The GenePattern Notebook environment, notebook.genepattern.org, integrates the Jupyter Notebook system with the GenePattern platform for integrative genomics analysis, making hundreds of analyses available within notebooks without the need for programming. Additional features allow publication and collaboration. A library of useful analysis notebook templates can be adapted to a scientist's needs.
Expression Atlas at EMBL-EBI provides free resources that facilitate submission, archival, reprocessing and visualisation of functional genomics data. This allows researchers a powerful way to identify where their favourite gene is expressed and how its expression changes in disease. Our tools are continuously updated to incorporate datasets using new technologies.
HiSCiAp is a user-friendly Galaxy setup to use ~80 Single Cell analysis modules from tools such as a Seurat, Scanpy, Monocle3, SCMap and others in QC, clustering, trajectory analysis and cell mapping. Tools are available at humancellatlas.usegalaxy.eu, can be installed on any Galaxy instance or used in command line.