Seurat Subset Barcode Pairwise comparisons are performed across these barcodes to identify those with a high percentage of shared fragments. Name of the assay corresponding to the initial input data.
Sep 01, 2020 · Criminal charges loom in California boat fire that killed 34. By BRIAN MELLEY and STEFANIE DAZIO September 1, 2020 GMT. 1 of 6.
@bgruening: @jkanche have you created a galaxy.yml in your config folder?
Additional resources. Many popular packages support Loom files out of the box, including scanpy from Fabian Theis lab, SCope from Stein Aerts lab, LoomR from Rahul Satij's lab, node-loompy for Java Script, LoomExperiment from Bioconductor, and scVI from Nir Yosef's lab.
To run velocity analysis on your own data, read your file (loom, h5ad, csv …) to an AnnData object with adata = scv.read('path/file.loom', cache=True). If you want to merge your loom file into an...
Wolf F.A. et al. (2018) SCANPY: large-scale single-cell gene expression data analysis. Genome Biol., 19, 15. [Europe PMC free article] [Google Scholar] Zerbino D.R. et al. (2014) WiggleTools: parallel processing of large collections of genome wide datasets for visualization and statistical analysis. Bioinformatics, 30, 1008–1009.
Setting compression to 'gzip' can save disk space but will slow down writing and subsequent reading. Prior to v0.6.16, this was the default for parameter compression . Generally, if you have sparse data that are stored as a dense matrix, you can dramatically improve performance and reduce disk space by converting to a csr_matrix :