logo
CRCD User Manual
CRC bioinformatics workshops
Initializing search
    GitHub
    GitHub
    • Back to crc.pitt.edu
    • User Manual Home
    • Getting Started
        • Your First Job
        • Running Python (OnDemand)
        • Running R (OnDemand)
      • Step 1- Getting an Account
      • Step 2- Login to Access Portals
        • Terminal SSH
        • Open OnDemand Web-portal
        • Linux Desktop Visualization
        • JupyterHub on Teach Cluster
      • Step 3- CRCD Ecosystem
        • Discovering Software
        • Requesting Resources
        • Managing Jobs
    • Hardware Profiles
        • SMP
        • HTC
        • MPI
        • GPU
        • Teach
        • Login Nodes
        • Viz
      • Storage Tiers
      • SSH Connection Using a Terminal
      • Open OnDemand
      • Jupyter on OnDemand
      • Linux Desktop Visualization (Viz)
      • Jupyter Hub
      • JupyterHub on the Teach Cluster
      • Create a virtual environment for JupyterHub
      • Psych (Psychiatry Department Web Portal)
      • HuGen / Teach Open OnDemand Portal
    • Running Jobs with Slurm
      • Interactive Jobs
      • Batch Jobs
      • Service Units
      • Job Limits & QoS
      • Preemptible Partitions
      • Job Arrays
      • Scratch Space
      • VS Code
    • Data Management
      • File Systems
      • File Permissions
      • File Transfer to CRCD
        • Globus
        • OneDrive (via Globus)
        • OneDrive (command line)
        • FileZilla
      • CRCD Software List
        • VS Code
      • Application Environment
      • Basic Slurm Commands
      • CRC Wrappers
      • Software Development
      • Python
      • NVIDIA CUDA-Q
      • 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
        • 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
        • Genome Browser
        • CLCBio Genomics Server
      • nf-core Pipelines
      • Alpha Fold 3
      • fMRI data analysis
      • Electronic Health Record data analysis
      • Ollama
      • Biomedical Image Analysis
      • VirtualGL
      • GitHub Copilot
    • Code Optimization
      • Persisting Sessions with tmux and nohup
      • Job Scheduling Policy
      • Hardware Investing Policy
      • Resource Descriptions For Writing Proposals
    • Citing CRCD
    • Glossary
    • 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

    Was this page helpful?
    Thanks for your feedback!
    Thanks for your feedback! Help us improve this page by creating an issue in our Github Repository.
    Previous
    MATLAB Remote Jobs Submission
    Next
    RNASeq Data Analysis
    Copyright © University of Pittsburgh. All rights reserved.
    Made with Material for MkDocs