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piano specifications

Information


Unique identifier OMICS_01558
Name piano
Alternative name Platform for Integrated Analysis of Omics data
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 2.0
Computer skills Advanced
Version 1.20.0
Stability Stable
Maintained Yes

Subtools


  • Consensus Gene Set Analysis tool
  • Gene set analysis
  • Microarray Differential Expression Analysis
  • Microarray Quality Check

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Documentation


Additional information


Some functionalities are also available at http://biomet-toolbox.chalmers.se/index.php?page=tools Tutorial: https://varemo.github.io/piano/quick_tutorial.html https://github.com/varemo/piano

Information


Unique identifier OMICS_01558
Name piano
Alternative name Platform for Integrated Analysis of Omics data
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Subtools


  • Consensus Gene Set Analysis tool
  • Gene set analysis
  • Microarray Differential Expression Analysis
  • Microarray Quality Check

Documentation


Additional information


Some functionalities are also available at http://biomet-toolbox.chalmers.se/index.php?page=tools Tutorial: https://varemo.github.io/piano/quick_tutorial.html https://github.com/varemo/piano

Publication for Platform for Integrated Analysis of Omics data

piano in pipelines

 (4)
2017
PMCID: 5320501
PMID: 28225009
DOI: 10.1038/srep42633

[…] go enrichment was additionally examined by using the differential expression-associated statistics obtained through linear modeling in a distinct directional gene set analysis (page) using the piano package. b. oleae expression data and array platform have been uploaded to the gene expression omnibus with accession number gse82037., selected detoxification and digestive genes […]

2017
PMCID: 5478895
PMID: 28634240
DOI: 10.1128/mBio.00857-17

[…] and fluxes, normalized and log-transformed counts were used, while correlation scores were calculated according to a previously described method ()., gene-set analysis was performed using the piano package () for r. go terms were obtained from reference , while those sets corresponding to “cellular localization” and gene sets with fewer than 5 or more than 500 genes were discarded. […]

2017
PMCID: 5683368
PMID: 29158777
DOI: 10.1186/s13068-017-0956-0

[…] of 1, similarity cut-off of 30%). classification into gene ontology (go) categories and interproscan were performed with blast2go software []. go enrichment tests were performed with the r package piano []. secretory proteins were predicted using the signalp 4.1 server [] or the wolf psort algorithm []. genes containing cazy domains were identified using dbcan release 5.0 [] which searches […]

2014
PMCID: 4322794
PMID: 25671108
DOI: 10.1186/2049-3002-2-21

[…] of 6,503 genes for further analysis. the log2 fold change (i.e., log2 of the fpkm ratio) was used as the gene-level statistic. the gene set analysis was carried out using the r/bioconductor package piano []. three types of gene set collections were used, describing the association between (i) genes and metabolites, (ii) genes and metabolic pathways, and (iii) gene ontology (go) terms., […]

piano in publications

 (55)
PMCID: 5930841
PMID: 29743953
DOI: 10.1186/s13068-018-1116-x

[…] [] from bioconductor (http://bioconductor.org), the two gene-level statistics summarization tests—fisher’s combined probability test [] and summarization of median gene-level fold changes—using piano package [] from bioconductor. statistical significance of the enrichment tests was estimated with 100,000 data permutations., the proteomic sample processing and data analysis in additional […]

PMCID: 5865380
PMID: 29588665
DOI: 10.1186/s13068-018-1076-1

[…] were similarly performed, namely c5 vs. c6 substrates as well as complex vs. simple substrates. functional enrichment (kegg and go) for specific substrates were performed through the r package piano [] as detailed previously []. a genome atlas was created that charted the abundance profiles of extracellular proteins across substrates—globally visualized in the context of the entire c. […]

PMCID: 5850081
PMID: 29556541
DOI: 10.1128/mSystems.00194-17

[…] it throws away potentially useful data, the extra reads from samples with greater sequencing depth. second, they adapt empirical bayesian methods developed to reduce false-positive results in microarray differential expression analysis by “borrowing” information across taxa on how taxa are distributed across samples. finally, they accommodate multivariate models that can be used […]

PMCID: 5820295
PMID: 29503662
DOI: 10.3389/fgene.2018.00052

[…] of snpgenesets, we also conducted test of pathway expression association with diabetes traits using different methods of gene set enrichment (; ), including wilcoxon rank-sum and fisher’s test from piano package () and gsea test () implemented in fgsea package (sergushichev, unpublished), and obtained p-value based on 10,000 permutations., meta-analysis was conducted using binomial test […]

PMCID: 5823973
PMID: 29452638
DOI: 10.1016/j.molcel.2018.01.034

[…] age (). the considered contrast were mt45 against mt7, mt80 against mt7 and mt80 against mt45. an enrichment analysis was performed with the resulting statistics of each considered contrast using the piano r package (). the gene set collections used were obtained from msigdb (c5.go.bp). each gene set collection was enriched independently. the consensus enrichment p value for each considered gene s […]

piano institution(s)
Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
piano funding source(s)
Supported by the Knut and Alice Wallenberg foundation, the Chalmers foundation, the Bioinformatics Infrastructure for Life Sciences (BILS).

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