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.

Last modified on October 25, 2023 at 1:41 pm by George Leaver