Rxivist combines preprints from bioRxiv with data from Twitter to help you find the papers being discussed in your field. Currently indexing 70,186 bioRxiv papers from 306,470 authors.
Assessing allele specific expression across multiple tissues from RNA-seq read data
Noah A Zaitlen,
Emmanouil T Dermitzakis,
Mark I McCarthy,
Manuel A. Rivas
Posted 17 Jul 2014
bioRxiv DOI: 10.1101/007211 (published DOI: 10.1093/bioinformatics/btv074)
Posted 17 Jul 2014
Motivation: RNA sequencing enables allele specific expression (ASE) studies that complement standard genotype expression studies for common variants and, importantly, also allow measuring the regulatory impact of rare variants. The Genotype-Tissue Expression project (GTEx) is collecting RNA-seq data on multiple tissues of a same set of individuals and novel methods are required for the analysis of these data. Results: We present a statistical method to compare different patterns of ASE across tissues and to classify genetic variants according to their impact on the tissue-wide expression profile. We focus on strong ASE effects that we are expecting to see for protein-truncating variants, but our method can also be adjusted for other types of ASE effects. We illustrate the method with a real data example on a tissue-wide expression profile of a variant causal for lipoid proteinosis, and with a simulation study to assess our method more generally. Availability: MAMBA software: http://birch.well.ox.ac.uk/~rivas/mamba/ R source code and data examples: http://www.iki.fi/mpirinen/ Contact: email@example.com firstname.lastname@example.org
- Downloaded 1,832 times
- Download rankings, all-time:
- Site-wide: 2,951 out of 70,230
- In bioinformatics: 588 out of 6,887
- Year to date:
- Site-wide: 32,286 out of 70,230
- Since beginning of last month:
- Site-wide: 63,063 out of 70,230
Downloads over time
Distribution of downloads per paper, site-wide
- 18 Dec 2019: We're pleased to announce PanLingua, a new tool that enables you to search for machine-translated bioRxiv preprints using more than 100 different languages.
- 21 May 2019: PLOS Biology has published a community page about Rxivist.org and its design.
- 10 May 2019: The paper analyzing the Rxivist dataset has been published at eLife.
- 1 Mar 2019: We now have summary statistics about bioRxiv downloads and submissions.
- 8 Feb 2019: Data from Altmetric is now available on the Rxivist details page for every preprint. Look for the "donut" under the download metrics.
- 30 Jan 2019: preLights has featured the Rxivist preprint and written about our findings.
- 22 Jan 2019: Nature just published an article about Rxivist and our data.
- 13 Jan 2019: The Rxivist preprint is live!