APOSTL: An Interactive Galaxy Pipeline for Reproducible Analysis of Affinity Proteomics Data.
With continuously increasing scale and depth of coverage in affinity proteomics (AP-MS) data, the analysis and visualization is becoming more challenging. A number of tools have been developed to identify high-confidence interactions; however, a cohesive and intuitive pipeline for analysis and visualization is still needed. Here we present Automated Processing of SAINT Templated Layouts (APOSTL), a freely available Galaxy-integrated software suite and analysis pipeline for reproducible, interactive analysis of AP-MS data. APOSTL contains a number of tools woven together using Galaxy workflows, which are intuitive for the user to move from raw data to publication-quality figures within a single interface. APOSTL is an evolving software project with the potential to customize individual analyses with additional Galaxy tools and widgets using the R web application framework, Shiny. The source code, data, and documentation are freely available from GitHub ( https://github.com/bornea/APOSTL ) and other sources.
Department of Drug Discovery, H. Lee Moffitt Cancer Center & Research Institute , Tampa, Florida 33612-9497, United States.|Cancer Biology Ph.D. Program, University of South Florida , Tampa, Florida 33620, United States.
Brent M
BM
Kuenzi
Department of Thoracic Oncology, H. Lee Moffitt Cancer Center & Research Institute , Tampa, Florida 33612-9497, United States.
Adam L
AL
Borne
Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute , Tampa, Florida 33612-9497, United States.
Jiannong
J
Li
Department of Thoracic Oncology, H. Lee Moffitt Cancer Center & Research Institute , Tampa, Florida 33612-9497, United States.
Eric B
EB
Haura
Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute , Tampa, Florida 33612-9497, United States.
Steven A
SA
Eschrich
Molecular Oncology, H. Lee Moffitt Cancer Center & Research Institute , Tampa, Florida 33612-9497, United States.
John M
JM
Koomen
Department of Drug Discovery, H. Lee Moffitt Cancer Center & Research Institute , Tampa, Florida 33612-9497, United States.
Uwe
U
Rix
Department of Thoracic Oncology, H. Lee Moffitt Cancer Center & Research Institute , Tampa, Florida 33612-9497, United States.
Paul A
PA
Stewart
D019295:Computational Biology / Q000379:methods; D040901:Proteomics / Q000379:methods*; D012984:Software; D014584:User-Computer Interface; D057188:Workflow
AP−MS; Galaxy; SAINT; SAINTexpress; affinity proteomics; data analysis; data visualization; pipeline; workflow
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