Transcriptional landscape of repetitive elements in single cells

Purpose

We quantified conventional features (GENCODE) as well as repetitive elements (RepeatMasker) from multiple single-cell RNA-seq datasets using several analytical approaches, and starting from raw data, and looked for association with known cell metadata (e.g. cell types).

This repository includes the count tables and cell embeddings as generated by `export_run_for_upload.R` from repeats_sc (bitbucket).

Files

Please check the `README.md` file for a full description of all files. Each tarball contains a set of `gz` compressed files, including cell embeddings, raw and normalized count matrices, and metadata at the feature and cell levels. Data are stored as either comma-separated values (CSV) or MatrixMarket files,  UTF8-encoded and with Unix EOLs.

Datasets

We reanalyzed sequencing (`fastq`) files generated by other researchers; this repository contains results from our reanalysis, and not the original raw data. We are very grateful to the original data producers and encourage checking their data release licenses and checking and citing their publication(s). The `README.md` has a full description of these datasets and their sources.

Source code

https://bitbucket.org/imallona/repeats_sc

Contact

izaskun dot mallona at gmail.com

Funding

Swiss National Science Foundation SNF Spark 190824 (CRSK-3_190824)