ISCVA: Interactive Single Cell Visual Analytics, a JavaScript-based visual analytics for analyzing scRNA-seq data: http://iscva.moffitt.org

The computational tool ISCVA is described in this paper:

Smalley I, Chen Z, Phadke M, Li J, Yu X, Wyatt C, Evernden B, Messina JL, Sarnaik A, Sondak VK, Zhang C, Law V, Tran N, Etame A, Macaulay RJB, Eroglu Z, Forsyth PA, Rodriguez PC, Chen YA, Smalley KSM. Single-Cell Characterization of the Immune Microenvironment of Melanoma Brain and Leptomeningeal Metastases. Clin Cancer Res. 2021 Jul 15;27(14):4109-4125.

Briefly, it consists of two major components.

The First component includes a collection of Bash and R scripts (utilizing many of the widely used algorithms in the single-cell community, including:

Seurat for general processing,
SingleR for cell-type recognition,
and Single-cell signature explorer for gene set signature scoring that processed the scRNA-seq data offline

The second is the Web-based component based upon state-of-the-art technologies, including react.js from Facebook, tensorflow.js from Google and Plotly.js, that allows convenient real-time interactive exploration and ad hoc node.js backend was also created to serve the on-demand queries of the Web application, allowing for real-time interactive investigation of genes expressed in selected samples or subsets of cells. (A note on web-browser: ISCVA is currently available on all web browsers, except for Safari)

ISCVA was used in these papers:

Phadke MS, Chen Z, Li J, Mohamed E, Davies MA, Smalley I, Duckett DR, PalveV, Czerniecki BJ, Forsyth PA, Noyes D, Adeegbe DO, Eroglu Z, Nguyen KT, Tsai KY, Rix U, Burd CE, Chen YA, Rodriguez PC, Smalley KSM. Targeted Therapy Given after Anti-PD-1 Leads to Prolonged Responses in Mouse Melanoma Models through Sustained Antitumor Immunity. Cancer Immunol Res. 2021 May;9(5):554-567. doi: 10.1158/2326-6066.CIR-20-0905. Epub 2021 Mar 2. PubMed PMID: 33653716; PubMed Central PMCID: PMC8102376.

Smalley I, Chen Z, Phadke M, Li J, Yu X, Wyatt C, EverndenB, Messina JL, Sarnaik A, Sondak VK, Zhang C, Law V, Tran N, Etame A, Macaulay RJB, Eroglu Z, Forsyth PA, Rodriguez PC, Chen YA, Smalley KSM. Single-Cell Characterization of the Immune Microenvironment of Melanoma Brain and Leptomeningeal Metastases. Clin Cancer Res. 2021 Jul 15;27(14):4109-4125. doi: 10.1158/1078-0432.CCR-21-1694. Epub 2021 May 25. PubMed PMID: 34035069; PubMed Central PMCID: PMC8282775.

Li J, Smalley I, Chen Z, Wu JY, Phadke MS, Teer JK, Nguyen T, Karreth FA, Koomen JM, Sarnaik AA, Zager JS, Khushalani NI, Tarhini AA, Sondak VK, Rodriguez PC, Messina JL, Chen YA, Smalley KSM. Single cell characterization of the cellular landscape of acral melanoma identifies novel targets for immunotherapy. Clin Cancer Res. 2022 Mar 4;. doi: 10.1158/1078-0432.CCR-21-3145. [Epub ahead of print] PubMed PMID: 35247927.

About ISCVA