Skip to content

@riverxdata RiverXData

Change the repository type filter

All

    Repositories list

    38 repositories

    • river-docs

      Public
      The public docs for riverxdata platform and related project. It will be merged into the river repo later after publication
      TypeScript
      •0•0•0•0•Updated Jan 8, 2026Jan 8, 2026

    • autodock-vina

      Public
      Autodock-vina on RIVER
      Shell
      •
      MIT License
      •0•0•0•0•Updated Jan 8, 2026Jan 8, 2026

    • river

      Public
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jan 7, 2026Jan 7, 2026

    • smartsensor

      Public
      The sensor utilizes a smartphone camera to analyze and characterize chemical compounds.
      Python
      •
      MIT License
      •2•0•0•0•Updated Dec 29, 2025Dec 29, 2025

    • bioinfor-sw-TFinder

      Public
      Python script to quickly extract promoter and terminator regions with the NCBI API. Search for the presence of individual pattern or transcription factor responsive elements with manual sequence (IUPAC) or JASPAR API.
      Python
      •
      MIT License
      •21•0•0•0•Updated Dec 28, 2025Dec 28, 2025

    • GWAS-Biobank

      Public
      The GWAS analysis on large scale biobanks UKB, All of US, etc
      GNU General Public License v3.0
      •0•0•0•0•Updated Dec 15, 2025Dec 15, 2025

    • miRNorms-cancer-panel

      Public
      miRNA expression profiles for cancers
      Python
      •
      MIT License
      •0•0•0•0•Updated Dec 7, 2025Dec 7, 2025

    • river-head_model

      Public
      Reproducible paper "Prediction of tissue-of-origin of early stage cancers using serum miRNomes"
      Python
      •
      Other
      •4•0•0•0•Updated Dec 7, 2025Dec 7, 2025

    • bioanalyzer

      Public
      Bioinformatics web analyzer
      Python
      •1•0•0•0•Updated Nov 14, 2025Nov 14, 2025

    • bioinfor-wf-snakemake-qc-ngs

      Public
      Proof of concepts to use snakemake in RIVER
      Shell
      •
      MIT License
      •0•0•0•0•Updated Nov 5, 2025Nov 5, 2025

    • bioinfor-wf-bashscipt-qc-ngs

      Public
      The proof of concepts for using fastqc+multiqc for NGS data in RIVER
      Shell
      •
      MIT License
      •0•0•0•0•Updated Nov 5, 2025Nov 5, 2025

    • batch-template-analysis

      Public template
      The template for analysis, easier for user to use this to create new tool from this template that can be run with river
      Shell
      •
      MIT License
      •0•0•0•0•Updated Nov 4, 2025Nov 4, 2025

    • data-sw-jupyterlab

      Public
      The Jupyterlab
      Shell
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Nov 3, 2025Nov 3, 2025

    • data-sw-rstudio

      Public
      RStudio that allows to run on HPC
      Shell
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Nov 3, 2025Nov 3, 2025

    • web-template-analysis

      Public template
      The web template that will simply run the streamlit to say "Hello world"
      Shell
      •
      MIT License
      •0•0•0•0•Updated Nov 3, 2025Nov 3, 2025

    • bioinfor-sw-Omics

      Public
      Build the dashboard with quality image for the publications using cBioportal datasets
      Shell
      •
      MIT License
      •0•0•0•0•Updated Oct 31, 2025Oct 31, 2025

    • data-sw-visual-studio-code-server

      Public
      Host the code-server(based on open source of vscode) on slurm job using sbatch.
      Shell
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Oct 31, 2025Oct 31, 2025

    • bioinfor-sw-CircNetVis

      Public
      CircNetVis: an interactive web application for visualizing interaction networks of circular RNAs
      HTML
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Oct 30, 2025Oct 30, 2025

    • bioinfor-sw-CARTAR

      Public
      Files and code used to generate the CARTAR app to identify and validate CAR targets for cancer treatment.
      Python
      •1•0•0•0•Updated Oct 17, 2025Oct 17, 2025

    • bioinfor-sw-igv

      Public
      IGV via RIVER platform
      Shell
      •
      MIT License
      •0•0•0•0•Updated Oct 17, 2025Oct 17, 2025

    • enhancer-predictor

      Public
      The nextflow pipeline for enhancer predicor based on ABC score
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Oct 10, 2025Oct 10, 2025

    • bioinfor-wf-template

      Public
      The template for bioinformatics project
      HTML
      •
      MIT License
      •0•0•0•0•Updated Aug 14, 2025Aug 14, 2025

    • riverxdata-nf-core-demo

      Public
      Demo
      Nextflow
      •
      MIT License
      •0•0•0•0•Updated Aug 8, 2025Aug 8, 2025

    • .github

      Public
      The overview of the RiverXData
      0•0•0•0•Updated Jul 8, 2025Jul 8, 2025

    • ABC-Enhancer-Gene-Prediction

      Public
      Cell type specific enhancer-gene predictions using ABC model (Fulco, Nasser et al, Nature Genetics 2019)
      Python
      •
      MIT License
      •74•0•0•0•Updated Jun 27, 2025Jun 27, 2025

    • river-slurm

      Public
      This repo for setting up the local infrastructure for bioinformatics analysis
      Jinja
      •
      GNU General Public License v3.0
      •1•2•0•0•Updated May 23, 2025May 23, 2025

    • nextflow

      Public
      A DSL for data-driven computational pipelines
      Groovy
      •
      Apache License 2.0
      •760•0•0•0•Updated May 22, 2025May 22, 2025

    • river-envs

      Public
      River utils for communication between the river web service and the computing resource (HPC-Slurm, Local)
      Python
      •
      MIT License
      •0•0•0•0•Updated May 21, 2025May 21, 2025

    • UKB-RAP-Notebooks-Genomics

      Public
      UKB-RAP optimization
      Jupyter Notebook
      •
      MIT License
      •5•0•0•0•Updated Apr 25, 2025Apr 25, 2025

    • bioinfor-wf-nipt-human-genetics

      Public
      The prototypes for running NIPT GWAS using nextflow
      Nextflow
      •
      MIT License
      •3•0•0•0•Updated Apr 24, 2025Apr 24, 2025