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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


No version available



  • person_outline Benilton Carvalho

Publication for CRLMM

CRLMM citations


Genomic analysis of head and neck cancer cases from two high incidence regions

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

[…] and 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 the Databas […]


Screening of candidate key genes associated with human osteosarcoma using bioinformatics analysis

PMCID: 5588164
PMID: 28928828
DOI: 10.3892/ol.2017.6519

[…] Copy number analysis of the raw data from the SNP profiling data was performed using the crlmm package ( () in Bioconductor package version 1.0.2. Then, genes with copy number gains/losses were additionally screened using t […]


Targeting and Regulating of an Oncogene via Nanovector Delivery of MicroRNA using Patient Derived Xenografts

PMCID: 5327642
PMID: 28255359
DOI: 10.7150/thno.16357

[…] rix protocols. Data were analyzed using R software (version 2.12). Raw probe intensity data (CEL Files) obtained from the GeneChip Scanner 3000 system (Affymetrix) were imported to R, segmented using CRLMM algorithm and copy number variantion was estimated by the VanillaICE and DNAcopy methods. […]


DNA methylation signature (SAM40) identifies subgroups of the Luminal A breast cancer samples with distinct survival

PMCID: 5352035
PMID: 27911866
DOI: 10.18632/oncotarget.13718

[…] Genome Atlas []. A total of 85 Luminal A subtype primary breast carcinoma tumors had all three types of measurement. Copy-number data from Affymetrix 6.0 SNP arrays were extracted with the R package crlmm []. Samples with signal-to-noise ratio of less than 5 were removed. Moreover, probes with a confidence limit less than 0.9 were removed. Samples were normalized to a mean of 2. Log ratios were s […]


Language Agnostic Reproducible Data Analysis Using Literate Programming

PLoS One
PMCID: 5053501
PMID: 27711123
DOI: 10.1371/journal.pone.0164023
call_split See protocol

[…] he Cancer Genome Atlas []. The data was processed anonymously. All TCGA data were preprocessed using Anduril []. We genotyped the probes, and estimated and normalized copy-number values to 2 with the CRLMM algorithm []. Copy-number data were segmented with the circular binary segmentation (CBS) algorithm using the R package DNAcopy (parameters undo.splits = sdundo, SD = 3, alpha = 0.01) []. Copy-n […]


A new model calling procedure for Illumina BeadArray data

BMC Genet
PMCID: 4921002
PMID: 27343118
DOI: 10.1186/s12863-016-0398-x

[…] g algorithms are imperatively needed to accurately infer genotypes. Recently, several popular calling algorithms have been designed for Illumina platform, such as: BEAGLE with BEAGLECALL software [], CRLMM [, ], GenCall [], GenoSNP [], and Iluminus []. In general, Illumina chip catalogs millions of SNPs and processes a large number of parallel samples, and the genotyping algorithms for the Illumin […]


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

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