Rxivist combines preprints from bioRxiv with data from Twitter to help you find the papers being discussed in your field. Currently indexing 54,968 bioRxiv papers from 253,677 authors.
We introduce alevin, an efficient pipeline for gene quantification from dscRNA-seq (droplet-based single-cell RNA-seq) data. Alevin is an end-to-end quantification pipeline that starts from sample-demultiplexed FASTQ files and generates gene-level counts for two popular droplet-based sequencing protocols (drop-seq , and 10x-chromium ). Importantly, alevin handles all processing internally, avoiding reliance on external pipeline programs, and the need to write large intermediate files to disk. Alevin adopts efficient algorithms for cellular-barcode whitelist generation, cellular-barcode correction, lightweight per-cell UMI deduplication and quantification. This integrated solution allows alevin to process data much faster (typically ~ 10 times faster) than other approaches, while also working within a reasonable memory budget. This enables full, end-to-end analysis for single-cell human experiment consisting of ~ 4500 cells with 335 Million reads with 13G of RAM and 8 threads (of an Intel Xeon E5-2699 v4 CPU) in 27 minutes.
- Downloaded 1,986 times
- Download rankings, all-time:
- Site-wide: 1,906 out of 54,968
- In bioinformatics: 398 out of 5,689
- Year to date:
- Site-wide: 1,190 out of 54,968
- Since beginning of last month:
- Site-wide: 7,172 out of 54,968
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!