Here is a changelog for the 2.2.0 version:
New features
- Five new species have been added:
- European amphioxus, `Branchiostoma lanceolatun` (assembly Bl71nemr; species key: `Bla`): http://vastdb.crg.eu/libs/vastdb.bla.01.12.18.tar.gz
- Centipede, `Strigamia maritima` (assembly Smar1; species key: `Sma`): http://vastdb.crg.eu/libs/vastdb.sma.01.12.18.tar.gz
- Fruit fly, `Drosophila melanogaster` (assembly BDGP6; species key: `Dme`): http://vastdb.crg.eu/libs/vastdb.dme.01.12.18.tar.gz
- Worm, `Caenorhabditis elegans` (assembly WBcel235; species key `Cel`): http://vastdb.crg.eu/libs/vastdb.cel.01.12.18.tar.gz
- Sea anemone, `Nematostella vectensis` (assembly GCA_000209225; species key `Nve`): http://vastdb.crg.eu/libs/vastdb.nve.01.12.18.tar.gz
Further information about the assemblies and species can be found in the source publication:
Torres-Méndez, A., Bonnal, S., Marquez, Y., Roth, J., Iglesias, M., Permanyer, J., Almudí, I., O’Hanlon, D., Guitart, T., Soller, M., Gingras, A.-C., Gebauer, F., Rentzsch, F., Blencowe, B.J.B., Valcárcel, J., Irimia, M. (2019). A novel protein domain in an ancestral splicing factor drove the evolution of neural microexons. Nature Ecol Evol, 3:691-701.
- Added official Docker container image at: https://cloud.docker.com/u/vastgroup/repository/docker/vastgroup/vast-tools.
- Included continuous integration tests with TravisCi: https://travis-ci.org/vastgroup/vast-tools.
- `tidy` allows filtering events by coverage using a groups config file. Using this option, the minimum number or fraction of samples with coverage (`--min_N` or `--min_Fr`) applies to EACH group of samples.
- `combine` allows to create tables of normalized cRPKMs using `normalizebetweenarrays` from the `limma` R package.
- `compare_expr` provides a list of ranked genes sorted by fold change to be used directly in GSEA (with rnk.txt extension).
- `compare` provides the list of all AS events with coverage, when the option `--GO` is provided.
Updates and fixes
- The VASTDB libraries for zebrafish (`Dre`) and sea urchin (`Spu`) have been updated (http://vastdb.crg.eu/libs/ vastdb.dre.01.12.18.tar.gz and http://vastdb.crg.eu/libs/vastdb.spu.01.12.18.tar.gz). A few new microexons are now included in the MIC module.
- Quality control to make sure the expression files have the same number of genes when combining.
- Improvements in README and help messages.
- Various other minor fixes and improvements.