added several datasets #11
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| @@ -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 | |||
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Is there a more defined name for this resource? I had in my radar as well but did not insert it yet.
Otherwise, we can just leave it as it is...
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I agree the name is not ideal, but I don't know what else to change it to. There is nothing on the website and in the original publication, they say "we therefore developed a user-friendly Web site (http://blood.stemcells.cam.ac.uk/single_cell_atlas.html) where users can explore the three-dimensional structure of the diffusion map graph as well as visualize expression profiles for any gene of interest and surface marker expression".
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Gotta admit that "single_cell_atlas.html" is somewhat... generic
README.md
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| @@ -66,6 +68,7 @@ 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](http://aifantislab.com/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 | |||
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Would it make more sense to link directly to the resource here? https://compbio.nyumc.org/niche/
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I was trying to match the publication for consistency. I am personally okay with either version. From personal experience, the nyumc.org one may be less stable long-term. On the other hand, this page can be edited at any time to fix any issues.
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I'd propose then you just use both 👍 there is no restriction in the links number
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Hi Igor! Thank you for the triplet of contribution - don't forget to add yourself to the contributors list ;) |
adjusted nichExplorer content
Please complete the following fields to make the reviewing process of the Pull Request as smooth as possible.
RESOURCE NAME: Gene and protein expression in adult haematopoiesis
LINK: http://blood.stemcells.cam.ac.uk/single_cell_atlas.html
(SHORT) DESCRIPTION: visualization of gene expression in 1,656 single HSPCs, accompanying
(if available) REFERENCE to the paper where this resource is used, with a link to DOI, PubMed, bioRxiv: https://doi.org/10.1182/blood-2016-05-716480
RESOURCE NAME: indeXplorer
LINK: http://steinmetzlab.embl.de/shiny/indexplorer/
(SHORT) DESCRIPTION: a web-based app for the explorative analysis of the hematopoietic stem cell dataset
(if available) REFERENCE to the paper where this resource is used, with a link to DOI, PubMed, bioRxiv: https://doi.org/10.1038/ncb3493
RESOURCE NAME: nichExplorer
LINK: http://aifantislab.com/niche
(SHORT) DESCRIPTION: an interactive browser for bone marrow microenvironment
(if available) REFERENCE to the paper where this resource is used, with a link to DOI, PubMed, bioRxiv: https://doi.org/10.1038/s41586-019-1104-8