PMID- 36284674 OWN - NLM STAT- PubMed-not-MEDLINE VI - 2 IP - 1 TI - STtools: A Comprehensive Software Pipeline for Ultra-high Resolution Spatial Transcriptomics Data. LA - eng PT - Journal Article PL - England TA - Bioinform Adv JT - Bioinformatics advances JID - 9918282081306676 IS - 2635-0041 (Electronic) LID - vbac061 [pii] LID - 10.1093/bioadv/vbac061 [doi] FAU - Xi, Jingyue AU - Xi J AD - Department of Biostatistics, School of Public Health, University of Michigan, 1415 Washington Heights, Ann Arbor, MI 48109, USA. FAU - Lee, Jun Hee AU - Lee JH AD - Department of Molecular & Integrative Physiology, University of Michigan Medical School, 109 Zina Pitcher Place, Ann Arbor, MI 48109. FAU - Kang, Hyun Min AU - Kang HM AD - Department of Biostatistics, School of Public Health, University of Michigan, 1415 Washington Heights, Ann Arbor, MI 48109, USA. FAU - Jun, Goo AU - Jun G AD - Department of Epidemiology, Human Genetics & Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston, 1200 Pressler St., Houston, TX 77030, USA. IS - 2635-0041 (Linking) PMC - PMC9590442 LR - 20230126 DP - 2022 DEP - 20220901 AB - Motivation: While there are many software pipelines for analyzing spatial transcriptomics data, few can process ultra high-resolution datasets generated by emerging technologies. There is a clear need for new software tools that can handle sub-micrometer resolution spatial transcriptomics data with computational scalability without compromising its resolution. Results: We developed STtools, a software pipeline that provides a versatile framework to handle spatial transcriptomics datasets with various resolutions, such as the ones produced by Seq-Scope (<1μm), Slide-seq (10μm) and VISIUM (100μm). It automatically processes raw FASTQ files and runs downstream analyses at several folds higher resolution than existing methods. It also generates various visualizations including transcriptome density, cell type mapping, marker gene highlighting, and subcellular architectures. Availability: STtools is publically available for download at https://github.com/seqscope/STtools.