Rxivist combines preprints from bioRxiv with data from Twitter to help you find the papers being discussed in your field. Currently indexing 65,690 bioRxiv papers from 290,986 authors.
Motivation: Hi-C experiments have been widely adopted to study chromatin spatial organization, which plays an important role in genome function. Well-established Hi-C readouts include A/B compartments, topologically associating domains (TADs) and chromatin loops. We have recently proposed another readout: frequently interacting regions (FIREs) and discovered them to be informative about tissue-specific gene expression. However, computational tools for detecting FIREs from Hi-C data are still lacking. Results: In this work, we have developed FIREcaller, a stand-alone, user-friendly R package for detecting FIREs from Hi-C data. FIREcaller takes raw Hi-C contact matrix as input, performs within-sample and cross-sample normalization via HiCNormCis and quantile normalization respectively, and outputs continuous FIRE scores, dichotomous FIREs and super-FIREs. Availability and implementation: The FIREcaller package is implemented in R, freely available at https://yunliweb.its.unc.edu/FIREcaller.
- Downloaded 218 times
- Download rankings, all-time:
- Site-wide: 44,481 out of 65,690
- In bioinformatics: 5,081 out of 6,504
- Year to date:
- Site-wide: 21,091 out of 65,690
- Since beginning of last month:
- Site-wide: 27,458 out of 65,690
Downloads over time
Distribution of downloads per paper, site-wide
- Top preprints of 2018
- Paper search
- Author leaderboards
- Overall metrics
- The API
- Email newsletter
- 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!