.github/ISSUE_TEMPLATE/user-dataset-submission.md

In shooshtarilab/scATAC.Explorer: A Collection of Single-cell ATAC Sequencing Datasets and Corresponding Metadata

name: New Dataset Submission about: Suggest a new dataset for inclusion to package title: "[Dataset] " labels: addition assignees: agibsonk

Note: R scripts are available under the .github of the package repository for R scripts to process some of the common scATAC-seq data formats for submission to the package.

Dataset description

Please provide a description of the dataset, such as what type of cells were sequenced, the number of cells, etc.

Link to the reference for the dataset

Please provide a DOI, article reference, pubmed ID, or other method of linking to the paper.

Link to the hosted dataset

This should be a link to the element(s) of the dataset. It can be a link to any file-hosting platform as long as the files are in the format outlined below.

• cell-by-peak matrix in a R dgCMatrix object saved as a .rds file
  • The rownames of the matrix should be the genomic regions in "chromosome-start-end" format
  • The column names of the matrix should be the names of the individual cells (this doesn't need to have a particular format, often they are barcodes)
  • The contents of the matrix should be the chromatin accessibility data
• Cell-type labels should be R dataframes saved in .rds files
  • Rownames of the dataframe should be the cell name
  • The first column should be named "cluster" and contain cluster assignments for the specified cell in the same row
  • The second column should be named "cell_label" and contain the cell type label for the cell in the same row

Metadata Table

Please fill all columns of the new_scATAC_metadata.csv and attached the completed document here.

shooshtarilab/scATAC.Explorer documentation built on Oct. 20, 2024, 8:20 p.m.