BASiCS statistics

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chevron_left Differential expression detection Normalization Read count simulation Variable gene detection chevron_right
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BASiCS specifications


Unique identifier OMICS_09027
Alternative name Bayesian Analysis of Single-Cell Sequencing data
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Stability Stable
Maintained Yes


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  • person_outline Catalina A. Vallejos <>
  • person_outline Nils Eling <>

Publications for Bayesian Analysis of Single-Cell Sequencing data

BASiCS in publications

PMCID: 5913682
PMID: 29373712
DOI: 10.1093/molbev/msx336

[…] were removed. prior to normalization, genes with >1,000,000 reads or <10 reads across all cells were removed. a tsne plot showing batch labels for each cell is presented in l, online., the basics package () was used to normalize read counts by incorporating ercc spike-ins for technical noise estimation. specific ercc spike-ins were removed if not detected in the data set. posterior […]

PMCID: 5030210
PMID: 27708664
DOI: 10.3389/fgene.2016.00163

[…] normalization tool fitting a gamma regression model between the reads (fpkm, rpkm, tpm) and spike-ins (ding et al., ). the trained model is then used to estimate gene expression from the reads. basics, another recent workflow, provides a bayesian model allowing to infer cell-specific normalization factor (vallejos et al., ). this workflow estimates the technical variability using spike-ins. […]

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BASiCS institution(s)
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, UK; Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, UK; Cambridge Institute for Medical Research, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK; MRC Biostatistics Unit, University of Cambridge, Cambridge Institute of Public Health, Forvie Site, Cambridge Biomedical Campus, Cambridge, UK; The Alan Turing Institute, British Library, London, UK; Department of Statistical Science, University College London, London, UK
BASiCS funding source(s)
Supported by the European Molecular Biology Laboratory (EMBL) international PhD programme, the MRC Skills Development Fellowship (MR/P014178/1), a MRC grant MC_UP_0801/1, a core support of Cancer Research UK, EMBL, The Alan Turing Institute and EPSRC grant EP/N510129/1.

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