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Amnah Siddiqa edited this page Nov 12, 2020 · 45 revisions

Welcome to the GCPFirebase_ImmuneData wiki!

ImmuneData--Database

ImmuneData is a NoSQL document-oriented database created using Cloud Firestore Intro to Firestore or wiki of this git repo .

We have three lists

  • Served (Up in Firestore - versioned )
  • Staged (sitting there waiting to cleaned and go up in version)
  • Enstage (waiting to be staged- might need extraction)

Everything after enstage has a version and a model category (pathways, gene sets)

Details on Added Data

Served

Details on Added Data Click on the link to view whats on GCP for now!

  • InnateDB models-- Done --Details to add

  • LI BTMs--Done --Details to add

  • Chaussabel-Modules--Done--Details to add

  • Nature immunology review John Wherry, U penn, immunotherapy gene sets

  • CELL MARKER DB--Done

  • Monaco et al 2019-- cell reports rna seq deconvolution data --Done details to add

  • IRIS -2005---Up on GCP * Alexandra-Chloé Villani,2018--Science -scRNAseq--(Aviv Regev)-- Up on GCP (Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors)--Done

    To check: (laeving them for now)
* Diego Calderon--Landscape of stimulation-responsive chromatin across diverse human immune cells--Nature Genetics--2019
* Biola M. Javierre--Lineage-Specific Genome Architecture Links Enhancers and Non-coding Disease Variants to Target Gene Promoters--2016
* Noa Novershtern-Densely interconnected transcriptional circuits control cell states in human hematopoiesis--2012 Cell

  • InnateDB models

  • LI BTMs

  • DC-Modules Gen1

  • DC-Modules Gen2

  • DC-Modules Gen3

  • CELL MARKER DB

  • Monaco et al 2019-- cell reports rna seq deconvolution data

  • DICE -- UP on GCP

    Schmiedel BJ, Singh D, Madrigal A, Valdovino-Gonzalez AG, White BM, Zapardiel-Gonzalo J, Ha B, Altay G, Greenbaum JA, McVicker G, Seumois G. Impact of genetic polymorphisms on human immune cell gene expression. Cell. 2018 Nov 29;175(6):1701-15.

Staged

  • Cell Pedia

Enstaged

  * Etienne Becht-2016-No time
  * Gabriela Bindea--Immunity-2013--No Time
  • Human Cell Atlas
  • scRNA seq---Pipeline (GitHub--pipeline--working) ---prediction --data sets ---- using GRN inference algorithms

Check scrNA seq Data here

https://www.ebi.ac.uk/gxa/sc/experiments

Ontologies to discuss

Clone this wiki locally