Mass spectrometry-based proteomics data amenable to analysis by PANOPLY includes isobaric label-based LC-MS/MS approaches like iTRAQ, TMT and TMTPro profiling the proteome and multiple PTM-omes including phospho-, acetyl-and ubiquitylomes. Most analysis modules include a report generation task that outputs a HTML interactive report summarizing results from the respective analysis tasks. PANOPLY provides a comprehensive collection of proteogenomic data analysis methods including sample QC (sample quality evaluation using profile plots and tumor purity scores (1), identify sample swaps, etc.), association analysis, RNA and copy number correlation (to proteome), connectivity map analysis (1 ,2), outlier analysis using BlackSheep (3), PTM-SEA (4), GSEA (5) and single-sample GSEA (6), consensus clustering, and multi-omic clustering using non-negative matrix factorization (NMF). The workspaces include all data, parameter settings and results. Terra workspaces showing case studies of applying PANOPLY to the analysis of CPTAC BRCA (7) and CPTAC LUAD (8) datasets.The PANOPLY_Tutorial workspace contains data and results from running the tuorial. A tutorial illustrating the application of PANOPLY to a published breast cancer dataset and demonstrating the practical relevance of PANOPLY by regenerating many of the results described in (Mertins et al) (1) with minimal effort. A GitHub wiki includes documentation and description of algorithms. Panoply org code#A GitHub repository that contains code for all PANOPLY tasks and workflows, including R code for implementing analysis algorithms, task module creation, and release management.An interactive Jupyter notebook (included in the Terra workspaces) that provides step-by-step instructions for uploading data, identifying data types, specifying parameters, and setting up the PANOPLY workspace for analyzing a new dataset.A Terra production workspace on PANOPLY_Production_Pipelines_v1_1 with a preconfigured unified workflow to automatically run all analysis tasks on proteomics (global proteome, phosphoproteome, acetylome, ubiquitylome), transcriptome and copy number data and an additional workspace that includes separate methods for each analysis component.PANOPLY v1.2 consists of the following components: A wide array of algorithms applicable to all cancer types have been implemented, and available in PANOPLY for analysis of cancer proteogenomic data. PANOPLY leverages Terra-a cloud-native platform for extreme-scale data analysis, sharing, and collaboration-to host proteogenomic workflows, and is designed to be flexible, automated, reproducible, scalable, and secure. PANOPLY is a platform for applying state-of-the-art statistical and machine learning algorithms to transform multi-omic data from cancer samples into biologically meaningful and interpretable results. A cloud-based platform for automated and reproducible proteogenomic data analysis Version 1.2 Our current dance-opera, Any Size Mirror is a Dictator,made in collaboration with Lindsey Drury and many other performance-makers will culminate September 5-October 19 at Momenta Art. PPL the project space and in Bushwick, hosts interdisciplinary performance practices and projects. Louis), 119 Gallery (Lowell, MA), Charlotte Street’s La Esquina Gallery (Kansas City), ACUD, KuLe Theater, and BLO Atelier (Berlin), The Pumpehuset (Copenhagen), and many festivals, fairs, public sites, and other contexts. Projects have been hosted by Glasshouse, Grace Exhibition Space, The Brick Theater, the cell, Dixon Place, Silent Barn, IV Soldiers, English Kills, AUNTS, Casita Maria, Bronx Arts Space, ABC No Rio, and Fitness Center for Arts and Tactics (to name a few in NYC) and Defibrillator Performance Art Gallery (Chicago), Contemporary Art Institute of Detroit, University of Kentucky, Ohio State, LA GALERIA at Villa Victoria (Boston), The Lemp (St. PPL’s engagements have included residencies like LMCC’s Swing Space, LPAC, University Settlement, incubation at IRT, chashama, Gruntaler9 (Berlin) and engagements with organizations across social spheres. Past projects have included a durational diner, a silviculture museum, full-length operas, workshops, dances, solo and duo actions, conferences, concerts, gallery exhibitions, and large-scale collaborative works of constructional institutional critique. Is a collective and space formed by Esther Neff and Brian McCorkle, is unbounded by discipline or field, we collect ourselves around processes, theorizing social systems, ideological structures, modes of production, and epistemic genealogies via actions, relational constructs, images, noise, text, interactions, and objects.
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