EDASeq protocols

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EDASeq specifications

Information


Unique identifier OMICS_01231
Name EDASeq
Alternative name Exploratory Data Analysis and Normalization for RNA-Seq
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data RNA-Seq read data
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License Artistic License version 2.0
Computer skills Advanced
Version 2.14.1
Stability Stable
Requirements
AnnotationDbi, methods, graphics, BiocGenerics, GenomicRanges, Biostrings, BiocStyle, edgeR, DESeq, biomaRt, GenomicFeatures, knitr, KernSmooth, Biobase(>=2.15.1), ShortRead(>=1.11.42), IRanges(>=1.13.9), aroma.light, Rsamtools(>=1.5.75), yeastRNASeq, leeBamViews
Maintained Yes

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EDASeq in pipelines

 (13)
2018
PMCID: 5869697
PMID: 29588458
DOI: 10.1038/s41598-018-23195-8

[…] as determined by the original tcga analysis using hierarchical cluster analysis. the genes were normalized within samples by gene length and between samples to correct for sequencing depth using the edaseq package (version 2.10.0). only genes which were expressed above 0.5 counts per million (cpm) in at least a sixth of all samples were retained, i.e. selection was irrespective of tissue type. […]

2017
PMCID: 5394545
PMID: 28417961
DOI: 10.1038/srep46577

[…] co., ltd. (guangzhou, china). paired-end reads were aligned to the mouse transcriptome with tophat2 as previously described. rna-seq data were normalized for gc (guanine-cytosine) content with edaseq software. the whole samples expression levels were presented as rpkm (expected number of reads per kilobase of transcript sequence per million base pairs sequenced), which is the recommended […]

2017
PMCID: 5610324
PMID: 28939884
DOI: 10.1038/s41467-017-00668-4

[…] with nextseq 500 mid output kit v2 (150 cycles)., the number of raw reads mapped to human mrna reference sequence for grch38/hg38 using rsem (rsem-1.2.4), bowtie2 (v2.2.5), and normalized with edaseq (v2.2.0). gene expression is expressed as “normalized tag count.” other downstream analyses were performed using glbase. in brief, differential expression between differentiation state […]

2016
PMCID: 4748411
PMID: 26861190
DOI: 10.1038/srep20837

[…] considered ‘absent’ and therefore removed from the dataset. as such, 13,599 genes were left. per sample, gc-content was corrected using full quantile normalization on bins of gc-content with the edaseq package from bioconductor for within-sample normalization. between-sample normalization was carried out to correct for library size and rna composition, as it is known that these are sources […]

2016
PMCID: 4824866
PMID: 26785728
DOI: 10.1074/mcp.M115.054122

[…] tool (life technologies) and reference genome grch37/hg19. statistical analysis was performed with r (). normalization and differential expression calculations were carried out using the r packages edaseq () and deseq (), respectively., phosphomannomutase activity was determined as the turnover rate of man-6-p to man-1,6-p in the presence of cofactor glu-1,6-p. twelve micrograms protein of cell […]


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EDASeq in publications

 (48)
PMCID: 5896901
PMID: 29649237
DOI: 10.1371/journal.pone.0194803

[…] from the gene expression omnibus database, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=gse79544., normalization of rna-sequences was obtained using the upper-quartile method provided by edaseq package in r bioconductor, followed by removing unwanted variation (ruv) technique using ruvg function provided by r bioconductor package ruvseq, where a set of 20 house keeping genes […]

PMCID: 5924522
PMID: 29587435
DOI: 10.3390/genes9040180

[…] libraries (the minimum number of libraries representing the two strains at a given time point). libraries were normalized for gc content and between-library sequencing depth using the r package edaseq [] and input as offsets along with the raw counts into edger []., differential expression analysis was done by fitting negative binomial generalized log-linear models in edger []. specific […]

PMCID: 5882306
PMID: 29662615
DOI: 10.18632/oncotarget.24634

[…] this analysis, technical replicates were combined and genes with less than 20 aligned reads across all samples were removed. expression levels were normalized by upper quartile normalisation using edaseq [, ]. differential expression was calculated using limma/voom [] (). volcano plots of differential gene expression data were created using the r plot function, and heat maps were produced […]

PMCID: 5864750
PMID: 29568081
DOI: 10.1038/s41598-018-23217-5

[…] fasta sequence and gene feature annotation files were obtained from thermo fisher and combined with mm10 reference information. gene level counts were upper-quartile normalized using the r package edaseq and converted to transcripts per million (tpm) using the gene effective length., precise plates were prepared for sequencing following manufacturer’s instructions for the bd precise™ reagents […]

PMCID: 5756345
PMID: 29304754
DOI: 10.1186/s12864-017-4423-x

[…] within-lane normalization procedures to adjust for gc-content effects on read counts and between-lane normalization procedures to adjust for distributional differences between lanes using the edaseq package [] as reported in [, ].table 1, for each cancer type, we performed a differential expression analysis (dea) between two classes, normal vs tumoural, using tcgabiolinks [, ], […]


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EDASeq institution(s)
Department of Statistical Sciences, University of Padua, Italy; Department of Genetics, Stanford University, Standford, CA, USA; Division of Biostatistics and Department of Statistics, University of California, Berkeley, CA, USA
EDASeq funding source(s)
This work was funded by grant R01 HG03468 from the NHGRI at the NIH and grant CPDA094285 from the University of Padua.

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