CellHeap: A Workflow for Optimizing COVID-19 Single-Cell RNA-Seq Data Processing in the Santos Dumont Supercomputer

[1]  Alexander Sczyrba,et al.  Severe COVID-19 Is Marked by a Dysregulated Myeloid Cell Compartment , 2020, Cell.

[2]  Brad T. Sherman,et al.  Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources , 2008, Nature Protocols.

[3]  Tanya Barrett,et al.  The Gene Expression Omnibus Database , 2016, Statistical Genomics.

[4]  S. Aksoy,et al.  Single-cell RNA sequencing of Trypanosoma brucei from tsetse salivary glands unveils metacyclogenesis and identifies potential transmission blocking antigens , 2020, Proceedings of the National Academy of Sciences.

[5]  Leandra M. Brettner,et al.  Microbial single-cell RNA sequencing by split-pool barcoding , 2019, Science.

[6]  Paul J. Hoffman,et al.  Comprehensive Integration of Single-Cell Data , 2018, Cell.

[7]  Evan Z. Macosko,et al.  Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets , 2015, Cell.

[8]  J. Lee,et al.  Single-cell RNA sequencing technologies and bioinformatics pipelines , 2018, Experimental & Molecular Medicine.

[9]  Wil M. P. van der Aalst,et al.  Flexible Workflow Management Systems: An Approach Based on Generic Process Models , 1999, DEXA.

[10]  C. Yao,et al.  Cell-Type-Specific Immune Dysregulation in Severely Ill COVID-19 Patients , 2020, Cell Reports.

[11]  I. Amit,et al.  Elevated Calprotectin and Abnormal Myeloid Cell Subsets Discriminate Severe from Mild COVID-19 , 2020, Cell.

[12]  Single-cell RNA sequencing of batch Chlamydomonas cultures reveals heterogeneity in their diurnal cycle phase. , 2021, The Plant cell.

[13]  Lavanya Ramakrishnan,et al.  The future of scientific workflows , 2018, Int. J. High Perform. Comput. Appl..

[14]  Thawfeek M. Varusai,et al.  The Reactome Pathway Knowledgebase , 2017, Nucleic acids research.

[15]  Nuno A. Fonseca,et al.  Expression Atlas update: from tissues to single cells , 2019, Nucleic Acids Res..

[16]  Pawel Zajac,et al.  Highly multiplexed and strand-specific single-cell RNA 5′ end sequencing , 2012, Nature Protocols.

[17]  Oscar Franzén,et al.  PanglaoDB: a web server for exploration of mouse and human single-cell RNA sequencing data , 2019, Database J. Biol. Databases Curation.

[18]  Joseph T. Roland,et al.  Unsupervised Trajectory Analysis of Single-Cell RNA-Seq and Imaging Data Reveals Alternative Tuft Cell Origins in the Gut. , 2017, Cell systems.

[19]  Andrew D. Rouillard,et al.  Enrichr: a comprehensive gene set enrichment analysis web server 2016 update , 2016, Nucleic Acids Res..

[20]  Matt Thomson,et al.  Low Dimensionality in Gene Expression Data Enables the Accurate Extraction of Transcriptional Programs from Shallow Sequencing. , 2016, Cell systems.

[21]  I. Amit,et al.  Host-Viral Infection Maps Reveal Signatures of Severe COVID-19 Patients , 2020, Cell.

[22]  Anushya Muruganujan,et al.  PANTHER version 16: a revised family classification, tree-based classification tool, enhancer regions and extensive API , 2020, Nucleic Acids Res..

[23]  A. Bhardwaj,et al.  In situ click chemistry generation of cyclooxygenase-2 inhibitors , 2017, Nature Communications.

[24]  Anna Zhukova,et al.  Modeling sample variables with an Experimental Factor Ontology , 2010, Bioinform..

[25]  Lin Cheng,et al.  Single-cell landscape of bronchoalveolar immune cells in patients with COVID-19 , 2020, Nature Medicine.

[26]  A. Tanay,et al.  MetaCell: analysis of single-cell RNA-seq data using K-nn graph partitions , 2019, Genome Biology.

[27]  Helga Thorvaldsdóttir,et al.  Molecular signatures database (MSigDB) 3.0 , 2011, Bioinform..