Standardizing workflows in imaging transcriptomics with the abagen toolbox.

ABSTRACT: Gene expression fundamentally shapes the structural and functional architecture of the human brain. Open-access transcriptomic datasets like the Allen Human Brain Atlas provide an unprecedented ability to examine these mechanisms in vivo; however, a lack of standardization across research groups has given rise to myriad processing pipelines for using these data. Here, we develop the abagen toolbox, an open-access software package for working with transcriptomic data, and use it to examine how methodological variability influences the outcomes of research using the Allen Human Brain Atlas. Applying three prototypical analyses to the outputs of 750,000 unique processing pipelines, we find that choice of pipeline has a large impact on research findings, with parameters commonly varied in the

SUBMITTER: Markello RD 

PROVIDER: S-EPMC8660024 | biostudies-literature | 2021 Nov

REPOSITORIES: biostudies-literature