FastQC
FastQC provides quality control checks of high throughput sequence data that identify areas of the data that may cause problems during further analysis.
Pitzer
Perl
Perl is a family of programming languages.
Cufflinks
Cufflinks is a program that analyzes RNA -Seq samples. It assembles aligned RNA-Seq reads into a set of transcripts, then inspects the transcripts to estimate abundances and test for differential expression and regulation in the RNA-Seq reads.
Apptainer (formerly Singularity)
Apptainer (formerly Singularity) is a container system designed for use on High Performance Computing (HPC) systems. It allows users to run both Docker and Singularity containers.
HTSlib
HTSlib is a C library used for reading and writing high-throughput sequencing data.
RELION
RELION (REgularised LIkelihood OptimisatioN) is a stand-alone computer program for the refinement of 3D reconstructions or 2D class averages in electron cryo-microscopy.
LAPACK
LAPACK (Linear Algebra PACKage) provides routines for solving systems of simultaneous linear equations, least-squares solutions of linear systems of equations, eigenvalue problems, and singular value problems.
Availability and Restrictions
A highly optimized implementation of LAPACK is available on all OSC clusters as part of the Intel Math Kernel Library (MKL). We recommend that you use MKL rather than building LAPACK for yourself. MKL is available to all OSC users.
FreeSurfer
FreeSurfer is a software package used to anaylze nueroimaging data.
Availability & Restrictions
Versions
The following versions of FreeSurfer are available on OSC clusters:
FSL
FSL is a library of tools for analyzing FMRI, MRI and DTI brain imaging data.
Availability and Restrictions
Versions
The following versions of FSL are available on OSC clusters:
HOWTO: Submit Homework to Repository at OSC
This page outlines a way a professor can set up a file submission system at OSC for his/her classroom project.
Usage for Professor
After connecting to OSC system, professor runs submit_prepare as
