
Preliminary study of consistency among public cancer drug response datasets
CSB5/skin_metatranscriptome