Software list

• adultHSPC10X - 2017-12-821413
• Bacnet - friendly platform for building multi-omics websites. Described in https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btaa828/5910544, source code available at https://github.com/becavin-lab/bacnet
• BioTuring Browser
• Blood RNAexpress Atlas
• BRAIN-SAT - publication available here: https://www.biorxiv.org/content/10.1101/750000v1, successor to GOAD
• Cell Guide - cell RNA-seq datasets in the web browser, with a demo available at https://cell.guide/app/?ds=Smillie2019&gene=CXCL2. Source code available at https://github.com/slowkow/cellguide
• Cellar - cell data analysis. Described in this publication https://doi.org/10.1038/s41467-022-29744-0, source code available at https://github.com/euxhenh/cellar
• CellView
• CeNGEN
• CHARTS - cell RNA-seq datasets; described in the publication https://www.biorxiv.org/content/10.1101/2020.09.23.310441v1, source code at https://github.com/mbernste/cancer-single-cell-biomarker
• COVID-19 Immune Atlas - 19 Immune Atlas, aiming to provide a comprehensive overview of the human immune response in COVID-19 disease; used to display the data in the linked papers https://covid19cellatlas.com/#/papers
• COVID Omics App - 19 Multi-Omics Data Dashboard; linked to Large-scale Multi-omic Analysis of COVID-19 Severity, for which the preprint is available at https://www.medrxiv.org/content/10.1101/2020.07.17.20156513v1
• DRSC RNA-seq Explorer
• DVEX
• epiviz
• Evo-devo mammalian organs - 019-1338-5.
• Expression Atlas - seq datasets
• gEAR - driven, multi-omic data exploration. An exemplary instance is available at https://nemoanalytics.org/. Source code available at https://github.com/IGS/gEAR, described in the preprint https://www.biorxiv.org/content/10.1101/2020.08.28.272039v1
• Giotto - cell spatial transcriptomic data. Publication about it is https://doi.org/10.1101/701680 - Giotto Viewer is http://spatial.rc.fas.harvard.edu/giotto-viewer/, while the pipeline is available at https://github.com/RubD/Giotto
• Haemosphere
• HCA Bone Marrow Viewer
• Human Cell Atlas Data Portals - 019-1652-y (HCA Liver instances: https://developmental.cellatlas.io/fetal-liver). Source code is available at https://github.com/DoruMP/Fast-data-portals-for-scRNAseq-data
• i2dash - based dashboards for visualization of omics data and results, available on CRAN at https://cran.r-project.org/web/packages/i2dash/index.html - preprint available at https://www.biorxiv.org/content/10.1101/2020.07.06.189563v1
• iMAC
• Innate T cell gradient - input and single-cell RNA-seq for human T cell subsets, visualized with Shiny. Nature Communications
• iSEE - Interactive SummarizedExperiment Explorer (dev version at https://github.com/iSEE/iSEE), with custom panels (https://github.com/iSEE/iSEE_custom). Publication available at https://f1000research.com/articles/7-741/v1
• Loupe Cell Browser
• Lung Aging Atlas - 019-08831-9
• Magellan - generation sequencing data with a focus on COVID-19. Single cell maps are provided for a number of datasets in the dedicated tab (e.g. the COVID-19 dataset is https://www.nature.com/articles/s41587-020-0602-4).
• Mammary Gland Development - 017-02001-5
• MERmaid
• Microglia Orthologoues Viewer
• Morpheus
• Mouse Gastrulation and Early Organogenesis - 019-0933-9
• Mouse Organogenesis - 017-0013-z
• Mouse Organogenesis Cell Atlas (MOCA) - 019-0969-x
• Mouse sci-ATAC-seq Atlas - atac/ukbb_visualization/, among others. Manuscript: https://doi.org/10.1016/j.cell.2018.06.052
• Mouse Visual Cortex Explorer - 017-0029-5 (Hrvatin et al., 2018)
• mRNA isoform atlas - joglekar.shinyapps.io/spatialviz/. Related to the package https://github.com/noush-joglekar/scisorseqr, preprint available at https://www.biorxiv.org/content/10.1101/2020.08.27.268730v1
• Multiple sclerosis gene atlas
• nichExplorer - 019-1104-8, with source code available at https://github.com/igordot/nichexplorer. Also available from http://aifantislab.com/niche
• OmicPioneer-sc - cell sequencing data, described in https://www.biorxiv.org/content/10.1101/2020.10.31.363580v1 - based on the NG-CHM toolbox https://github.com/MD-Anderson-Bioinformatics/NG-CHM, with a demo available here https://bioinformatics.mdanderson.org/TCGA/NGCHMPortal/NGCHM/chm.html?map=d897cc0d4d2cd5c94801a3187996d3023e3b1f28
• Oncoscape - 023-31180-z; source code avilable at https://github.com/FredHutch/OncoscapeV3
• OpenTargets Browser - 020-15543-y, apps are https://cytokines.cellgeni.sanger.ac.uk/ and on cellxgene: https://cytokines.cellgeni.sanger.ac.uk/resting + https://cytokines.cellgeni.sanger.ac.uk/simulated
• PAWER - described in publication: https://www.biorxiv.org/content/10.1101/692905v1
• plae
• Planaria Single Cell Atlas
• PlaqView - Cell Portal for Cardiovascular Research - composed of a scRNA-seq portal (http://plaqviewv2.uvadcos.io/) and a scATAC-seq portal (http://plaqviewatac.uvadcos.io/). Described in https://doi.org/10.1016/j.atherosclerosis.2021.11.025, source code available at https://github.com/MillerLab-CPHG/PlaqView
• ProteinPaint - resources/technology-licensing/technologies/proteinpaint-web-application-for-visualizing-genomic-data-sj-15-0021.html, original publication here: https://www.nature.com/articles/ng.3466. Used e.g. to deploy Mouse Retina Development data, https://proteinpaint.stjude.org/F/mm10/2019.mouse.retina.scRNA.html
• ProTrack - described in the preprint https://doi.org/10.1101/2020.02.05.935650. Source code is (should be) available at https://github.com/WangLab/ProTrack-ccrcc (currently not found?)
• puma_gtex - specific functions of miRNAs (as described in the PUMA preprint, https://www.biorxiv.org/content/10.1101/2019.12.18.874065v1)
• Reptilian pallium - department/software-techniques.html
• RNA_vs_protein
• SCHNAPPs - pasteur-fr/UTechSCB-SCHNAPPs. Could be extended as in https://github.com/baj12/SCHNAPPsContributions
• shinyMethyl
• ShinyOmics - data. Described in https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-3360-x, with source code available at https://github.com/dsurujon/ShinyOmics
• Single Cell Expression Atlas - Seq studies (total: 882958 cells), across 11 different species. Publication: https://academic.oup.com/nar/article/47/D1/D711/5144130
• Single Cell Portal - of-human-blood-dendritic-cells-and-monocytes#study-visualize - Source code available here: https://github.com/broadinstitute/single_cell_portal_core
• Slide-seq Portal
• SpatialDB - article/doi/10.1093/nar/gkz934/5622703
• TCGABrowser
• TILAtlas - infiltrating CD8 lymphocytes in B16 melanoma tumors with single-cell RNA-Seq. Based on iSEE. Publication available at https://www.tandfonline.com/doi/full/10.1080/2162402X.2020.1737369 - alternative address: https://tilatlas.shinyapps.io/B16_CD8TIL_10X/
• Transcriptome Dynamics for CD4+ T-cells in Experimental Malaria
• UCSC Cell Browser - seq data. Documentation at https://cellbrowser.readthedocs.io. Preprint available at https://www.biorxiv.org/content/10.1101/2020.10.30.361162v1, described also in https://www.ncbi.nlm.nih.gov/pubmed/30407534
• VDJView - omics data. Preprint available at https://www.biorxiv.org/content/10.1101/613083v2.full
• VirtualCytometry
• VisCello
• WIlsON - bn.mpg.de
• Zebrafish single cell development atlas
• Fate Bias Inference in Lymphoid progenitors - single-cell RNA-seq data of murine hematopoietic progenitors
• AMP RA - seq and CyTOF for human synovial tissue from patients with rheumatoid arthritis (RA) or osteoarthritis (OA), visualized with Shiny. bioRxiv
• AMP SLE - seq for human kidney biopsies from patients with systemic lupus erythematosus (SLE) patients, visualized with Shiny. bioRxiv
• Brain Cell RNA-seq Browser
• cellxgene - muris-senis.ds.czbiohub.org) - a simpler browser is available at https://tabula-muris.ds.czbiohub.org. Another example of this in action is http://mouse.retina.gofflab.org, for the Developing Mouse Retina https://doi.org/10.1016/j.neuron.2019.04.010
• cerebro - seq data. bioRxiv -> now published here: https://doi.org/10.1093/bioinformatics/btz877
• COPD Cell Atlas
• DISCO - Cell Omics data. Described in https://doi.org/10.1093/nar/gkab1020, source code (for FastIntegration) available at https://github.com/JinmiaoChenLab/FastIntegration
• DropViz
• dseqr - seq data. Project website available at https://docs.dseqr.com/
• FireBrowse
• GenePattern
• GEPIA
• Human Liver Cell Atlas - 019-1373-2 - currently not working?
• IPF Cell Atlas
• iS-CellR - seq data. R Shiny app. Manuscript available at https://academic.oup.com/bioinformatics/article/34/24/4305/5048937
• iSTARTRAC - A Shiny web-application accompanying https://doi.org/10.1038/s41597-019-0131-5. Source code available at https://github.com/Japrin/STARTRAC
• Microglia Single Cell Atlas
• MouseLight Neuron Browser
• Neuroexpresso - 17.2017
• OmicLoupe - dataset visualizations for omic data; demo running at http://130.239.81.217:3838/omicloupe/, source code at https://github.com/ComputationalProteomics/OmicLoupe, described in the preprint https://www.biorxiv.org/content/10.1101/2020.10.22.349944v1
• Pan-cancer tumor infiltrating myeloid cells atlas - cancer single-cell transcriptional atlas of tumor infiltrating myeloid cells" (https://doi.org/10.1016/j.cell.2021.01.010); source available at https://github.com/Sijin-ZhangLab/PanMyeloid
• Planarian Digiworm
• rakaia - browser expression analysis of spatial data types, https://github.com/camlab-bioml/rakaia. Available as a preprint on bioRxiv, https://www.biorxiv.org/content/10.1101/2025.08.15.670550v1
• RNA-Seq Viewer
• scbrowse - a single-cell ATAC-seq browser that enables to simultaneously explore a 2D cell-embedding and accessibility profiles across the genome. Live example: https://scbrowse.mdc-berlin.de
• scClustViz - focused on exploring clustering results, paper here: https://f1000research.com/articles/7-1522/v2
• scSVA - cell Scalable Visualization and Analytics, presented in this publication https://www.biorxiv.org/content/10.1101/512582v1 - some documentation presented as videos, e.g. https://www.youtube.com/watch?v=W_U9swh468U
• SCelVis - seq data. Preprint: https://www.biorxiv.org/content/10.1101/713008v1
• SCV (Single Cell Viewer)
• scViewer - cell data viewer shiny application. Published in https://doi.org/10.3390/cells12111489
• scX - friendly tool for scRNA-seq exploration. Documentation available at https://chernolabs.github.io/scX/, related publication (preprint) at https://arxiv.org/abs/2311.00012
• SeuratWizard - web-based interactive application to perform a guided single-cell RNA-seq data analysis and clustering based on Seurat. Based on the Nasqar platform (http://nasqar.abudhabi.nyu.edu)
• SeuratV3Wizard - successor of SeuratWizard (above) for Seurat v3
• ShinyCell - cell gene expression data; described in https://doi.org/10.1093/bioinformatics/btab209 (preprint: https://www.biorxiv.org/content/10.1101/2020.10.25.354100v1). Source available at https://github.com/SGDDNB/ShinyCell, demo/tutorial available at http://shinycell1.ddnetbio.com/
• Single Cell Explorer - 019-6053-y. Demos available at http://18.204.165.197, source code at https://github.com/d-feng/scExplorer
• spatialLIBD - frontal cortex (DLPFC) spatial transcriptomics data generated with the 10x Genomics Visium platform - described in the preprint https://www.biorxiv.org/content/10.1101/2020.02.28.969931v1. Source available at https://github.com/LieberInstitute/spatialLIBD
• Spatial Mouse Atlas - described in the paper https://www.nature.com/articles/s41587-021-01006-2. App source and analysis scripts available at https://github.com/MarioniLab/SpatialMouseAtlas2020.
• ST Viewer
• TISCH - cell Hub 2 - source code available at https://github.com/DongqingSun96/TISCH
• VISION - cell RNA-seq. Source code available at https://github.com/YosefLab/VISION, described in https://doi.org/10.1038/s41467-019-12235-0
• Brain RNA-Seq - related RNA-seq datasets
• scRNASeqDB - Seq gene expression profiles in human single cells. Publication https://www.mdpi.com/2073-4425/8/12/368, available at https://bioinfo.uth.edu/scrnaseqdb/
• indeXplorer - based app for the explorative analysis of the hematopoietic stem cell dataset, accompanying https://doi.org/10.1038/ncb3493, with source code available at https://git.embl.de/velten/indeXplorer
• HTSVis
• ASAP - cell Analysis Pipeline (https://doi.org/10.1093/bioinformatics/btx337)
• Mouse Cell Atlas - seq, companion to https://doi.org/10.1016/j.cell.2018.02.001
• Mousebrain.org - Manuscript: https://www.sciencedirect.com/science/article/pii/S009286741830789X
• islet regulome - 019-0524-6, browser described in https://www.frontiersin.org/articles/10.3389/fgene.2017.00013/full. Source code is available at https://github.com/mireia-bioinfo/plotRegulome (plotting functions as a package!) and https://github.com/mireia-bioinfo/isletregulome_shiny (app)
• ALS Spatiotemporal gene expression Atlas
• cBioPortal
• eyeIntegration - seq datasets reprocessed and made available with a reactive Shiny app
• PanglaoDB - franzen/PanglaoDB (not the source code of the resource itself)
• PEAC RNA-seq - seq of early rheumatoid arthritis individuals and their clinical data. Linked to the publication https://doi.org/10.1016/j.celrep.2019.07.091
• scfind - source code available here: https://github.com/hemberg-lab/scfind, described in the publication https://www.biorxiv.org/content/10.1101/788596v1
• Xena Browser
• Allen Brain Atlases - for example, referred to in this recent publication on whole brain spatial transcriptomics (https://www.biorxiv.org/content/10.1101/784181v1)
• Brain Immune Atlas - cell RNA sequencing datasets that together capture the diversity of the brain immune compartment. Publication related: https://www.nature.com/articles/s41593-019-0393-4; source code: https://github.com/saeyslab/brainimmuneatlas/
• CancerSCEM - cell Expression Map - a database of single-cell expression map across various human cancers. Described in https://doi.org/10.1093/nar/gkab905, source code not linked in any of the online resources
• ChickHeartAtlas
• CRI iATLAS - oncology research. Source code available at https://github.com/CRI-iAtlas/shiny-iatlas, with the publication describing it at https://f1000research.com/articles/9-1028/v1
• Gene and protein expression in adult haematopoiesis - 2016-05-716480
• MicrobiomeDB
• MicrobiomeExplorer - described in https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btaa838/5909986, source code available at https://github.com/zoecastillo/microbiomeExplorer
• NCI Patient Derived Model Repository
• oposSom-Browser - dimensional data portraying", generated via self-organizing maps (e.g. through oposSOM). Demo instance available at https://apps.health-atlas.de/opossom-browser/ (source not available?), described in https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-03806-w
• ORDER - wide gene expression data during the floral transition in the allopolyploid crop Brassica napus (oilseed rape, OSR). This website also allows users to search using sequence similarity to Arabidopsis genes or to user submitted sequences. Any time series data, regardless of origin, can be visualised using this website. Publication can be found here: https://bmcplantbiol.biomedcentral.com/articles/10.1186/s12870-020-02509-x
• pRolocGUI
• SCPortalen - cell centric database. Published at https://doi.org/10.1093/nar/gkx949
• SCope - scale scRNA-seq datasets. Has some datasets preprocessed to showcase, allows own data (in the .loom format) to be uploaded. Source code: https://github.com/aertslab/SCope. Original publication where this is found: https://www.sciencedirect.com/science/article/pii/S0092867418307207
• Seattle Organismal Molecular Atlases
• Spaniel
• starmapVR - based visualisation of single cell spatial omic data. Source code available at https://github.com/holab-hku/starmapVR, described in the preprint https://www.biorxiv.org/content/10.1101/2020.09.01.277079v1
• Vidjil - Throughput Analysis
• Vitessce - cell experiment data. Some demos are available, e.g. http://vitessce.io/?dataset=linnarsson-2018 - source code is available at https://github.com/hubmapconsortium/vitessce

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