Reference: C. Soderlund (2019) Transcriptome computational workbench (TCW): analysis of single and comparative transcriptomes. Published at BioRxiv.
Description: For single-transcriptome (singleTCW) - similarity search against annotation databases, GO annotation, ORF finding and differential analysis. For multi-transcriptome (multiTCW) - compute similar pairs, provide statistics for pairs, compute clusters, provide statistics for clusters. Both singleTCW and multiTCW provide graphical interfaces for extensive query and display of the results.
Requirements: Java and MySQL to build the database and view the results. R for differential analysis. All other external software used by TCW is contained in the package tar file.
TCW package: To use TCW, download the TCW package from the link at the top. The tar file contains all necessary jar files, R scripts and demo files. Follow the instructions at http://www.agcol.arizona.edu/software/tcw/doc/.
TCW github code: This site does not include the external packages; you will need to extract them from the TCW package or provide them yourself. The necessary Java classes are provided, see TCW/java/README.