Difference between revisions of "AltAnalyze"
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==System Variables== | ==System Variables== | ||
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory | ||
Latest revision as of 19:14, 10 June 2022
Description
AltAnalyze is an extremely user-friendly and open-source analysis toolkit that can be used for a broad range of genomics analyses. These analyses include the direct processing of raw RNASeq or microarray data files, advanced methods for single-cell population discovery, differential expression analyses, analysis of alternative splicing/promoter/polyadenylation and advanced isoform function prediction analysis (protein, domain and microRNA targeting). Multiple advanced visualization tools and à la carte analysis methods are supported in AltAnalyze (e.g., network, pathway, splicing graph). AltAnalyze is compatible with various data inputs for RNASeq data (FASTQ, BAM, BED), microarray platforms (Gene 1.0, Exon 1.0, junction and 3' arrays). This software requires no advanced knowledge of bioinformatics programs or scripting or advanced computer hardware. User friendly videos, online tutorials and blog posts are also available.
Environment Modules
Run module spider altanalyze to find out what environment modules are available for this application.
System Variables
- HPC_ALTANALYZE_DIR - installation directory
Additional Information
This is a GUI software. Follow the instructions at https://wiki.rc.ufl.edu/doc/GUI_Programs
Basic usage:
module load gui launch_gui_session --module altanalyze -e AltAnalyze.py
Connect with xpra locally using the xpra command
xpra attach ssh:jdoe@i111a-s222.rc.ufl.edu:3713
Citation
If you publish research that uses altanalyze you have to cite it as follows:
http://altanalyze.readthedocs.io/en/latest/References/