CRLMM protocols

View CRLMM computational protocol

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CRLMM specifications


Unique identifier OMICS_00717
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Illumina, Affymetrix
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License Artistic License version 2.0
Computer skills Advanced
Version 1.18.0
Stability Stable
methods, stats, BiocGenerics, splines, utils, R(>=2.14.0), lattice, RUnit, ff, oligoClasses(>=1.21.12), preprocessCore(>=1.17.7), Biobase(>=2.15.4), affyio(>=1.23.2), illuminaio, ellipse, mvtnorm, SNPchip, foreach, RcppEigen, matrixStats, hapmapsnp6, genomewidesnp6Crlmm(>=1.0.7), GGdata, snpStats
Maintained Yes


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  • person_outline Benilton Carvalho <>

Publication for CRLMM

CRLMM in pipeline

PMCID: 3468603
PMID: 23071531
DOI: 10.1371/journal.pone.0045950

[…] the samples were run on an automatic sequencer and analyzed with the gene scan program (abi-prism, perkin elmer)., the total and allele-specific copy numbers were computed for each sample using the crlmm algorithm , . the correction of the total copy number waves was based on the gc-content of the probes and targeted dna regions. the total copy numbers from the tumor samples were normalized […]

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CRLMM in publications

PMCID: 5940695
PMID: 29740118
DOI: 10.1038/s41598-018-25659-3

[…] and respectively 4000 s. the xps spectra look similar, suggesting no major changes of chemical concentrations. besides xps characteristic peaks for cu(2p,2s), cr(2p,2s) and o1s, auger okll culmm and crlmm peaks are present in the spectra. the positions of cu2p peaks (1/2 at 932.6 ev and 3/2 at 952.5 ev) do not vary upon annealing. the distance between them is 19.9 ev, a clear indication […]

PMCID: 5898725
PMID: 29652911
DOI: 10.1371/journal.pone.0194842

[…] and the coastal city of monastir) were genotyped in a previous study [] using the affymetrixchip 6.0 genotyping array. genotyping data were generated after the variants calling performed with r crlmm package []. the study was approved by the ethics committee of the institut pasteur (tunis, tunisia-registration numbers irb00005445, fwa00010074, and pv09/06, irb# 0000000044). all participants […]

PMCID: 5788352
PMID: 29377909
DOI: 10.1371/journal.pone.0191701

[…] biological replicates for quality control and validation. microarray data are available in the arrayexpress database ( under accession number e-mtab-4863. the r package crlmm [] was used for pre-processing, genotyping and calculation of circular binary segmentation to estimate the normalized copy number. germline copy number alterations were removed using […]

PMCID: 5681527
PMID: 29163558
DOI: 10.3389/fpls.2017.01788

[…] nomenclature or allelic variants of the same gene. this uncertainty arises from researchers using different crosses, different isolates and different marker systems. for example the genes lmr1, crlmm, rlm4, crlmrb, and lem1 were all mapped on chromosome a7 in b. napus using australian cultivars shiralee, maluka, skipton and the french cultivar major, respectively (ferreira et al., ; […]

PMCID: 5585301
PMID: 28874807
DOI: 10.1038/s41598-017-11029-y

[…] extracted, amplified and hybridized onto an affymetrix genome-wide human snp array 6.0 according to the manufacturer’s instructions (affymetrix inc.). first, r packages of hapmapsnp6, oligoclasses, crlmm and ff were used to read the primary data (in cel format) of affy snp 6.0 array, in addition to spotting the sites of snps. second, r package of pd.genomewidesnp.6 was used to obtain […]

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CRLMM institution(s)
Department of Biostatistics, Johns Hopkins University, Baltimore, MD, USA

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