A hybrid metagenomic assembler which combines the advantages of short and long-read technologies to provide high quality assemblies, addressing issues of low contiguity for short-read only assemblies, and low base-pair quality for long-read only assemblies.
fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data. Sensitive to rare variants (<1%).
Accurate single molecule reads using nanopore sequencing
A highly sensitive and accurate mapper for long, error-prone reads
Consensus module for raw de novo DNA assembly of long uncorrected reads.
Chemical utilized probing interrogated using nanopores
A MinION-based pipeline for fast and cost-effective DNA barcoding
Robust, Computational Identification of Influenza Reassortments via Graph Mining
Modelling microbial community dynamics based on longitudinal metagenomic sequencing data (16S or shotgun-metagenomics). It is based on the commonly used generalized Lotka-Volterra modelling (gLVM) framework.
Learning directed microbial interactions from cross-sectional microbiome profiling data based on the generalized Lotka-Volterra model (gLVM).
SVM/regex abstract parser for identification of microbial interactions
Pre-classification of Long-reads for Memory Efficient Taxonomic assignment
Task uncertainty guided domain adaptation for robust generalization of cancer drug response prediction from in in vitro to in vivo settings
OncoIMPACT is a first-in-class algorithmic framework that nominates patient-specific driver genes by integratively modeling genomic mutations (point, structural and copy-number) and the resulting perturbations in transcriptional programs via defined molecular networks.
Cancer Drug Response prediction using a Recommender System (CaDRReS) is based on the matrix factorization approach to predict which drugs are sensitive for an unseen cell line.
A framework for analyzing drug response heterogeneity based on single-cell RNA-seq data
Experimental Design in Differential Abundance analysis (EDDA) is a tool for systematic assessment of the impact of experimental design and the statistical test used on the ability to detect differential abundance.
A Nextflow re-implementation of the original pipeline used by MTMS at the Genome Institute of Singapore (GIS).
a remake of the original 16S pipeline developed with in the Genome Institute of Singapore, designed for Illumina shotgun sequencing of 16S rRNA amplicon sequences.
A collection of scripts used for the analysis of RNA viruses, based on LoFreq
Decontaminate FastQ files by mapping with BWA-MEM against a given source.
Pipeline for mutation benchmarking of various softwares.
a proof-of-concept 3D model to explore the hospital microbiome survey data
Shared signatures and divergence in skin microbiomes of children with atopic dermatitis and their adult caregivers
Metagenome-wide association analysis identifies microbial determinants of post-antibiotic ecological recovery in the gut
Evaluating cancer driver prediction methods and compare them against predictions obtained from 18 different existing methods on 15 TCGA cancer types
Analyzing data from the SPLASH protocol for generating in vivo RNA interactome maps
