release_20230412

release 04/12/2023

NetBID2_2.1.1

Add license and categories to CWL implementation

NetBID2_2.1.0

Add automation and implementation for the Cancer Genomics Cloud (CGC). Add a non-interactive Dockerfile.

NetBID2_2.0.3

add draw.oncoprint

Version 2.0.2

Major changes:

1. Add funcEnrich.GSEA()
2. Add processDriverProfile()
3. Modify draw.GSEA() draw.GSEA.NetBID.GS()
4. Fix bug in getDE.BID.2G() and modify demo1/driver/DATA/

Version 2.0.1

Major changes:

• Add draw.emb.kmeans() to replace draw.umap.kmeans and draw.pca.kmeans
• Add boxplot option in draw.eset.QC()
• Fix bug in generate.masterTable()
• User-defined color code with two options: use_color,pre_define passed to get.class.color().
  The modified functions are: draw.2D(), draw.2D.interactive(), draw.2D.text(), draw.3D(), draw.2D.ellipse(), draw.eset.QC(), draw.heatmap(), draw.categoryValue().
• Re-wrote the cal.Activity(), add in Matrix Cross Products, which accelerates the calculation time but consumes more memory. memory_constrain is an option to reduce memory usage to sacrifice some features.
• Modifed the draw.eset.QC(), added correlation plot. Modify draw.network.QC(), add html_info_limit.
• Modified the option name target_list in generate.masterTable()
• Rebuilt on R 3.6.0

Additions

• Created two "lazy mode" functions, NetBID.lazyMode.DriverVisualization(),NetBID.lazyMode.DriverEstimation().
• Added warning message for all functions.
• Added package information in calling functions to avoid possible conflict of function names.
• Added draw.2D.interactive(), and add option "2D.interactive" to draw.pca.kmeans(), draw.umap.kmeans().
• Added functions to judge abnormal values.
• Added option geneSymbol_column for SJAracne.prepare()

Version 2.0.0

This is the first release of NetBID version 2.0.

Major changes compared with version 1.0.0

• Significant refactoring of the code
• Many pre-processing, QC and visualization features have been added
• Pack the code to an R package

Version 1.0.0

This is a backup release of NetBID that has been published in the following Nature paper.

Reference

Du X, Wen J, Wang Y, Karmaus PWF, Khatamian A, Tan H, Li Y, Guy C, Nguyen TM, Dhungana Y, Neale G, Peng J, Yu J*, Chi H*. Hippo/Mst signaling couples metabolic state and immune function of CD8α+ dendritic cells. Nature. 2018;558(7708):141-5. DOI: 10.1038/s41586-018-0177-0. PubMed PMID: 29849151. * Corresponding authors

Note that this version is not actively maintained by Yu Lab due to its significant changes compared with version 2.0.0+. It is highly recommended to use the newest version to perform your analysis.