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illuminaio specifications

Information


Unique identifier OMICS_07516
Name illuminaio
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Illumina
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Version 0.22.0
Stability Stable
Requirements
BiocGenerics, BiocStyle, RUnit, base64, IlluminaDataTestFiles(>=1.0.2)
Maintained Yes

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Documentation


Maintainer


  • person_outline Kasper Daniel Hansen <>

Publication for illuminaio

illuminaio in pipeline

2018
PMCID: 5907140
PMID: 29671397
DOI: 10.1186/s12859-018-2096-3

[…] intensities for each probe, ii) *.txt data, which is usually got after simple preprocessing and is easier to access. both file formats can be handled by r packages: *.idat files can be read by illuminaio package [] and *.txt files can be dealt with minfi [], watermelon [] et al. we use three datasets for expounding our framework., dataset 1: illumina 450k dataset from dedeurwaerder et al. […]

illuminaio in publications

 (7)
PMCID: 5907140
PMID: 29671397
DOI: 10.1186/s12859-018-2096-3

[…] intensities for each probe, ii) *.txt data, which is usually got after simple preprocessing and is easier to access. both file formats can be handled by r packages: *.idat files can be read by illuminaio package [] and *.txt files can be dealt with minfi [], watermelon [] et al. we use three datasets for expounding our framework., dataset 1: illumina 450k dataset from dedeurwaerder et al. […]

PMCID: 5747338
PMID: 29333246
DOI: 10.5256/f1000research.13583.r27972

[…] downloaded from http://bioinf.wehi.edu.au/egsea/arraydata.zip into the current working directory. illumina beadarray data can be read in directly using the readidat and readbgx functions from the illuminaio package . however, a more convenient way is via the read.idat function in limma which uses these illuminaio functions and outputs the data as an elistraw object for further processing., […]

PMCID: 4916993
PMID: 27347385
DOI: 10.5256/f1000research.9514.r14245

[…] ## [86] rcurl_1.95-4.8 ## [87] nnet_7.3-12 ## [88] tibble_1.2 ## [89] rmarkdown_1.3 ## [90] data.table_1.10.4 ## [91] digest_0.6.12 ## [92] xtable_1.8-2 ## [93] httpuv_1.3.3 ## [94] illuminaio_0.16.0 ## [95] r.utils_2.5.0 ## [96] openssl_0.9.6 ## [97] munsell_0.4.3 ## [98] registry_0.3 ## [99] biasedurn_1.07 ## [100] quadprog_1.5-5 , competing interests: i am the primary […]

PMCID: 5503549
PMID: 28418867
DOI: 10.18632/oncotarget.16258

[…] analysis to identify dmrs in gastric cancer samples (n = 295) from the cancer genome atlas project (tcga) and gastritis controls (n = 20) from perĂº., we imported the data into r using the illuminaio package []. for data normalization we used the minfi package to apply the noob background subtraction and dye-bias correction [] followed by normalization and identification of dmrs […]

PMCID: 4574526
PMID: 26316348
DOI: 10.1186/s13059-015-0741-y

[…] on geo under the accession number [geo:gse49629]., for the 450 k-fibroblast and 450 k-prad datasets, we downloaded the idat files containing the raw intensities. we read the data into r using the illuminaio package []. for data normalization, we use the minfi package [] to apply the noob background subtraction and dye-bias correction [] followed by functional normalization []. […]

illuminaio institution(s)
CRUK Cambridge Institute, Li Ka Shing Centre, The University of Cambridge, Cambridge, UK; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA; Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia

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