Adding software to package management systems can increase their citation by 280%

A growing number of biomedical methods and protocols are being disseminated as open-source software packages. When put in concert with other packages, they can execute in-depth and comprehensive computational pipelines. Therefore, their integration with other software packages plays a prominent role in their adoption in addition to their availability. Accordingly, package management systems are developed to standardize the discovery and integration of software packages. Here we study the impact of package management systems on software dissemination and their scholarly recognition. We study the citation pattern of more than 18,000 scholarly papers referenced by more than 23,000 software packages hosted by Bioconda, Bioconductor, BioTools, and ToolShed—the package management systems primarily used by the Bioinformatics community. Our results suggest that there is significant evidence that the scholarly papers’ citation count increases after their respective software was published to package management systems. Additionally, our results show that the impact of different package management systems on the scholarly papers’ recognition is of the same magnitude. These results may motivate scientists to distribute their software via package management systems, facilitating the composition of computational pipelines and helping reduce redundancy in package development. Significance Statement Software packages are the building blocks of computational pipelines. A myriad of packages are developed; however, the lack of integration and discovery standards hinders their adoption, leaving most scientists’ scholarly contributions unrecognized. Package management systems are developed to facilitate software dissemination and integration. However, developing software to meet their code and packaging standards is an involved process. Therefore, our study results on the significant impact of the package management systems on scholarly paper’s recognition can motivate scientists to invest in disseminating their software via package management systems. Dissemination of more software via package management systems will lead to a more straightforward composition of computational pipelines and less redundancy in software packages.