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    34 repositories

    • acdc_py_data

      Public
      0•0•0•0•Updated Jan 25, 2025Jan 25, 2025

    • acdc_py

      Public
      scanpy-compatible suite for automated clustering of scRNA-seq data in python
      pythonbioinformaticsclusteringsingle-cell-rna-seq
      Jupyter Notebook
      •
      MIT License
      •0•0•7•0•Updated Jan 20, 2025Jan 20, 2025

    • ARACNe3

      Public
      Faster & theoretically redesigned implementation of ARACNe
      C++
      •
      Other
      •0•2•0•0•Updated Jan 16, 2025Jan 16, 2025

    • VIPERKernel

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Jan 9, 2025Jan 9, 2025

    • PISCES_networks

      Public
      Repository of networks from the PISCES project
      0•0•0•0•Updated Nov 12, 2024Nov 12, 2024

    • Immune-Nets-Snakemake-Pipeline

      Public
      Python
      •0•0•0•0•Updated Oct 29, 2024Oct 29, 2024

    • MAPK_Experimental_Signature

      Public
      This repository contains an example of code to generate a MAPK Experimental Signature from PlateSeq data
      R
      •0•0•0•0•Updated Aug 30, 2024Aug 30, 2024

    • vespa.tutorial

      Public
      Tutorials on how to use the VESPA algorithm
      R
      •0•0•0•0•Updated Mar 1, 2024Mar 1, 2024

    • vespa.net

      Public
      VESPA (Virtual Enrichment-based Signaling Protein-activity Analysis) signaling network inference module
      Python
      •0•0•0•0•Updated Mar 1, 2024Mar 1, 2024

    • vespa.db

      Public
      VESPA (Virtual Enrichment-based Signaling Protein-activity Analysis) supplementary data package
      R
      •
      Other
      •0•0•0•0•Updated Mar 1, 2024Mar 1, 2024

    • vespa.aracne

      Public
      VESPA (Virtual Enrichment-based Signaling Protein-activity Analysis) ARACNe module
      Java
      •
      Other
      •0•0•0•0•Updated Mar 1, 2024Mar 1, 2024

    • vespa

      Public
      VESPA (Virtual Enrichment-based Signaling Protein-activity Analysis) algorithm
      R
      •
      Other
      •0•1•0•0•Updated Mar 1, 2024Mar 1, 2024

    • acdc

      Public
      suite for clustering of scRNA-seq data (beta version)
      R
      •0•0•0•0•Updated Jun 11, 2023Jun 11, 2023

    • ARACNe-AP

      Public
      Network Reverse Engineering through AP inference of Mutual Information
      Java
      •
      Other
      •24•82•15•2•Updated Mar 6, 2023Mar 6, 2023

    • NaRnEA

      Public
      NaRnEA (Nonparametric analytical Rank-based Enrichment Analysis)
      R
      •
      Other
      •4•9•0•0•Updated Mar 2, 2023Mar 2, 2023

    • Olive_926-mouse-screen

      Public
      LJV analysis code for IPI 926 mouse drug screening data from the Olive lab.
      R
      •0•0•0•0•Updated Feb 28, 2023Feb 28, 2023

    • NDP-KO-SC

      Public
      Analysis code for collaboration with the Kuo lab. Single-cell analysis of NDP KO mice w/ and w/ out L6-F4-2 therapeutic agent.
      R
      •1•1•0•0•Updated Feb 16, 2023Feb 16, 2023

    • PISCES

      Public
      R package for Protein activity analysis of single-cell RNAseq.
      R
      •24•80•20•1•Updated Dec 15, 2022Dec 15, 2022

    • SHARP-SCABC-2022

      Public
      Hands-on session code and data from the 2022 SHARP Single Cell Analysis Boot Camp.
      Python
      •0•0•0•0•Updated Jul 27, 2022Jul 27, 2022

    • MOMA

      Public
      R
      •3•6•1•0•Updated Apr 9, 2021Apr 9, 2021

    • Statistical_Rethinking_with_brms_ggplot2_and_the_tidyverse_2_ed

      Public
      The bookdown version lives here:
      HTML
      •
      Creative Commons Zero v1.0 Universal
      •39•0•0•0•Updated Mar 26, 2021Mar 26, 2021

    • OncoSig

      Public
      Code to run OncoSig Analyses
      R
      •5•18•0•0•Updated Sep 30, 2020Sep 30, 2020

    • SEARCHIN

      Public
      Systematic Elucidation and Assessment of Regulatory Cell-to-cell Interaction Networks (SEARCHIN)
      R
      •
      Other
      •3•0•0•0•Updated Sep 18, 2020Sep 18, 2020

    • COSMA

      Public
      Final code for the cosma collaboration (for paper submission).
      R
      •1•0•1•0•Updated Jun 6, 2020Jun 6, 2020

    • moma.gbmexample

      Public
      Example gbm multi-omic data for moma package vignette
      R
      •0•0•0•0•Updated Apr 3, 2020Apr 3, 2020

    • single-cell-pipeline

      Public
      HTML
      •8•44•11•1•Updated Jan 16, 2020Jan 16, 2020

    • GTEx-Networks

      Public
      Tissue specific network for GTEx tissue data (TPM normalized).
      2•5•0•0•Updated Oct 14, 2019Oct 14, 2019

    • gbm-multiomic-data

      Public
      Data for the MOMA Bioconductor package
      0•0•0•0•Updated Sep 11, 2019Sep 11, 2019

    • CZI

      Public
      CZI Project Results
      R
      •
      Other
      •1•1•0•0•Updated Apr 15, 2019Apr 15, 2019

    • ADVOCATE

      Public
      ADVOCATE
      R
      •
      Other
      •1•3•2•0•Updated Jan 31, 2019Jan 31, 2019