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) is a container system designed for use on High Performance Computing (HPC) systems. It allows users to run both Docker and Singularity containers.
HTSlib is a C library used for reading and writing high-throughput sequencing data.
RELION (REgularised LIkelihood OptimisatioN) is a stand-alone computer program for the refinement of 3D reconstructions or 2D class averages in electron cryo-microscopy.
FreeSurfer is a software package used to anaylze nueroimaging data.
The following versions of FreeSurfer are available on OSC clusters:
FSL is a library of tools for analyzing FMRI, MRI and DTI brain imaging data.
The following versions of FSL are available on OSC clusters:
VirtualGL allows OpenGL applications to run with 3D hardware accerlation.
The following versions of VirtualGL are available on OSC clusters:
From julialang.org:
"Julia is a high-level, high-performance dynamic programming language for numerical computing. It provides a sophisticated compiler, distributed parallel execution, numerical accuracy, and an extensive mathematical function library. Julia’s Base library, largely written in Julia itself, also integrates mature, best-of-breed open source C and Fortran libraries for linear algebra, random number generation, signal processing, and string processing. In addition, the Julia developer community is contributing a number of external packages through Julia’s built-in package manager at a rapid pace. IJulia, a collaboration between the Jupyter and Julia communities, provides a powerful browser-based graphical notebook interface to Julia."
MATLAB allows matrix manipulations, plotting of functions and data, implementation of algorithms, creation of user interfaces, and interfacing with programs written in other languages, including C, C++, C#, Java, Fortran and Python.
All the desktop apps can be found within the 'Interactive Apps' dropdown in our OnDemand web portal as shown in the image below:
RStudio is an integrated development environment (IDE) for R. It includes a console, syntax-highlighting editor that supports direct code execution, as well as tools for plotting, history, debugging and workspace management.
All the desktop apps can be found within the 'Desktop Apps' dropdown in our OnDemand web portal as shown in the image below:
