GRM specifications

Information


Unique identifier OMICS_07585
Name GRM
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Version 0.1
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Wei Wang <>

Publication for GRM

GRM in publications

 (2)
PMCID: 5499114
PMID: 28468817
DOI: 10.1534/g3.117.040683

[…] per kilobase of transcript per million mapped reads (fpkm) (), upper quartile (uq) (), trimmed mean of m-values (tmm) (), deseq (), removed unwanted variation (ruv) (), and gamma regression model (grm) (). most of these methods were developed for bulk rna-seq, and then applied directly to scrna-seq analysis. the performance of these methods was assessed on bulk (; ), but not on scrna-seq, data […]

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

[…] the abundance difference of transcripts or genes between the cells. when experiments are designed with ercc spike-ins, ercc can be used as internal controls and serve as anchors for normalization. grm is a scrna-seq 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 […]


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GRM institution(s)
Department of Chemistry and Biochemistry, University of California, La Jolla, CA, USA

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