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Quick start – First steps

  • Creating an account
  • Connecting to the clusters
  • Introduction to Linux
  • Copying files
  • Editing files
  • Submitting jobs with Slurm
  • Glossary
  • Acknowledging the CÉCI

Managing files

  • Disk space
  • Transferring files to and from the clusters
  • Using the Common Storage
  • Sharing files among CÉCI users
  • Copy files and folders to the /CECI/proj partition
  • Making your files Secure
  • Making your files safe
  • Long term data storage
  • Encrypting files

Using software and libraries

  • Using pre-installed software
  • Software installed in the clusters
  • Compiling and installing software from source
  • Installing software by yourself
  • Singularity Container
  • Visualization server
  • Jupyter
  • Login shell

Submitting jobs to the cluster

  • Submitting jobs with Slurm
  • Slurm F.A.Q
  • Slurm priorities
  • A job submission helper on Hercules: ssubmit
  • Getting Job Efficiency
  • Slurm limits
  • Workflow management
  • Slurm interactive jobs
  • Using Visual Studio Code inside a job

Software-specific documentation

  • Matlab
  • R
  • Python
CÉCI
  • Docs »
  • PLINK

PLINK¶

Description¶

PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. The focus of PLINK is purely on analysis of genotype/phenotype data, so there is no support for steps prior to this (e.g. study design and planning, generating genotype or CNV calls from raw data). Through integration with gPLINK and Haploview, there is some support for the subsequent visualization, annotation and storage of results.

More information¶

  • Homepage: http://zzz.bwh.harvard.edu/plink/

Availability¶

Module NIC5 Hercules2 Dragon2 Lemaitre3 Dragon1
PLINK/1.07-foss-2020b       ✓  
PLINK/2.00a3.7-foss-2022a ✓        

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