Cytoscape single-cell analysis

Trainer: Scooter Morris

Overview: This session describes a network analysis workflow for differentially expressed genes from an RNA-Seq experiment.

Learning outcomes:

By the end of the session you will be able to:

  • Find a set of differentially expressed genes
  • Retrieve relevant networks from public databases
  • Work on integration and visualisation of experimental data
  • Use network functional enrichment analysis
  • Export network visualisations

Materials:

Tools filter Upload Data @ Show Sections Seurat FilterCells filter cells in a Seurat object Filter with scanpy Filter FASTA on the headers and/or the sequences Filter Combined Transcripts using tracking file filter-annotated-entries Split entries into two files based on whether they overlap annotations in a bed file filter-by-energy Split entries over two files based on the estimated energy Filter Tabular Scater: filter SCE with user-defined parameters or PCA Scanpy FilterCells based on counts and numbers of genes expressed Scanpy FilterGenes based on counts and numbers of cells expressed Filter FASTQ reads by quality score and length FilterSamReads include or exclude aligned and unaligned reads and read lists filtlong Filtering long reads by quality Filter data on any column using simple expressions find in reference filter peptides that are present in proteins Filter BED on splice Scanpy FilterCells based on counts and numbers of genes expressed (Galaxy Version 1.7.2+galaxyO) Input object in AnnData/Loom format D 69: Scanpy FilterCells on data 59: Filtered cells AnnData (input-object-file) Format of input object AnnData format hdf5 (--input-format) Format of output object AnnData format (--output-format) Name of the column in •anndata.var• that contains gene name Favorite & Versions • Options Used for flagging mitochondria genes (starting with 'MT-I). Leave empty if gene table already has a boolean column called 'mito' that flags MT genes Parameters to select cells to keep 1: Parameters to select cells to keep Name of parameter to filter on n_genes for example n_genes or n_counts Min value Cells with value below min will be discarded. Max value 1000000000.0 Cells with value above max will be discarded. + Insert Parameters to select cells to keep Categories to select cells to keep (unless negate is checked) + Insert Categories to select cells to keep (unless negate is checked) Subsets to select cells to keep + Insert Subsets to select cells to keep Force recalculation of QC vars C) No filter here! so se up as you Tick this to If set, it will recalculate pcts and other existing QC vars, overwriting existing ones. Save to IOx mtx format C) No say YES If enabled, it will generate in addition to the main output in Loom or AnnData an export in IOx format. (--export-mtx) Email notification