GDC Datasets version update

As of March 11, 2022, GDC datasets available through the Data Browser and the API correspond to GDC Data Release 31.

Recently published apps

We have added four apps to our public apps gallery:

• Single cell RNA-seq velocity analysis with scVelo 0.2.4 workflow that performs preprocessing, marker gene analysis, and velocity analysis of single-cell expression data. It is based on SingleCellExperiment, Seurat, scran, scater, AnnotationHub, scuttle, and scVelo.
• Velocyto.py – Velocyto 0.17.17 is a package for the analysis of expression dynamics in single cell RNAseq data. In particular, it enables estimations of RNA velocities of single cells by distinguishing unspliced and spliced mRNAs in standard single-cell RNA sequencing protocols. Velocyto.py is a command line tool (distributed with the package) that is used to generate spliced/unspliced count matrices.
• SBG single cell object convertor tool that performs conversion of single cell data object type for commonly used formats: Seurat, AnnotatedData, and SingleCellExperiment.
• Single cell RNA-seq trajectory analysis with slingshot and tradeSeq, a tool that performs single cell trajectory analysis with slingshot 2.0.0, and differential expression testing on inferred trajectories with tradeSeq 1.6.0. Slingshot takes advantage of single cell data principal components analysis (PCA) and clustering to infer probable paths of cell development.

Marko Marinkovic