Merge pull request #11 from igordot/patch-1

added several datasets
federicomarini · Oct 22, 2019 · 2b5ab01 · 2b5ab01
2 parents f8d2472 + 9339441
commit 2b5ab01
Showing 1 changed file with 3 additions and 0 deletions.
diff --git a/README.md b/README.md
@@ -34,6 +34,7 @@ A curated list of software and resources for exploring and visualizing (browsing
 - [FASTGenomics](https://fastgenomics.org), an online platform to share single-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://prod.fastgenomics.org/ (allows anonymous login)
 - [Fate Bias Inference in Lymphoid progenitors](http://hematopoietic-progenitors.ie-freiburg.mpg.de), from the lab of Dominic Grün - single-cell RNA-seq data of murine hematopoietic progenitors
 - [FireBrowse](http://firebrowse.org), developed by the Broad Institute on top of Firehose
+- [Gene and protein expression in adult haematopoiesis](http://blood.stemcells.cam.ac.uk/single_cell_atlas.html), visualization of gene expression in 1,656 single HSPCs, accompanying https://doi.org/10.1182/blood-2016-05-716480
 - [GenePattern](http://genepattern-notebook.org), Gene Pattern Notebook Environment (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5572818/)
 - [GEPIA](http://gepia.cancer-pku.cn/) Gene Expression Profiling Interactive Analysis, a web server for cancer and normal gene expression profiling and interactive analyses. (https://academic.oup.com/nar/article/45/W1/W98/3605636)
 - [Giotto](http://spatial.rc.fas.harvard.edu), a complete pipeline for integrative analysis and visualization of single-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
@@ -44,6 +45,7 @@ A curated list of software and resources for exploring and visualizing (browsing
 - [Human Cell Atlas Data Portals](https://developmentcellatlas.ncl.ac.uk/datasets/hca_liver/), for exploring gene expression and developmental trajectories, showcased in this publication https://doi.org/10.1038/s41586-019-1652-y (HCA Liver instances: https://developmentcellatlas.ncl.ac.uk/datasets/hca_liver/). Source code is available at https://github.com/DoruMP/Fast-data-portals-for-scRNAseq-data
 - [Human Liver Cell Atlas](http://human-liver-cell-atlas.ie-freiburg.mpg.de), related to https://dx.doi.org/10.1038/s41586-019-1373-2 - *currently not working?*
 - [iMAC](https://www.stemformatics.org/atlas), an interactive atlas to explore phenotypic differences between macrophage cells. Puiblication available at https://www.biorxiv.org/content/10.1101/719237v1
+- [indeXplorer](http://steinmetzlab.embl.de/shiny/indexplorer/), a web-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](https://immunogenomics.io/itc), low-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](http://ipfcellatlas.com), the Idiopathic Pulmonary Fibrosis Cell Atlas. Linked to the publications https://www.biorxiv.org/content/10.1101/753806v1 and https://www.biorxiv.org/content/10.1101/759902v2
 - [iS-CellR](https://github.com/immcore/iS-CellR), for analysing and visualising scRNA-seq data. R Shiny app. Manuscript available at https://academic.oup.com/bioinformatics/article/34/24/4305/5048937
@@ -67,6 +69,7 @@ A curated list of software and resources for exploring and visualizing (browsing
 - [Multiple sclerosis gene atlas](http://msatlas.compbio.sdu.dk), companion to https://www.biorxiv.org/content/10.1101/584920v1
 - [NCI Patient Derived Model Repository](https://pdmdb.cancer.gov/pls/apex/f?p=101:1:0::NO) expression and whole exome data on >350 patients xenografts and patient tissue samples.
 - [Neuroexpresso](http://neuroexpresso.org), for the analysis of brain cell type expression profiles. Source available here, https://github.com/PavlidisLab/neuroexpresso, publication: https://www.eneuro.org/content/4/6/ENEURO.0212-17.2017
+- [nichExplorer](https://compbio.nyumc.org/niche/), an interactive browser for bone marrow microenvironment, accompanying https://doi.org/10.1038/s41586-019-1104-8, with source code available at https://github.com/igordot/nichexplorer. Also available from http://aifantislab.com/niche
 - [PanglaoDB](https://panglaodb.se), a database for the exploration of single cell RNA sequencing experiments from mouse and human. Publication at https://academic.oup.com/database/article/doi/10.1093/database/baz046/5427041, GitHub repo: https://github.com/oscar-franzen/PanglaoDB (not the source code of the resource itself)
 - [PAWER](https://biit.cs.ut.ee/pawer/), a software tool for analysing protein microarray data - described in publication: https://www.biorxiv.org/content/10.1101/692905v1
 - [PEAC RNA-seq](https://peac.hpc.qmul.ac.uk), for exploring RNA-seq of early rheumatoid arthritis individuals and their clinical data. Linked to the publication https://doi.org/10.1016/j.celrep.2019.07.091