Research Tools
EPSCoR Research Server
The CI team maintains a research server to handle the data storage and computational needs of Missouri Transect researchers. Accounts on the server are available for all Missouri Transect participants.
Software List
Below is a list of software currently installed on the research server. If you need software that is not listed here, please contact the CI team about getting it installed.
Data Transfer
Computational Software / General Scientific Data / Image Processing
- MATLAB
- Matplotlib
- NetCDF with Ncview
- NumPy
- Python Imaging Library (PIL)
- R with RStudio
- SciPy
- UDUNITS
Genomics Analysis
- BamTools
- Bedtools
- BioPerl
- BLAST
- Bowtie
- Burrows-Wheeler Aligner
- Cufflinks
- FastQC
- FastqMcf
- FastX-Toolkit
- GATK
- GeneMerge
- HTSeq
- HTSlib
- Integrative Genomics Viewer (IGV)
- Platypus
- Samtools
- SolexaQA
- TopHat
- VCFtools
Weather Data Tools
Tutorials
Several tutorials have been written for Missouri Transect participants that explain step-by-step how to use the available research tools. These tutorials include instructions on connecting to the EPSCoR Research server, running programs on the server, and transferring data between the server and a personal machine. Additionally, information is available on using external resources, such as iPlant.
