├── .github └── workflows │ └── main.yml ├── Human ├── Adult │ ├── Brain_AllenBrainAtlas.RData │ ├── Brain_Darmanis.RData │ ├── BreastCancer_Wu.RData │ ├── Colon_HCA.RData │ ├── Decidua_HCA.RData │ ├── Esophagus_HCA.RData │ ├── Gut_HCA.RData │ ├── Heart_HCA.RData │ ├── Ileum_Wang.RData │ ├── ImmuneCensus_HCA.RData │ ├── ImmuneTumor_safeTME.RData │ ├── Kidney_HCA.RData │ ├── Liver_HCA.RData │ ├── Lung_COPD_Adams.RData │ ├── Lung_Control_Adams.RData │ ├── Lung_HCA.RData │ ├── Lung_IPF_Adams.RData │ ├── Muscle_DeMicheli.RData │ ├── Pancreas_HCA.RData │ ├── Placenta_HCA.RData │ ├── Prostate_Henry.RData │ ├── Rectum_Wang.RData │ ├── Retina_HCA.RData │ ├── Skin_HCA.RData │ ├── Spleen_HCA.RData │ └── Testis_Guo.RData ├── COVID-Infected │ ├── Bronchoalveolar_lavage_fluid_COVID19_cellAtlas.RData │ ├── Covid_Airway_COVID19_cellAtlas.RData │ ├── Immunodeficiency_Nasal_Swabs_COVID19_cellAtlas.RData │ ├── Immunodeficiency_PBMCs_COVID19_cellAtlas.RData │ ├── MGH_Broad_COVID19_cellAtlas.RData │ └── PBMCs_COVID19_cellAtlas.RData ├── Fetal │ ├── Adrenal_Descartes.RData │ ├── Cerebellum_Descartes.RData │ ├── Cerebrum_Descartes.RData │ ├── Eye_Descartes.RData │ ├── Heart_Descartes.RData │ ├── Intestine_Descartes.RData │ ├── Kidney_Descartes.RData │ ├── Liver_Descartes.RData │ ├── Lung_Descartes.RData │ ├── Muscle_Descartes.RData │ ├── Pancreas_Descartes.RData │ ├── Placenta_Descartes.RData │ ├── Spleen_Descartes.RData │ ├── Stomach_Descartes.RData │ └── Thymus_Descartes.RData ├── HumanAdult_CellTypes.xlsx ├── HumanCOVID-Infected_CellTypes.xlsx ├── HumanFetal_CellTypes.xlsx └── Human_datasets_metadata.csv ├── LICENSE ├── Mouse ├── Adult │ ├── Bladder_MCA.RData │ ├── BoneMarrow_MCA.RData │ ├── BoneMarrow_cKit_MCA.RData │ ├── Brain_AllenBrainAtlas.RData │ ├── Brain_MCA.RData │ ├── ImmuneAtlas_ImmGen.RData │ ├── ImmuneAtlas_ImmGen_cellFamily.RData │ ├── Kidney_MCA.RData │ ├── Liver_MCA.RData │ ├── Lung_MCA.RData │ ├── MammaryGland_Involution_MCA.RData │ ├── MammaryGland_Lactation_MCA.RData │ ├── MammaryGland_Pregnancy_MCA.RData │ ├── MammaryGland_Virgin_MCA.RData │ ├── Muscle_MCA.RData │ ├── Ovary_MCA.RData │ ├── Pancreas_MCA.RData │ ├── PeripheralBlood_MCA.RData │ ├── Placenta_MCA.RData │ ├── Prostate_MCA.RData │ ├── SmallIntestine_MCA.RData │ ├── Spleen_MCA.RData │ ├── Stomach_MCA.RData │ ├── Testis_MCA.RData │ ├── Thymus_MCA.RData │ └── Uterus_MCA.RData ├── Fetal │ ├── E14.5 │ │ ├── Brain_MCA.RData │ │ ├── EmbryonicMesenchyme_MCA.RData │ │ ├── Intestine_MCA.RData │ │ ├── Liver_MCA.RData │ │ ├── Lung_MCA.RData │ │ └── Stomach_MCA.RData │ └── E9.5-13.5 │ │ └── FetalAtlas_MOCA.RData ├── MouseAdult_CellTypes.xlsx ├── MouseFetal_CellTypes.xlsx ├── MouseNeonatal_CellTypes.xlsx ├── Mouse_datasets_metadata.csv └── Neonatal │ ├── Calvaria_MCA.RData │ ├── Heart_MCA.RData │ ├── Muscle_MCA.RData │ ├── Pancreas_MCA.RData │ ├── Rib_MCA.RData │ └── Skin_MCA.RData └── README.md /.github/workflows/main.yml: -------------------------------------------------------------------------------- 1 | on: 2 | issues: 3 | types: [opened] 4 | 5 | 6 | jobs: 7 | welcome: 8 | runs-on: ubuntu-latest 9 | steps: 10 | - uses: EddieHubCommunity/gh-action-community/src/welcome@main 11 | with: 12 | github-token: ${{ secrets.GITHUB_TOKEN }} 13 | issue-message: "Thank you for contacting us about our tools! To receive assistance, kindly email support.spatial@bruker.com with detailed information about your issue. If applicable, attach a screenshot of any encountered errors and include a copy of the modified script in Notepad. 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However, if You fail to comply with this Public License, then Your rights under this Public License terminate automatically. 71 | Where Your right to use the Licensed Material has terminated under Section 6(a), it reinstates: 72 | 73 | automatically as of the date the violation is cured, provided it is cured within 30 days of Your discovery of the violation; or 74 | upon express reinstatement by the Licensor. 75 | For the avoidance of doubt, this Section 6(b) does not affect any right the Licensor may have to seek remedies for Your violations of this Public License. 76 | For the avoidance of doubt, the Licensor may also offer the Licensed Material under separate terms or conditions or stop distributing the Licensed Material at any time; however, doing so will not terminate this Public License. 77 | Sections 1, 5, 6, 7, and 8 survive termination of this Public License. 78 | Section 7 – Other Terms and Conditions. 79 | 80 | The Licensor shall not be bound by any additional or different terms or conditions communicated by You unless expressly agreed. 81 | Any arrangements, understandings, or agreements regarding the Licensed Material not stated herein are separate from and independent of the terms and conditions of this Public License. 82 | Section 8 – Interpretation. 83 | 84 | For the avoidance of doubt, this Public License does not, and shall not be interpreted to, reduce, limit, restrict, or impose conditions on any use of the Licensed Material that could lawfully be made without permission under this Public License. 85 | To the extent possible, if any provision of this Public License is deemed unenforceable, it shall be automatically reformed to the minimum extent necessary to make it enforceable. If the provision cannot be reformed, it shall be severed from this Public License without affecting the enforceability of the remaining terms and conditions. 86 | No term or condition of this Public License will be waived and no failure to comply consented to unless expressly agreed to by the Licensor. 87 | Nothing in this Public License constitutes or may be interpreted as a limitation upon, or waiver of, any privileges and immunities that apply to the Licensor or You, including from the legal processes of any jurisdiction or authority. 88 | -------------------------------------------------------------------------------- /Mouse/Adult/Bladder_MCA.RData: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/CellProfileLibrary/9698cc40641940581eac92a2bf21cdcbadb49367/Mouse/Adult/Bladder_MCA.RData -------------------------------------------------------------------------------- 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-------------------------------------------------------------------------------- 1 | Profile Matrix,Tissue,Species,Strain,Age,Age Group,URL,Citation 2 | MCA,Bladder,Mouse,C57BL/6,6-10 weeks,Adult,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)." 3 | MCA,BoneMarrow,Mouse,C57BL/6,6-10 weeks,Adult,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)." 4 | MCA,BoneMarrow_cKit,Mouse,C57BL/6,6-10 weeks,Adult,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)." 5 | AllenBrainAtlas,Brain,Mouse,"C57BL/6J, Nkx2.1-CreERT2;Ai14",8 weeks,Adult,"https://www.biorxiv.org/content/10.1101/2020.03.30.015214v1.full#F1 6 | https://portal.brain-map.org/atlases-and-data/rnaseq/mouse-whole-cortex-and-hippocampus-10x","Yao, Z. et al. A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation. bioRxiv 2020.03.30.015214 (2020) doi:10.1101/2020.03.30.015214." 7 | MCA,Brain,Mouse,"C57BL/6","6-10 weeks",Adult,"https://pubmed.ncbi.nlm.nih.gov/29474909/","Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)." 8 | ImmGen,ImmuneAtlas,Mouse,"C57BL/6, B6.Rorc.tm2Litt",5-6 weeks,Adult,https://pubmed.ncbi.nlm.nih.gov/30686579/,"Yoshida, H. et al. The cis-Regulatory Atlas of the Mouse Immune System. Cell 176, 897-912.e20 (2019)." 9 | ImmGen_cellFamily,ImmuneAtlas,Mouse,"C57BL/6, B6.Rorc.tm2Litt",5-6 weeks,Adult,https://pubmed.ncbi.nlm.nih.gov/30686579/,"Yoshida, H. et al. The cis-Regulatory Atlas of the Mouse Immune System. Cell 176, 897-912.e20 (2019)." 10 | MCA,Kidney,Mouse,C57BL/6,6-10 weeks,Adult,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)." 11 | MCA,Liver,Mouse,C57BL/6,6-10 weeks,Adult,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)." 12 | MCA,Lung,Mouse,C57BL/6,6-10 weeks,Adult,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)." 13 | MCA,MammaryGland_Involution,Mouse,C57BL/6,6-10 weeks,Adult,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)." 14 | MCA,MammaryGland_Lactation,Mouse,C57BL/6,6-10 weeks,Adult,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)." 15 | MCA,MammaryGland_Pregnancy,Mouse,C57BL/6,6-10 weeks,Adult,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)." 16 | MCA,MammaryGland_Virgin,Mouse,C57BL/6,6-10 weeks,Adult,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)." 17 | MCA,Muscle,Mouse,C57BL/6,6-10 weeks,Adult,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)." 18 | MCA,Ovary,Mouse,C57BL/6,6-10 weeks,Adult,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)." 19 | MCA,Pancreas,Mouse,C57BL/6,6-10 weeks,Adult,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)." 20 | MCA,PeripheralBlood,Mouse,C57BL/6,6-10 weeks,Adult,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)." 21 | MCA,Placenta,Mouse,C57BL/6,6-10 weeks,Adult,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)." 22 | MCA,Prostate,Mouse,C57BL/6,8-10 weeks,Adult,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)." 23 | MCA,SmallIntestine,Mouse,C57BL/6,6-10 weeks,Adult,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)." 24 | MCA,Spleen,Mouse,C57BL/6,6-10 weeks,Adult,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)." 25 | MCA,Stomach,Mouse,C57BL/6,6-10 weeks,Adult,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)." 26 | MCA,Testis,Mouse,C57BL/6,8-10 weeks,Adult,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)." 27 | MCA,Thymus,Mouse,C57BL/6,6-10 weeks,Adult,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)." 28 | MCA,Uterus,Mouse,C57BL/6,6-10 weeks,Adult,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)." 29 | MCA,EmbryonicMesenchyme,Mouse,C57BL/6,14.5 days,Fetal/E14.5,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)." 30 | MOCA,FetalAtlas,Mouse,C57BL/6,9.5 and 13.5 days,Fetal/E9.5-13.5,"https://doi.org/10.1038/s41586-019-0969-x 31 | https://oncoscape.v3.sttrcancer.org/atlas.gs.washington.edu.mouse.rna/downloads","Cao, J. et al. The single cell transcriptional landscape of mammalian organogenesis. Nature 566, 496–502 (2019)." 32 | MCA,Brain,Mouse,C57BL/6,14.5 days,Fetal/E14.5,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)." 33 | MCA,Intestine,Mouse,C57BL/6,14.5 days,Fetal/E14.5,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)." 34 | MCA,Liver,Mouse,C57BL/6,14.5 days,Fetal/E14.5,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)." 35 | MCA,Lung,Mouse,C57BL/6,14.5 days,Fetal/E14.5,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)." 36 | MCA,Stomach,Mouse,C57BL/6,14.5 days,Fetal/E14.5,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)." 37 | MCA,Calvaria,Mouse,C57BL/6,1 day,Neonatal,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)." 38 | MCA,Heart,Mouse,C57BL/6,1 day,Neonatal,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)." 39 | MCA,Muscle,Mouse,C57BL/6,1 day,Neonatal,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)." 40 | MCA,Pancreas,Mouse,C57BL/6,1 day,Neonatal,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)." 41 | MCA,Rib,Mouse,C57BL/6,1 day,Neonatal,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)." 42 | MCA,Skin,Mouse,C57BL/6,1 day,Neonatal,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)." 43 | -------------------------------------------------------------------------------- /Mouse/Neonatal/Calvaria_MCA.RData: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/CellProfileLibrary/9698cc40641940581eac92a2bf21cdcbadb49367/Mouse/Neonatal/Calvaria_MCA.RData -------------------------------------------------------------------------------- /Mouse/Neonatal/Heart_MCA.RData: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/CellProfileLibrary/9698cc40641940581eac92a2bf21cdcbadb49367/Mouse/Neonatal/Heart_MCA.RData -------------------------------------------------------------------------------- /Mouse/Neonatal/Muscle_MCA.RData: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/CellProfileLibrary/9698cc40641940581eac92a2bf21cdcbadb49367/Mouse/Neonatal/Muscle_MCA.RData -------------------------------------------------------------------------------- /Mouse/Neonatal/Pancreas_MCA.RData: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/CellProfileLibrary/9698cc40641940581eac92a2bf21cdcbadb49367/Mouse/Neonatal/Pancreas_MCA.RData -------------------------------------------------------------------------------- /Mouse/Neonatal/Rib_MCA.RData: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/CellProfileLibrary/9698cc40641940581eac92a2bf21cdcbadb49367/Mouse/Neonatal/Rib_MCA.RData -------------------------------------------------------------------------------- /Mouse/Neonatal/Skin_MCA.RData: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/CellProfileLibrary/9698cc40641940581eac92a2bf21cdcbadb49367/Mouse/Neonatal/Skin_MCA.RData -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | ## Overview 2 | 3 | This repo contains a library of "cell profile matrices" - matrices giving the average expression profiles of all cell types found in a tissue. 4 | Each matrix in the library was derived from a single scRNA-seq experiment. These matrices can be used with cell type deconvolution packages like SpatialDecon to get cell type proportions or identities. 5 | 6 | SpatialDecon [Manuscript](https://www.nature.com/articles/s41467-022-28020-5) and [Package](https://bioconductor.org/packages/release/bioc/html/SpatialDecon.html) 7 | 8 | ![SpatialDecon_workflow](https://user-images.githubusercontent.com/40255151/128901535-54a8d912-d7ea-4774-9b71-46f396f6bce3.PNG) 9 | 10 | 11 | Each RData file contains 3 file types: 12 | 13 | 1. Cell Profile Matrix 14 | 15 | 2. Cell Groups 16 | 17 | 3. Dataset Metadata 18 | 19 | ## File Types 20 | 21 | **Cell Profile Matrix**: Average expression profile of all cell types found in a tissue. 22 | 23 | ![cellProfileMatrix](https://user-images.githubusercontent.com/40255151/126808635-a3c6c839-5872-4995-a870-6def7137ffb6.png) 24 | 25 | **Cell Groups**: Suggested binning of cell types for simpiler figures. In this example,there are six different hepatacyte cell types that can be collapsed into one group. Some datasets have more than one suggested grouping depending on aggressiveness in binning. The less aggressive binning is the default with the additional ones having "_binType" appended to the variable name. 26 | 27 | ![cellTypeBin](https://user-images.githubusercontent.com/40255151/126808762-c92983ae-9ed2-46fe-990b-73d633824a70.png) 28 | 29 | 30 | **Metadata**: Includes database, tissue, age, and paper info 31 | 32 | ## Usage 33 | 34 | These matrices can be downloaded directly. 35 | 36 | In addition, they can be downloaded within an R session using the "download_profile_matrix" function from the SpatialDecon package v1.4+. 37 | 38 | 39 | ## Details on methods 40 | 41 | "Matrices were generated using published datasets that had annotated cell types in human and mouse. Datasets were normalized, by total gene count, if raw data was used otherwise the publication’s normalization used. These datasets were filtered for cells expressing (count > 0) at least 100 genes and only calculated cell type profiles for cell types with 15+ viable cells. Profiles were created by taking the average expression of each gene across all viable cells of each cell type. The gene list was subset for genes that were expressed at least one cell type and was present in NanoString’s GeoMx Human Whole Transcriptome Atlas or Mouse Whole Transcriptome Atlas in addition to GeoMx COVID-19 Immune Response Atlas spike-in depending on dataset. A function to create custom profile matrices from scRNA-seq data using this method was realeased in SpatialDecon v1.4. 42 | 43 | Cell Groups were made using dataset’s cell annotations if applicable. Other groupings were made when original cell types were differentiated by numbers (“gamma-delta T cells 1” and “gamma-delta T cells 2”), different high genes (“Endothelial cell_Cldn5 high” and “Endothelial cell_Tm4sf1 high”), or specific gene expression (“MARCO- macrophage” and “MARCO+ macrophage”). When straight-forward groupings were not present cell types were also grouped by similarly named cell types (“lymphatic endothelial cell” and “maternal endothelial cell”) but this was done sparingly as not to oversimplify the data. These groupings are optional and can be changed by the user if they see fit." 44 | 45 | ## Archival info 46 | 47 | For versions of SpatialDecon <= v1.3 and the SpatialDecon plugin, csv files can be downloaded manually from the archive branch in this repository or the profile matrix in the RData file can be converted to a csv. 48 | ``` 49 | load(".RData file") 50 | write.csv(x = profile_matrix, file = "outputFileLocation/matrixName.csv", 51 | row.names = TRUE, quote = FALSE) 52 | ``` 53 | 54 | ## License Information 55 | 56 | The modified datasets in this repo are licensed under the terms of the Creative Commons Attribution 4.0 license. 57 | 58 | No original datasets were generated by NanoString Technologies or the authors of this repository. Please see metadata files for location of published data. [Human](Human/Human_datasets_metadata.csv) & [Mouse](Mouse/Mouse_datasets_metadata.csv) 59 | --------------------------------------------------------------------------------