baySeq protocols

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baySeq specifications

Information


Unique identifier OMICS_01299
Name baySeq
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 3.0, GNU General Public License version 2.0
Computer skills Advanced
Version 2.14.0
Stability Stable
Requirements
methods, parallel, BiocGenerics, GenomicRanges, BiocStyle, edgeR, R(>=2.3.0), abind
Maintained Yes

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Maintainer


  • person_outline Thomas J. Hardcastle <>

Publication for baySeq

baySeq in pipelines

 (10)
2018
PMCID: 5808219
PMID: 29467736
DOI: 10.3389/fmicb.2018.00120

[…] to the corresponding genome; and for h7858, 93% of the reads mapped to the genome., differential expression (de) of protein-coding genes and non-coding rna (ncrnas) features was analyzed using the bayseq package for r version 2.2.0 (hardcastle and kelly, ) based on the total coverage obtained for each gene or feature. six different de analyses were performed to compare transcript levels […]

2018
PMCID: 5878008
PMID: 29440499
DOI: 10.1073/pnas.1718263115

[…] were inferred from the sum of the number of reads assigned to the genes in the lowest 75 percentile of expressed genes for each library (). analyses of the data were carried out using the r package bayseq (), and clustering based on the posterior probabilities was acquired from this package and the clusterseq package (). the go enrichment analysis on grafting-specific genes was done […]

2016
PMCID: 4754846
PMID: 26880300
DOI: 10.1186/s12864-016-2432-9

[…] and antisense strands were analyzed separately using samtools []., differential expression of genes in the two different strains (δbchl::prha and δbchl::prha-sigh) was initially analyzed using the bayseq package for r version 2.2.0 []. genes were considered differentially expressed if the fdr (false discovery rate) was < 0.05 and the fc (fold change) was > 2.0 or < 0.5 (fc = average […]

2016
PMCID: 4949241
PMID: 27486438
DOI: 10.3389/fmicb.2016.01074

[…] and figure ). transcription of aprab, encoding the subunits of aps reductase, was correlated with sulfur metabolism rates (r2 = 0.99), and aprab was the only sulfur metabolism gene identified by the bayseq model as significantly up-regulated in hd incubations (fdr = 0.006; table ). multiple studies of free-living and endosymbiotic dissimilatory sulfur-metabolizing bacteria have found that aprab […]

2016
PMCID: 5080296
PMID: 27833590
DOI: 10.3389/fmicb.2016.01668

[…] 2) program (langmead and salzberg, ) using the implemented end-to-end mode, which requires the entire read align from one end to the other. differential expression analyses were performed with the bayseq program (mortazavi et al., ). genes with a fold change in expression of ≥2.0, a likelihood value of ≥0.9, and an adjusted p-value of ≤ 0.05 (the p-value was corrected by the false discovery […]


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baySeq in publications

 (107)
PMCID: 5889388
PMID: 29626212
DOI: 10.1038/s41598-018-23601-1

[…] treatment groups using an anova (p = 0.2387).table 1, as shown in supplementary fig. , 2540 hits were significantly changed as demonstrated by all three statistical tests (deseq. 2, edger, and bayseq) between the lg/bsa and lg/pa groups. of these, 740 were down-regulated while 1800 were up-regulated. the protein-coding genes with the largest log2fold changes are reported in table .table […]

PMCID: 5892942
PMID: 29570727
DOI: 10.1371/journal.ppat.1006942

[…] tbl20 as compared to bl20 with a cutoff of adjusted p value < 0.05. in order to increase the confidence level and limit our analysis to the most significantly de mirnas we used a second pipeline, bayseq []. both deseq2 and bayseq are highly specific and sensitive tools for the detection of differential expression []. we consider a mirna differentially expressed (de) following two criteria: a) […]

PMCID: 5845109
PMID: 29556248
DOI: 10.3389/fgene.2018.00058

[…] platform at the university of lethbridge facility. statistical comparisons between the control and pdx-bearing groups were performed using the deseq bioconductor package (version 1.8.3) and the bayseq bioconductor package (version 1.10.0). clustering of the samples was analyzed with multidimensional scaling (mds) plots, built using the plotmds function from the edger bioconductor package. […]

PMCID: 5831220
PMID: 29507534
DOI: 10.1186/s12575-018-0067-8

[…] both of which are provided in the r/bioconductor package tcc [–]. tcc implements a robust normalization strategy (called deges []) that uses functions provided in four widely used packages (bayseq [], edger [, ], deseq [], and deseq2) []. for simplicity and/or the algorithmic advantage [, ], we only used tcc for the de analysis of rna-seq data. specifically, we used the default de […]

PMCID: 5817962
PMID: 29491871
DOI: 10.3389/fpls.2018.00108

[…] been tackled recently by gierlinski et al. (). the authors recommend the use of tools based on the negative binomial distribution. these tools include edger, deseq, deseq2, cuffdiff, cuffdiff 2, and bayseq (anders and huber, ; hardcastle and kelly, ; robinson et al., ; trapnell et al., , ; love et al., ). there are also some non-parametric methods that can be used as alternatives when the data […]


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baySeq institution(s)
Department of Plant Sciences, University of Cambridge, Cambridge, UK
baySeq funding source(s)
Supported by European Research Council Advanced Investigator Grant ERC-2013-AdG 340642 – TRIBE.

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