Giotto
– Integrative data analysis and visualization toolkit for spatial transcriptomic data

smfishHmrf
– A Python package for single-molecule FISH machine learning analyses. Includes SVM-based cell type mapping
from scRNAseq to seqFISH and spatial pattern mining using hidden Markov random field.

CUT&RUNTools
– A customizable workflow for performing analyses of CUT&RUN data. Besides reads trimming, alignment, peak calling,
it includes de novo motif finding, motif footprinting, and transcription factor binding site predictions.

SEEK
– Search-based exploration of expression compendium. A coexpressed gene search and visualization system.

ModSEEK
– Model organism extension of SEEK. Covers transcriptome compendia in fly, worm, mouse, zebrafish, and yeast.