Showing papers by "Rehan Akbani published in 2022"
TL;DR: In this paper , integrative transcriptomic and proteomic analyses on emerging immuno-oncology targets across multiple clinical cohorts of melanoma under anti-PD-1 treatment, on both bulk and single-cell levels, reveal a surprising role of tumor-intrinsic SIRPA in enhancing antitumor immunity.
4 citations
TL;DR: Five HCC subtypes are correlated with genomic phenotypes and clinical outcomes and highly conserved in pre-clinical models, providing a framework for selecting the most appropriate models for preclinical studies.
3 citations
TL;DR: The RPPA SPACE R package is presented, a substantially improved successor to SuperCurve that allows exclusion of poor-quality samples from the normalization process to improve the quality of the remaining samples and features a novel quality-control metric, "noise," that estimates the level of random errors present in each RPPA slide.
Abstract: Abstract Summary Reverse-Phase Protein Array (RPPA) is a robust high-throughput, cost-effective platform for quantitatively measuring proteins in biological specimens. However, converting raw RPPA data into normalized, analysis-ready data remains a challenging task. Here, we present the RPPA SPACE (RPPA Superposition Analysis and Concentration Evaluation) R package, a substantially improved successor to SuperCurve, to meet that challenge. SuperCurve has been used to normalize over 170 000 samples to date. RPPA SPACE allows exclusion of poor-quality samples from the normalization process to improve the quality of the remaining samples. It also features a novel quality-control metric, ‘noise’, that estimates the level of random errors present in each RPPA slide. The noise metric can help to determine the quality and reliability of the data. In addition, RPPA SPACE has simpler input requirements and is more flexible than SuperCurve, it is much faster with greatly improved error reporting. Availability and implementation The standalone RPPA SPACE R package, tutorials and sample data are available via https://rppa.space/, CRAN (https://cran.r-project.org/web/packages/RPPASPACE/index.html) and GitHub (https://github.com/MD-Anderson-Bioinformatics/RPPASPACE). Supplementary information Supplementary data are available at Bioinformatics online.