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    • Capturing signaling pathways using scRNA-seq data.
      R
      GNU General Public License v3.0
      1100Updated Feb 20, 2026Feb 20, 2026
    • ccafv2_R

      Public
      ccAFv2 cell cycle classifier R pacakge
      C
      GNU General Public License v3.0
      1601Updated Nov 20, 2025Nov 20, 2025
    • ccAFv2_py

      Public
      Python package for ccAFv2
      Python
      GNU General Public License v3.0
      1010Updated Jul 18, 2025Jul 18, 2025
    • METAFlux

      Public
      HTML
      Other
      13000Updated Jun 19, 2025Jun 19, 2025
    • miR4975p

      Public
      Python
      0000Updated Dec 16, 2024Dec 16, 2024
    • ccAFv2

      Public
      Single cell RNA-seq cell cycle classifier
      R
      GNU General Public License v3.0
      1400Updated Nov 21, 2024Nov 21, 2024
    • cytospace

      Public
      CytoSPACE: Optimal mapping of scRNA-seq data to spatial transcriptomics data
      Python
      Other
      20000Updated Dec 4, 2023Dec 4, 2023
    • OncoMerge

      Public
      Systematic integration of protein affecting mutations, gene fusions, and copy number alterations into a comprehensive somatic mutational profile
      Python
      GNU General Public License v3.0
      3300Updated May 18, 2023May 18, 2023
    • Code to convert single cell expression data into medioids for CIBERSORT deconvolution analysis.
      Python
      GNU General Public License v3.0
      0000Updated Feb 21, 2023Feb 21, 2023
    • Jupyter Notebook
      0000Updated Nov 20, 2022Nov 20, 2022
    • ccAF

      Public
      Cell cycle classifier for scRNA-seq data.
      Python
      GNU General Public License v3.0
      1700Updated Aug 10, 2022Aug 10, 2022
    • mpm_web

      Public
      Website to explore the mpmSYGNAL network.
      Python
      GNU General Public License v3.0
      0040Updated May 9, 2022May 9, 2022
    • Single cell RNA-seq pipeline for 10X data.
      Dockerfile
      GNU General Public License v3.0
      0000Updated Oct 21, 2021Oct 21, 2021
    • CONICSmat

      Public
      Clone of CONICSmat with a key change!
      R
      0000Updated Oct 21, 2021Oct 21, 2021
    • Dockerized RNA-seq pipeline with cutadapt, STAR alignment, and htseq-count for a complete analysis pipeline. Also builds the STAR index for Homo sapiens GRCh38.…
      Python
      0000Updated Sep 21, 2021Sep 21, 2021
    • Docker build file for miRge2_0
      Dockerfile
      GNU General Public License v3.0
      0000Updated Oct 12, 2020Oct 12, 2020
    • A dockerized version of the SYstems Genetics Network AnaLysis (SYGNAL) pipeline.
      Dockerfile
      GNU General Public License v3.0
      0000Updated Aug 27, 2020Aug 27, 2020
    • Instructions to build an image which can run the software to compute RNA velocity.
      Dockerfile
      GNU General Public License v3.0
      0000Updated Aug 26, 2020Aug 26, 2020
    • Neural G0: a quiescent-like state found in neuroepithelial-derived cells and glioma
      R
      GNU General Public License v3.0
      1700Updated Aug 12, 2020Aug 12, 2020
    • Docker image with programs to analyze exome-seq data.
      Dockerfile
      GNU General Public License v3.0
      0000Updated Mar 5, 2020Mar 5, 2020
    • sygnal

      Public
      SYstems Genetic Network AnaLysis (SYGNAL) pipeline
      Python
      4000Updated Feb 4, 2020Feb 4, 2020
    • Boolean Network Modeling
      Python
      Other
      28000Updated Jan 31, 2020Jan 31, 2020
    • Dockerfile
      0000Updated Jan 10, 2020Jan 10, 2020
    • A dockerized version of cMonkey2.
      Dockerfile
      GNU General Public License v3.0
      0000Updated Jan 9, 2020Jan 9, 2020
    • Dockerfile
      GNU General Public License v3.0
      0100Updated Jan 9, 2020Jan 9, 2020
    • Molecular, Cellular and Tissue Bioengineering Single Cell Symposium R Code
      R
      GNU General Public License v3.0
      1300Updated Jun 3, 2019Jun 3, 2019
    • Contains scripts for analyzing and understanding the output from OncoMerge including value added assessments.
      Python
      0000Updated Apr 2, 2019Apr 2, 2019
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