Ecosyste.ms: Awesome

An open API service indexing awesome lists of open source software.

awesome-expression-browser

😎 A curated list of software and resources for exploring and visualizing (browsing) expression data 😎
https://github.com/federicomarini/awesome-expression-browser

  • AMP RA - seq and CyTOF for human synovial tissue from patients with rheumatoid arthritis (RA) or osteoarthritis (OA), visualized with Shiny. [bioRxiv](https://doi.org/10.1101/351130)
  • AMP SLE - seq for human kidney biopsies from patients with systemic lupus erythematosus (SLE) patients, visualized with Shiny. [bioRxiv](https://doi.org/10.1101/363051)
  • adultHSPC10X - 2017-12-821413
  • Allen Brain Atlases - for example, referred to in this recent publication on whole brain spatial transcriptomics (https://www.biorxiv.org/content/10.1101/784181v1)
  • ALS Spatiotemporal gene expression Atlas
  • ASAP - cell Analysis Pipeline (https://doi.org/10.1093/bioinformatics/btx337)
  • 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 Cell RNA-seq Browser
  • 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/
  • Brain RNA-Seq - related RNA-seq datasets
  • BRAIN-SAT - publication available here: https://www.biorxiv.org/content/10.1101/750000v1, successor to GOAD
  • 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
  • cBioPortal
  • 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
  • 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
  • CeNGEN
  • cerebro - seq data. [bioRxiv](https://www.biorxiv.org/content/10.1101/631705v1) -> now published here: https://doi.org/10.1093/bioinformatics/btz877
  • 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
  • ChickHeartAtlas
  • COPD Cell Atlas
  • 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
  • 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
  • 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
  • DRSC RNA-seq Explorer
  • dseqr - seq data. Project website available at https://docs.dseqr.com/
  • DVEX
  • epiviz
  • Evo-devo mammalian organs - 019-1338-5.
  • Expression Atlas - seq datasets
  • eyeIntegration - seq datasets reprocessed and made available with a reactive Shiny app
  • FASTGenomics - cell RNA sequencing data and analyses using reproducible workflows. Users can upload their own data and generate reproducible workflows ([Scholz et al. 2018](https://doi.org/10.1101/272476)). GitHub: [@fastgenomics](https://github.com/fastgenomics). A free demo instance is reachable at https://beta.fastgenomics.org/ (allows anonymous login)
  • Fate Bias Inference in Lymphoid progenitors - single-cell RNA-seq data of murine hematopoietic progenitors
  • FireBrowse
  • 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
  • Gene and protein expression in adult haematopoiesis - 2016-05-716480
  • GenePattern
  • GEPIA
  • 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
  • GTEx Portal - Tissue Expression (GTEx) project
  • Haemosphere
  • HCA Bone Marrow Viewer
  • HTSVis
  • 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
  • Human Liver Cell Atlas - 019-1373-2 - *currently not working?*
  • 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
  • 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
  • Innate T cell gradient - input and single-cell RNA-seq for human T cell subsets, visualized with Shiny. [Nature Communications](https://doi.org/10.1038/s41467-019-08604-4)
  • IPF Cell Atlas
  • iS-CellR - seq data. R Shiny app. Manuscript available at https://academic.oup.com/bioinformatics/article/34/24/4305/5048937
  • 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
  • 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)
  • iSTARTRAC - A Shiny web-application accompanying https://doi.org/10.1038/s41597-019-0131-5. Source code available at https://github.com/Japrin/STARTRAC
  • 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).
  • Malaria Cell Atlas
  • Mammary Gland Development - 017-02001-5
  • MERmaid
  • 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
  • Microglia Orthologoues Viewer
  • Microglia Single Cell Atlas
  • Morpheus
  • Mousebrain.org - Manuscript: https://www.sciencedirect.com/science/article/pii/S009286741830789X
  • Mouse Cell Atlas - seq, companion to https://doi.org/10.1016/j.cell.2018.02.001
  • Mouse Gastrulation and Early Organogenesis - 019-0933-9
  • MouseLight Neuron Browser
  • 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
  • NCI Patient Derived Model Repository
  • Neuroexpresso - 17.2017
  • nichExplorer - 019-1104-8, with source code available at https://github.com/igordot/nichexplorer. Also available from http://aifantislab.com/niche
  • 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
  • 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
  • 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
  • PanglaoDB - franzen/PanglaoDB (not the source code of the resource itself)
  • 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
  • PAWER - described in publication: https://www.biorxiv.org/content/10.1101/692905v1
  • 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
  • plae
  • Planaria Single Cell Atlas
  • Planarian Digiworm
  • 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
  • pRolocGUI
  • 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-Seq Viewer
  • RNA_vs_protein
  • 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
  • scfind - source code available here: https://github.com/hemberg-lab/scfind, described in the publication https://www.biorxiv.org/content/10.1101/788596v1
  • SCPortalen - cell centric database. Published at https://doi.org/10.1093/nar/gkx949
  • 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/
  • 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
  • SCHNAPPs - pasteur-fr/UTechSCB-SCHNAPPs. Could be extended as in https://github.com/baj12/SCHNAPPsContributions
  • 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
  • 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
  • Seattle Organismal Molecular Atlases
  • 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/
  • 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 Explorer - 019-6053-y. Demos available at http://18.204.165.197, source code at https://github.com/d-feng/scExplorer
  • 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
  • singlecellVR - cell data in virtual reality, preprint available at https://www.biorxiv.org/content/10.1101/2020.07.30.229534v1. Source code available at https://github.com/pinellolab/singlecellvr
  • Slide-seq Portal
  • Spaniel
  • SpatialDB - article/doi/10.1093/nar/gkz934/5622703
  • 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.
  • 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
  • ST Viewer
  • 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/
  • TISCH - cell Hub 2 - source code available at https://github.com/DongqingSun96/TISCH
  • 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
  • Vidjil - Throughput Analysis
  • VirtualCytometry
  • VisCello
  • VISION - cell RNA-seq. Source code available at https://github.com/YosefLab/VISION, described in https://doi.org/10.1038/s41467-019-12235-0
  • 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
  • WIlsON - bn.mpg.de
  • Xena Browser
  • Zebrafish single cell development atlas
  • @federicomarini
  • @csoneson
  • @kevinrue
  • @kevinblighe
  • @DCGenomics
  • @shazanfar
  • @davemcg
  • @slowkow
  • @patidarr
  • @crazyhottommy
  • @mvonpapen
  • @igordot
  • @wkopp
  • @ruthkr
Programming Languages
R 10 C++ 2 Python 2 JavaScript 2 r 1 HTML 1
Keywords
single-cell 3 shiny 3 r 3 single-cell-rna-seq 3 scrna-seq 2 single-cell-genomics 2 single-cell-analysis 2 shiny-apps 2 seurat 2 visualization 2 dataviz 1 scientific 1 transcriptomics 1 bulk-rna-seq 1 drug-repurposing 1 rna-seq 1 clustering-evaluation 1 differential-expression 1 scrna-seq-analysis 1 scrnaseq 1 ui 1 webapplication 1 bioinformatics 1 webapp 1