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. |