Release 5: 2020-02-12
Optimized asap_run docker, migration of v.2.7 python scripts to v.3.0.
Updated Ensembl data in asap_data database.
Updated Ensembl data in asap_data database.
| Tool/DB | Tool type | Reference | Version |
|---|---|---|---|
| ASAP_run image | Docker | https://hub.docker.com/r/fabdavid/asap_run/tags | v5 |
| ASAP_data PostgreSQL database | Database | Link | v5 |
| JSC [Java statistical API] | Java | http://www.jsc.nildram.co.uk/api/index.html | 1.0 |
| h5py | Python | http://docs.h5py.org/en/latest/build.html | 2.10.0 |
| scikits.learn | Python | http://scikit-learn.org/stable/ | 0.22.1 |
| numpy | Python | http://www.numpy.org/index.html | 1.18.1 |
| scipy | Python | https://www.scipy.org/ | 1.4.1 |
| Java JDK | Java | http://www.oracle.com/technetwork/java/javase/downloads | 11.0.6 |
| Python | Python | https://www.python.org/ | 3.7.6 |
| R version & default packages [stats] (K-means, PCA, Hierarchical clustering, distance, correlation) | R | https://www.r-project.org/ | 3.6.0 |
| SC3 | R | Kiselev VY, Kirschner K, Schaub MT, Andrews T, Yiu A, Chandra T, Natarajan KN, Reik W, Barahona M, Green AR and Hemberg M (2016). “SC3 - consensus clustering of single-cell RNA-Seq data.” bioRxiv. doi: 10.1101/036558, http://biorxiv.org/content/early/2016/09/02/036558. | 1.14.0 |
| Silhouette Plot [cluster package] | R | Maechler, M., Rousseeuw, P., Struyf, A., Hubert, M., Hornik, K.(2016). cluster: Cluster Analysis Basics and Extensions. | 2.1.0 |
| Rtsne | R | L.J.P. van der Maaten and G.E. Hinton. Visualizing High-Dimensional Data Using t-SNE. Journal of Machine Learning Research 9(Nov):2579-2605, 2008. | 0.15 |
| Limma / Voom | R | Charity W Law, Yunshun Chen, Wei Shi and Gordon K Smyth, voom: precision weights unlock linear model analysis tools for RNA-seq read counts, Genome Biology, 15:R29, 2014 DOI: 10.1186/gb-2014-15-2-r29 | 3.42.2 |
| DESeq2 | R | Love MI, Huber W and Anders S (2014). “Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.” Genome Biology, 15, pp. 550. doi: 10.1186/s13059-014-0550-8. | 1.26.0 |
| NA | NA | NA | 0.3.10 |
| data.table | R | https://github.com/Rdatatable/data.table/wiki | 1.12.8 |
| Gene Ontology | Database | http://geneontology.org/ | 2020-Jan |
| Ensembl vertebrates | Database | https://www.ensembl.org | 99 |
| Ensembl genomes | Database | http://ensemblgenomes.org | 46 |