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CRCD User Manual
CRC bioinformatics workshops
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    • Back to crc.pitt.edu
    • User Manual Home
    • Getting Started
      • Step 1- Getting an Account
      • Step 2- Login to Access Portals
        • SSH using a terminal
        • Linux Desktop Web-portal
        • Open OnDemand Web-portal
        • JupyterHub Web-portal
        • JupyterHub on Teach Cluster
      • Step 3- CRCD Ecosystem
        • Discovering Software
        • Requesting Resources
        • Managing Jobs
      • GPU
      • SMP
      • MPI
      • HTC
      • TEACH
      • VIZ
      • Login Nodes
      • Job Scheduling Policy
      • Hardware Investing Policy
      • Resource Descriptions For Writing Proposals
      • SSH Connection using a terminal
      • Open OnDemand
      • Jupyter on Ondemand User Guide
      • VIZ
      • Jupyter Hub
      • JupyterHub on the Teach Cluster
      • Psych (Psychiatry Department Web Portal)
      • hugen or teach Open Ondemand webportal on the teach cluster
      • Slurm Overview
      • Slurm Batch Jobs
      • Service Units
      • Interactive Jobs
      • PBS to Slurm Commands
      • Scavenger Partitions
      • Submitting Multiple Jobs to the Clusters
      • Interactive / Remote Computing with VS Code
      • Utilizing Scratch Space for Faster IO Operations
    • Acknowledge CRCD Resources and Assistance in Your Papers
      • File Systems
      • File Permissions and Ownership
    • File Transfer Methods
      • Globus
      • Globus for Microsoft OneDrive
      • Microsoft OneDrive
      • CRCD Software List
      • Application Environment
      • Basic Slurm Commands
      • CRC Wrappers
      • Compilers
      • Python
      • R and RStudio
      • RStudio Server on the GPU Cluster
      • Introduction to Singularity
        • ANSYS
        • COMSOL Multiphysics
        • Lumerical Photonics Simulation Suite (ANSYS)
        • Mathematica Software
        • Vienna Ab Initio Simulation Package (VASP)
          • MATLAB Software
          • MATLAB Remote Jobs Submission
      • CRC bioinformatics workshops
        • nf-core Pipelines
        • RNASeq Data Analysis
        • Variant Calling
        • Single Cell Data Analaysis
        • Spatial Transcriptomics
        • ChIP-Seq Data Analysis
        • ATACSeq Data Analysis
        • Methylation data analysis
        • Cromwell/WDL and ENCODE Pipelines
        • Snakemake
        • Genome Browser
        • CLCBio Genomics Server
      • Alpha Fold 3
      • fMRI data analysis
      • Electronic Health Record data analysis
    • Supporting Code Optimization
    • Frequently Asked Questions

    CRC bioinformatics workshopsΒΆ

    Semester Links
    Spring 2025 Bioinformatics workshop materials
    Fall 2024 Bioinformatics workshop materials
    Spring 2024 Bioinformatics workshop materials
    Fall 2023 Bioinformatics workshop materials
    Spring 2023 Bioinformatics workshop materials
    Fall 2022 Bioinformatics workshop materials
    Summer 2022 Bioinformatics workshop materials
    Spring 2022 Bioinformatics workshop materials
    Fall 2021 Bioinformatics workshop materials
    Summer 2021 Bioinformatics workshop materials
    Spring 2021 Bioinformatics workshop materials
    Fall 2020 Bioinformatics workshop materials
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