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.
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