A-Z List of Software
Not all software is accessible to all users. Where restrictions apply, typically licensing, this is detailed in the documentation.
| PACKAGE | NOTES |
|---|---|
| Anaconda Scientific Python | A scientific python distribution |
| BCFtools | Variant call manipulation in BCF (and VCF) files. |
| Bedops | A fast, flexible toolset for genome arithmetic. |
| Bedtools | A fast, flexible toolset for genome arithmetic. |
| Bioconductor (in R) | Tools for analysis and comprehension of high-throughput genomic data |
| Bowtie | Sequence alignment |
| Bowtie2 | Sequence alignment |
| bwa | Burrows-Wheeler Aligner, genome sequence mapper |
| Clojure | Java-based dynamic programming language |
| Compilers – GNU | gcc, g++ and gfortran |
| Cufflinks | Sequence assembly |
| EEGLab | MATLAB toolbox for EEG/MEG data processing and viz |
| Ensembl Tools | Varient Effect Predictor script in perl |
| fgwas | Tool for integrating functional genomic information into a GWAS |
| gauss | Numerical and statistical computation, visualization and programming |
| HiCUP | Genome mapping |
| ImageJ and Fiji | Image processing (Java) applications. |
| IPython Notebook | Interactive remote execution with web-based viewing of Python (not supported, please use jupyter notebook) |
| Julia | Interactive scientific programming language |
| Jupyter Notebook | Interactive remote execution with web-based viewing of Python (access from the nyx5,6,7 linux virtual dedktop) |
| MATLAB | Numerical computation, visualization and programming |
| MEGAN6 | Tool for studying the taxonomic content of a set of DNA reads |
| MOE | Molecular Operating Environment |
| MRIcroGL | 3D GPU Medical Imaging |
| MRIcron | Medical Imaging |
| NetBeans | Java-based IDE |
| NetLogo | Multi-agent modelling environment |
| p7zip | 7zip Unix port |
| R | Statistical computing and graphics |
| RStudio | GUI-based development environment for R |
| SAMtools | Sequence alignment and mapping tools |
| SAS | Data analysis and statistics |
| Singularity | Containers |
| Stata | Data analysis and statistical software |
| tabix | Generic indexer for TAB-delimited genome position files |
| TADtool | Hi-C data topological domain analysis |
| tensorflow | Data flow graph processing |
| tophat | Splice junction mapper |
| UKBioBank Helper | Environment variables to help access UK BioBank full-release datasets. |
| vcftools | Package for working with VCFfiles |
| VMD | Visual Molecular Dynamics molecule viewer/GUI. |