The recent growth in volume and complexity of biological data has simultaneously pushed the development of computational pipelines used in corresponding analyses. Over the last several years, numerous tools and packages have been developed for such purposes. In this article, we provide an overview of software strategies geared towards omics (e.g., genomics, transcriptomics, and proteomics) and bioimage data processing and investigation. We first introduce practical approaches for working with DNA (ChIP-seq and GWAS) and RNA (DNA-chip and RNA-seq) sequence information. Subsequently, we describe recent pipelines aimed at recognizing molecular features in proteins and conclude with a brief introduction to bioimage informatics.