scFlowData

A supplementary data package for scFlow.

Installation

You can install scFlowData from GitHub with:

# install.packages("devtools")
devtools::install_github("combiz/scFlowData")

Developers

You may need to install scFlowData using a Personal Access Token (Github->Settings->Developer Settings): -

# install.packages("devtools")
devtools::install_github("combiz/scFlowData", auth_token = "YOURTOKEN")

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Contents

Raw data files are stored in inst/extdata: -

Folder Organization

Folder	Description
ctd	ctd RDS files for reference cell type annotations generated by EWCE
pathway_database	Database RDS files for pathway enrichment analysis
vignette_data	RDS files and raw data folders for vignette

File Descriptions

FILE	Description
ensembl_mappings.tsv	A tsv file with biomart mappings between human ensembl_gene_id, gene_biotype, external_gene_name
human_protein_coding_genome.tsv	A tsv file with human protein coding gene symbols to be used as reference gene list in pathway enrichment analysis
de_result_table.tsv	A tsv file with example list of differentially expressed gene, their fold-change, pvalue, adjusted pvalue