ST Pipeline: an automated pipeline for spatial mapping of unique transcripts. - José Fernández Navarro; Joel Sjöstrand; Fredrik Salmén; Joakim Lundeberg; Patrik L. Ståhl (Bioinform., 2017)

ST Spot Detector: a web-based application for automatic spot and tissue detection for spatial Transcriptomics image datasets. - Kim Wong; José Fernández Navarro; Ludvig Bergenstråhle; Patrik L. Ståhl; Joakim Lundeberg (Bioinform., 2018)

ST viewer: a tool for analysis and visualization of spatial transcriptomics datasets. - José Fernández Navarro; Joakim Lundeberg; Patrik L. Ståhl (Bioinform., 2019)

Semla: a versatile toolkit for spatially resolved transcriptomics analysis and visualization. - Ludvig Larsson; Lovisa Franzén; Patrik L. Ståhl; Joakim Lundeberg (Bioinform., 2023)

Lokatt: a hybrid DNA nanopore basecaller with an explicit duration hidden Markov model and a residual LSTM network. - Xuechun Xu; Nayanika Bhalla; Patrik L. Ståhl; Joakim Jaldén (BMC Bioinform., 2023)