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    46 repositories

    • SPMP_Phages

      Public
      Scripts associated with the manuscript "GuFi phages represent the most prevalent viral family-level clusters in the human gut microbiome"
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Mar 16, 2026Mar 16, 2026

    • csb5.github.io

      Public
      github pages for csb5
      SCSS
      •3•1•0•0•Updated Feb 22, 2026Feb 22, 2026

    • lofreq

      Public
      LoFreq Star: Sensitive variant calling from sequencing data
      C
      •
      Other
      •36•113•78•0•Updated Oct 16, 2025Oct 16, 2025

    • XNA_Basecaller

      Public
      NCB Sequencing. Code for paper: "Direct high-throughput deconvolution of non-canonical bases via nanopore sequencing and bootstrapped learning"
      Python
      •
      MIT License
      •0•3•0•0•Updated Jul 31, 2025Jul 31, 2025

    • skin_metatranscriptome

      Public
      R
      •
      MIT License
      •1•0•0•0•Updated Jul 16, 2025Jul 16, 2025

    • ASMP_Dermotype

      Public
      Scripts to generate figures for the manuscript titled "Large-scale skin metagenomics reveals extensive prevalence, coordination, and functional adaptation of sk…
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Jun 23, 2025Jun 23, 2025

    • FFPE_kitome

      Public
      Metagenomic sequencing conducted on blank paraffin blocks or extraction controls.
      MIT License
      •0•0•0•0•Updated May 4, 2025May 4, 2025

    • SG90

      Public
      HTML
      •1•4•0•0•Updated Aug 14, 2024Aug 14, 2024

    • Recovery_Determinants_Study

      Public
      Data and scripts of Antibiotic Recovery Study
      R
      •
      MIT License
      •4•5•0•0•Updated Jul 15, 2024Jul 15, 2024

    • OPERA-MS

      Public
      OPERA-MS - Hybrid Metagenomic Assembler
      C++
      •
      Other
      •16•102•22•0•Updated Jul 3, 2024Jul 3, 2024

    • food_centre_microbiome

      Public
      City-wide metagenomic surveillance of food centres reveals location-specific microbial signatures and enrichment of antibiotic resistance genes
      Python
      •
      MIT License
      •0•1•0•0•Updated Mar 5, 2024Mar 5, 2024

    • AD-caregiver-manuscript

      Public
      Files and scripts to generate figures for the manuscript titled "Shared signatures and divergence in skin microbiomes of children with atopic dermatitis and the…
      Assembly
      •0•0•0•0•Updated Sep 12, 2023Sep 12, 2023

    • Candida_auris_CladeVI

      Public
      WGS analysis for Candida auris
      Jupyter Notebook
      •4•4•0•0•Updated Jul 31, 2023Jul 31, 2023

    • CaDRReS

      Public
      Cancer Drug Response prediction using a Recommender System
      Python
      •
      GNU General Public License v3.0
      •15•43•3•2•Updated Jul 6, 2023Jul 6, 2023

    • SPMP

      Public
      Singapore Platinum Metagenomes Project
      Jupyter Notebook
      •
      MIT License
      •3•3•0•0•Updated Mar 13, 2023Mar 13, 2023

    • shotgunmetagenomics-nf

      Public
      Python
      •
      MIT License
      •6•4•0•0•Updated Nov 11, 2022Nov 11, 2022

    • MetageNN

      Public
      MetageNN is a proof of concept neural network used to obtain a memory-efficient taxonomic classifier robust to sequencing errors and missing genomes
      Python
      •0•5•0•0•Updated Sep 26, 2022Sep 26, 2022

    • TUGDA

      Public
      TUGDA is a novel multi-task unsupervised domain adaptation method that leverages transfer learning from tasks/domains in a unified framework.
      Jupyter Notebook
      •3•5•0•0•Updated Sep 26, 2022Sep 26, 2022

    • CPE-microbiome

      Public
      Jupyter Notebook
      •0•1•0•0•Updated May 10, 2022May 10, 2022

    • CaDRReS-Sc

      Public
      CaDRReS-Sc is a framework for analyzing drug response heterogeneity based on single-cell RNA-seq data
      tumorscrna-seqdrug-response-prediction
      tumorscrna-seqdrug-response-predictiongene-expression-profilecadrres-sc
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •4•19•2•0•Updated May 7, 2022May 7, 2022

    • OncoIMPACT

      Public
      Cancer-omics Data Integration
      Perl
      •
      MIT License
      •4•7•1•0•Updated Mar 27, 2022Mar 27, 2022

    • EDDA

      Public
      Power Your Design
      R
      •3•2•0•0•Updated Dec 13, 2020Dec 13, 2020

    • BEEM-static

      Public
      BEEM-Static: An R package for inferring microbial interactions based on generalized Lotka-Volterra models
      R
      •
      MIT License
      •8•10•0•0•Updated Nov 25, 2020Nov 25, 2020

    • INC-Seq

      Public
      INC-Seq: Accurate single molecule reads using nanopore sequencing
      Python
      •
      Other
      •4•16•2•0•Updated Sep 11, 2020Sep 11, 2020

    • PLoT-ME

      Public
      Clustering of Genomic databases (RefSeq) for high memory reduction of taxonomic classifiers (Kraken2, Centrifuge). Designed to pre-processing long DNA reads (N…
      Python
      •
      Other
      •1•1•0•0•Updated Jul 9, 2020Jul 9, 2020

    • BEEM

      Public
      BEEM: Estimating Lotka-Volterra models from time-course microbiome sequencing data
      R
      •
      MIT License
      •4•9•0•0•Updated Jul 5, 2020Jul 5, 2020

    • hospital_microbiome_explorer

      Public
      R
      •1•5•0•0•Updated Jun 12, 2020Jun 12, 2020

    • hospital_microbiome

      Public
      HTML
      •
      MIT License
      •9•10•2•0•Updated Jun 9, 2020Jun 9, 2020

    • drug_response_consistency

      Public
      Preliminary study of consistency among public cancer drug response datasets
      Jupyter Notebook
      •0•0•0•0•Updated Jan 15, 2020Jan 15, 2020

    • driver_evaluation

      Public
      cancergenomicdriver-gene-prediction
      cancergenomicdriver-gene-prediction
      Perl
      •1•4•0•0•Updated Oct 23, 2019Oct 23, 2019
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