Literature DB >> 33795888

Modular, efficient and constant-memory single-cell RNA-seq preprocessing.

Páll Melsted1, A Sina Booeshaghi2, Lauren Liu3, Fan Gao4,5, Lambda Lu4, Kyung Hoi Joseph Min6, Eduardo da Veiga Beltrame4, Kristján Eldjárn Hjörleifsson3, Jase Gehring7, Lior Pachter8,9.   

Abstract

We describe a workflow for preprocessing of single-cell RNA-sequencing data that balances efficiency and accuracy. Our workflow is based on the kallisto and bustools programs, and is near optimal in speed with a constant memory requirement providing scalability for arbitrarily large datasets. The workflow is modular, and we demonstrate its flexibility by showing how it can be used for RNA velocity analyses.
© 2021. The Author(s), under exclusive licence to Springer Nature America, Inc.

Year:  2021        PMID： 33795888     DOI： 10.1038/s41587-021-00870-2

Source DB:  PubMed          Journal:  Nat Biotechnol        ISSN： 1087-0156            Impact factor:   54.908


  1 in total

1.  Benchmark analysis of algorithms for determining and quantifying full-length mRNA splice forms from RNA-seq data.

Authors:  Katharina E Hayer; Angel Pizarro; Nicholas F Lahens; John B Hogenesch; Gregory R Grant
Journal:  Bioinformatics       Date:  2015-09-03       Impact factor: 6.937
  1 in total
  42 in total

1.  Breast Cancer Endocrine Therapy Promotes Weight Gain With Distinct Adipose Tissue Effects in Lean and Obese Female Mice.

Authors:  Rebecca L Scalzo; Rebecca M Foright; Sara E Hull; Leslie A Knaub; Stevi Johnson-Murguia; Fotobari Kinanee; Jeffrey Kaplan; Julie A Houck; Ginger Johnson; Rachel R Sharp; Austin E Gillen; Kenneth L Jones; Anni M Y Zhang; James D Johnson; Paul S MacLean; Jane E B Reusch; Sabrina Wright-Hobart; Elizabeth A Wellberg
Journal:  Endocrinology       Date:  2021-11-01       Impact factor: 5.051

2.  RNA velocity unraveled.

Authors:  Gennady Gorin; Meichen Fang; Tara Chari; Lior Pachter
Journal:  PLoS Comput Biol       Date:  2022-09-12       Impact factor: 4.779

3.  Thymic epithelial cells co-opt lineage-defining transcription factors to eliminate autoreactive T cells.

Authors:  Daniel A Michelson; Koji Hase; Tsuneyasu Kaisho; Christophe Benoist; Diane Mathis
Journal:  Cell       Date:  2022-06-16       Impact factor: 66.850

4.  CD8 memory precursor cell generation is a continuous process.

Authors:  Helena Todorov; Margaux Prieux; Daphne Laubreton; Matteo Bouvier; Shaoying Wang; Simon de Bernard; Christophe Arpin; Robrecht Cannoodt; Wouter Saelens; Arnaud Bonnaffoux; Olivier Gandrillon; Fabien Crauste; Yvan Saeys; Jacqueline Marvel
Journal:  iScience       Date:  2022-08-13

5.  A mechanism for red coloration in vertebrates.

Authors:  Matthew B Toomey; Cristiana I Marques; Pedro M Araújo; Delai Huang; Siqiong Zhong; Yu Liu; Gretchen D Schreiner; Connie A Myers; Paulo Pereira; Sandra Afonso; Pedro Andrade; Małgorzata A Gazda; Ricardo J Lopes; Ivan Viegas; Rebecca E Koch; Maureen E Haynes; Dustin J Smith; Yohey Ogawa; Daniel Murphy; Rachel E Kopec; David M Parichy; Miguel Carneiro; Joseph C Corbo
Journal:  Curr Biol       Date:  2022-08-31       Impact factor: 10.900

6.  scSNV: accurate dscRNA-seq SNV co-expression analysis using duplicate tag collapsing.

Authors:  Gavin W Wilson; Mathieu Derouet; Gail E Darling; Jonathan C Yeung
Journal:  Genome Biol       Date:  2021-05-07       Impact factor: 13.583

7.  A functional cellular framework for sex and estrous cycle-dependent gene expression and behavior.

Authors:  Joseph R Knoedler; Sayaka Inoue; Daniel W Bayless; Taehong Yang; Adarsh Tantry; Chung-Ha Davis; Nicole Y Leung; Srinivas Parthasarathy; Grace Wang; Maricruz Alvarado; Abbas H Rizvi; Lief E Fenno; Charu Ramakrishnan; Karl Deisseroth; Nirao M Shah
Journal:  Cell       Date:  2022-01-21       Impact factor: 41.582

8.  BUTTERFLY: addressing the pooled amplification paradox with unique molecular identifiers in single-cell RNA-seq.

Authors:  Johan Gustafsson; Jonathan Robinson; Jens Nielsen; Lior Pachter
Journal:  Genome Biol       Date:  2021-06-08       Impact factor: 13.583

9.  Transcriptomic Profiling of Control and Thyroid-Associated Orbitopathy (TAO) Orbital Fat and TAO Orbital Fibroblasts Undergoing Adipogenesis.

Authors:  Dong Won Kim; Kamil Taneja; Thanh Hoang; Clayton P Santiago; Timothy J McCulley; Shannath L Merbs; Nicholas R Mahoney; Seth Blackshaw; Fatemeh Rajaii
Journal:  Invest Ophthalmol Vis Sci       Date:  2021-07-01       Impact factor: 4.799

10.  Tumor-derived NKG2D ligand sMIC reprograms NK cells to an inflammatory phenotype through CBM signalosome activation.

Authors:  Payal Dhar; Fahmin Basher; Zhe Ji; Lei Huang; Si Qin; Derek A Wainwright; Jerid Robinson; Shaye Hagler; Jing Zhou; Sean MacKay; Jennifer D Wu
Journal:  Commun Biol       Date:  2021-07-22
View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.