{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,9,19]],"date-time":"2025-09-19T11:00:04Z","timestamp":1758279604446,"version":"3.41.2"},"reference-count":15,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2023,5,23]],"date-time":"2023-05-23T00:00:00Z","timestamp":1684800000000},"content-version":"vor","delay-in-days":22,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100003006","name":"ETH","doi-asserted-by":"publisher","award":["PHRT-510"],"award-info":[{"award-number":["PHRT-510"]}],"id":[{"id":"10.13039\/501100003006","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,5,4]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Recently, CITE-seq emerged as a multimodal single-cell technology capturing gene expression and surface protein information from the same single cells, which allows unprecedented insights into disease mechanisms and heterogeneity, as well as immune cell profiling. Multiple single-cell profiling methods exist, but they are typically focused on either gene expression or antibody analysis, not their combination. Moreover, existing software suites are not easily scalable to a multitude of samples. To this end, we designed gExcite, a start-to-end workflow that provides both gene and antibody expression analysis, as well as hashing deconvolution. Embedded in the Snakemake workflow manager, gExcite facilitates reproducible and scalable analyses. We showcase the output of gExcite on a study of different dissociation protocols on PBMC samples.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>gExcite is open source available on github at https:\/\/github.com\/ETH-NEXUS\/gExcite_pipeline. The software is distributed under the GNU General Public License 3 (GPL3).<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btad329","type":"journal-article","created":{"date-parts":[[2023,5,24]],"date-time":"2023-05-24T00:03:57Z","timestamp":1684886637000},"source":"Crossref","is-referenced-by-count":2,"title":["gExcite: a start-to-end framework for single-cell gene expression, hashing, and antibody analysis"],"prefix":"10.1093","volume":"39","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3817-7613","authenticated-orcid":false,"given":"Linda","family":"Grob","sequence":"first","affiliation":[{"name":"ETH Zurich, NEXUS Personalized Health Technologies , 8952 Schlieren, Switzerland"},{"name":"SIB Swiss Institute of Bioinformatics , Zurich, Switzerland"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0691-0489","authenticated-orcid":false,"given":"Anne","family":"Bertolini","sequence":"additional","affiliation":[{"name":"ETH Zurich, NEXUS Personalized Health Technologies , 8952 Schlieren, Switzerland"},{"name":"SIB Swiss Institute of Bioinformatics , Zurich, Switzerland"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8559-8296","authenticated-orcid":false,"given":"Matteo","family":"Carrara","sequence":"additional","affiliation":[{"name":"ETH Zurich, NEXUS Personalized Health Technologies , 8952 Schlieren, Switzerland"},{"name":"SIB Swiss Institute of Bioinformatics , Zurich, Switzerland"}]},{"given":"Ulrike","family":"Lischetti","sequence":"additional","affiliation":[{"name":"Department of Biomedicine, University Hospital Basel and University of Basel , 4031 Basel, Switzerland"}]},{"given":"Aizhan","family":"Tastanova","sequence":"additional","affiliation":[{"name":"Department of Dermatology, University of Zurich, University of Zurich Hospital , 8952 Schlieren, Switzerland"}]},{"given":"Christian","family":"Beisel","sequence":"additional","affiliation":[{"name":"Department of Biosystems Science and Engineering, ETH Zurich , 4058 Basel, Switzerland"}]},{"given":"Mitchell P","family":"Levesque","sequence":"additional","affiliation":[{"name":"Department of Dermatology, University of Zurich, University of Zurich Hospital , 8952 Schlieren, Switzerland"}]},{"given":"Daniel J","family":"Stekhoven","sequence":"additional","affiliation":[{"name":"ETH Zurich, NEXUS Personalized Health Technologies , 8952 Schlieren, Switzerland"},{"name":"SIB Swiss Institute of Bioinformatics , Zurich, Switzerland"}]},{"given":"Franziska","family":"Singer","sequence":"additional","affiliation":[{"name":"ETH Zurich, NEXUS Personalized Health Technologies , 8952 Schlieren, Switzerland"},{"name":"SIB Swiss Institute of Bioinformatics , Zurich, Switzerland"}]}],"member":"286","published-online":{"date-parts":[[2023,5,23]]},"reference":[{"key":"2023053023011314500_btad329-B2","doi-asserted-by":"crossref","first-page":"e1010097","DOI":"10.1371\/journal.pcbi.1010097","article-title":"scAmpi\u2014a versatile pipeline for single-cell RNA-seq analysis from basics to clinics","volume":"18","author":"Bertolini","year":"2022","journal-title":"PLoS Comput Biol"},{"key":"2023053023011314500_btad329-B3","doi-asserted-by":"crossref","first-page":"272","DOI":"10.1038\/s41592-020-01050-x","article-title":"Joint probabilistic modeling of single-cell multi-omic data with totalVI","volume":"18","author":"Gayoso","year":"2021","journal-title":"Nat Methods"},{"key":"2023053023011314500_btad329-B4","doi-asserted-by":"crossref","first-page":"2667","DOI":"10.1038\/s41467-018-05083-x","article-title":"Detection and removal of barcode swapping in single-cell RNA-seq data","volume":"9","author":"Griffiths","year":"2018","journal-title":"Nat Commun"},{"key":"2023053023011314500_btad329-B5","doi-asserted-by":"crossref","first-page":"3573","DOI":"10.1016\/j.cell.2021.04.048","article-title":"Integrated analysis of multimodal single-cell data","volume":"184","author":"Hao","year":"2021","journal-title":"Cell"},{"key":"2023053023011314500_btad329-B6","doi-asserted-by":"crossref","first-page":"4137","DOI":"10.1093\/bioinformatics\/btaa282","article-title":"CiteFuse enables multi-modal analysis of CITE-Seq data","volume":"36","author":"Kim","year":"2020","journal-title":"Bioinformatics"},{"key":"2023053023011314500_btad329-B7","doi-asserted-by":"crossref","first-page":"129","DOI":"10.1016\/j.copbio.2019.03.001","article-title":"Beyond bulk: a review of single cell transcriptomics methodologies and applications","volume":"58","author":"Kulkarni","year":"2019","journal-title":"Curr Opin Biotechnol"},{"key":"2023053023011314500_btad329-B9","doi-asserted-by":"crossref","first-page":"409","DOI":"10.1038\/s41592-019-0392-0","article-title":"Expanding the CITE-seq tool-kit: detection of proteins, transcriptomes, clonotypes and CRISPR perturbations with multiplexing, in a single assay","volume":"16","author":"Mimitou","year":"2019","journal-title":"Nat Methods"},{"key":"2023053023011314500_btad329-B10","doi-asserted-by":"crossref","first-page":"W372","DOI":"10.1093\/nar\/gkaa437","article-title":"CReSCENT: CanceR Single Cell ExpressioN Toolkit","volume":"48","author":"Mohanraj","year":"2020","journal-title":"Nucleic Acids Res"},{"key":"2023053023011314500_btad329-B11","doi-asserted-by":"crossref","first-page":"33","DOI":"10.12688\/f1000research.29032.2","article-title":"Sustainable data analysis with snakemake","volume":"10","author":"M\u00f6lder","year":"2021","journal-title":"F1000Res"},{"key":"2023053023011314500_btad329-B13","doi-asserted-by":"crossref","first-page":"224","DOI":"10.1186\/s13059-018-1603-1","article-title":"Cell hashing with barcoded antibodies enables multiplexing and doublet detection for single cell genomics","volume":"19","author":"Stoeckius","year":"2018","journal-title":"Genome Biol"},{"key":"2023053023011314500_btad329-B14","doi-asserted-by":"crossref","first-page":"865","DOI":"10.1038\/nmeth.4380","article-title":"Simultaneous epitope and transcriptome measurement in single cells","volume":"14","author":"Stoeckius","year":"2017","journal-title":"Nat Methods"},{"key":"2023053023011314500_btad329-B15","doi-asserted-by":"crossref","first-page":"5814","DOI":"10.1093\/nar\/gkaa314","article-title":"BREM-SC: a Bayesian random effects mixture model for joint clustering single cell multi-omics data","volume":"48","author":"Wang","year":"2020","journal-title":"Nucleic Acids Res"},{"key":"2023053023011314500_btad329-B16","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1186\/s13059-017-1382-0","article-title":"SCANPY: large-scale single-cell gene expression data analysis","volume":"19","author":"Wolf","year":"2018","journal-title":"Genome Biol"},{"key":"2023053023011314500_btad329-B17","doi-asserted-by":"crossref","first-page":"14049","DOI":"10.1038\/ncomms14049","article-title":"Massively parallel digital transcriptional profiling of single cells","volume":"8","author":"Zheng","year":"2017","journal-title":"Nat Commun"},{"key":"2023053023011314500_btad329-B18","doi-asserted-by":"crossref","first-page":"53763","DOI":"10.18632\/oncotarget.17893","article-title":"Advances in single-cell RNA sequencing and its applications in cancer research","volume":"8","author":"Zhu","year":"2017","journal-title":"Oncotarget"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btad329\/50425553\/btad329.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/39\/5\/btad329\/50492066\/btad329.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/39\/5\/btad329\/50492066\/btad329.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,30]],"date-time":"2023-05-30T23:01:36Z","timestamp":1685487696000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/doi\/10.1093\/bioinformatics\/btad329\/7176365"}},"subtitle":[],"editor":[{"given":"Tobias","family":"Marschall","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2023,5,1]]},"references-count":15,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2023,5,4]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btad329","relation":{},"ISSN":["1367-4811"],"issn-type":[{"type":"electronic","value":"1367-4811"}],"subject":[],"published-other":{"date-parts":[[2023,5,1]]},"published":{"date-parts":[[2023,5,1]]},"article-number":"btad329"}}