Bioinformatic scripts used to analyze fungal metabarcoding data obtained from Vitis vinifera leaves (ICPSR doi:10.15454/WLHBP6)

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Part 1: Document Description
Part 2: Study Description
Part 3: Data Files Description
Part 4: Variable Description
Part 5: Other Study-Related Materials
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Document Description

Citation

Title:

Bioinformatic scripts used to analyze fungal metabarcoding data obtained from Vitis vinifera leaves

Identification Number:

doi:10.15454/WLHBP6

Distributor:

Portail Data INRAE

Date of Distribution:

2020-02-18

Version:

1

Bibliographic Citation:

Vacher, Corinne, 2020, "Bioinformatic scripts used to analyze fungal metabarcoding data obtained from Vitis vinifera leaves", https://doi.org/10.15454/WLHBP6, Portail Data INRAE, V1, UNF:6:LYk3rj9ck7B/6LlcF6oIcQ== [fileUNF]

Study Description

Citation

Title:

Bioinformatic scripts used to analyze fungal metabarcoding data obtained from Vitis vinifera leaves

Identification Number:

doi:10.15454/WLHBP6

Authoring Entity:

Vacher, Corinne (INRA - Institut National de la Recherche Agronomique)

Distributor:

Portail Data INRAE

Access Authority:

Vacher, Corinne

Depositor:

Vacher, Corinne

Date of Deposit:

2020-02-18

Study Scope

Keywords:

Biodiversity and Ecology

Abstract:

Bioinformatic scripts used to sort, filter and analyze fungal raw sequence data obtained by metabarcoding foliar, bark and ground cover samples collected in an untreated vineyard at INRA Villenave d'Ornon (France). Amplicon sequence variant (ASV) tables obtained for vine leaves and environmental sources (senescing leaves, bark and ground cover).

Kind of Data:

Software

Methodology and Processing

Sources Statement

Data Access

Notes:

<img src="https://www.etalab.gouv.fr/wp-content/uploads/2011/10/licence-ouverte-open-licence.gif" alt="Licence Ouverte" height="100"><a href="https://www.etalab.gouv.fr/licence-ouverte-open-licence">Licence Ouverte / Open Licence Version 2.0</a> compatible CC BY

Other Study Description Materials

Related Publications

Citation

Bibliographic Citation:

Pauvert, C., Fort, T., Calonnec, A., Faivre d' Arcier, J., Chancerel, E., Massot, M., Chiquet, J., Robin, S., Bohan, D., Vallance, J., Vacher, C. Microbial association networks give relevant insights into plant pathobiomes. Submitted

File Description--f98272

File: learn-biocontrol.metadata_all_run.tab

  • Number of cases: 383

  • No. of variables per record: 21

  • Type of File: text/tab-separated-values

Notes:

UNF:6:LYk3rj9ck7B/6LlcF6oIcQ==

Variable Description

List of Variables:

Variables

Label

f98272 Location:

Variable Format: character

Notes: UNF:6:zOVXBLLG4JlW5OxlIuyQGw==

Sample

f98272 Location:

Variable Format: character

Notes: UNF:6:hrFijsxd7h/E+lkYwMa6tQ==

Treatment

f98272 Location:

Variable Format: character

Notes: UNF:6:Ybta81EmfhZuYA7ilQ7t+Q==

Date

f98272 Location:

Variable Format: character

Notes: UNF:6:dm1xWrWeerdBzUKqNJ3SJQ==

Replicate

f98272 Location:

Summary Statistics: Mean 2.5172413793103448; Max. 4.0; Valid 377.0; Min. 1.0; StDev 1.1134309767494919

Variable Format: numeric

Notes: UNF:6:EOexrFM9EkkgT+DF+c5knw==

LeafAge

f98272 Location:

Summary Statistics: Max. 27.0; Min. 16.0; Mean 21.43874643874644; Valid 351.0; StDev 3.051197913903438;

Variable Format: numeric

Notes: UNF:6:W4Dv2EDFvfvpjFYoKQNYEg==

SLA

f98272 Location:

Summary Statistics: Min. 9.89960959286113; Max. 62.2405660377358; Valid 352.0; Mean 19.833554961384987; StDev 4.304222114549673

Variable Format: numeric

Notes: UNF:6:hgYZwkKOx5ftXSUkLpBc1Q==

LeafWaterContent

f98272 Location:

Summary Statistics: StDev 0.030113827655507196; Max. 0.866881188118812; Mean 0.719167192253061; Valid 352.0; Min. 0.451122448979592

Variable Format: numeric

Notes: UNF:6:VZwA36XA6lIP2WE1ZPi5Kg==

MeanTempSinceFlush

f98272 Location:

Summary Statistics: Mean 17.891194872050374; Valid 351.0; StDev 1.4368838640129702; Min. 16.2227272727273; Max. 19.425

Variable Format: numeric

Notes: UNF:6:puizFc6e3pvOUL9ZmERQDw==

VarTempSinceFlush

f98272 Location:

Summary Statistics: Min. 4.78223333333333; Valid 351.0; Max. 13.0819117647059; StDev 3.031863585335045; Mean 7.867692664125817

Variable Format: numeric

Notes: UNF:6:gsndJHX+FjPJuJNpr7vRPQ==

MeanVPDSinceFlush

f98272 Location:

Summary Statistics: Mean 2093.3964127141467; StDev 195.97471022670538; Min. 1867.79568592152; Max. 2297.49557354769; Valid 351.0

Variable Format: numeric

Notes: UNF:6:TnrbKtod43uw7+TTCVr/uQ==

VarVPDSinceFlush

f98272 Location:

Summary Statistics: Mean 164781.67030234306; StDev 86489.7833110916; Min. 73539.8995998982; Valid 351.0; Max. 301800.890124522;

Variable Format: numeric

Notes: UNF:6:eUM0eDGDzU963WSOwq6c3w==

RainyDaysSinceFlush

f98272 Location:

Summary Statistics: StDev 2.5815380346488452; Max. 16.0; Min. 7.0; Valid 351.0; Mean 11.962962962962957

Variable Format: numeric

Notes: UNF:6:quf0TN5HxHGPk9FD149QnA==

Run

f98272 Location:

Summary Statistics: StDev 0.4324411146294605; Max. 2.0; Min. 1.0; Valid 383.0; Mean 1.2480417754569193;

Variable Format: numeric

Notes: UNF:6:GKNJtguhumNRBGhBpRgU5Q==

Source

f98272 Location:

Variable Format: character

Notes: UNF:6:U6st0UMscG+uTy+j3cKDnA==

AbsoluteABD

f98272 Location:

Summary Statistics: StDev 830342.2668608585; Mean 263743.114942529; Valid 348.0; Min. 145.0; Max. 6491720.0

Variable Format: numeric

Notes: UNF:6:6ABOnxoSEFYrdn5Z4ODUGQ==

LeafID

f98272 Location:

Variable Format: character

Notes: UNF:6:/uS476D8bO4fxF+rIJn35w==

LeafState

f98272 Location:

Variable Format: character

Notes: UNF:6:Oq4hGy0UEAL9koipb2MBbw==

Zone

f98272 Location:

Variable Format: character

Notes: UNF:6:ByiiJRKz8/ZaJ5yXNHi2DQ==

D_inoc

f98272 Location:

Summary Statistics: Max. 401.0; Valid 353.0; Mean 140.60623229461757; Min. 9.0; StDev 88.57236169653999

Variable Format: numeric

Notes: UNF:6:0VyZI1OsTLVi0Vtm+gED9A==

PM

f98272 Location:

Summary Statistics: StDev 5.5184382949848265; Max. 18.0; Min. 0.0; Mean 5.804532577903682; Valid 353.0

Variable Format: numeric

Notes: UNF:6:rgCgxSB0m0AFWpyCEsCS/Q==

Other Study-Related Materials

Label:

ASV_phyloseq_LearnBiocontrol.RDS

Text:

Fungal ASV table (phyloseq format) corresponding to 20-days old grapevine leaves

Notes:

application/gzip

Other Study-Related Materials

Label:

prep_data_reseq.R

Text:

R script used to filter the raw fungal ASV table corresponding to 20-days old grapevine leaves and generate a phyloseq object

Notes:

type/x-r-syntax

Other Study-Related Materials

Label:

prep_data_sources.R

Text:

R script used to filter the raw ASV table corresponding to environmental sources (senescing leaves, bark and ground cover) and generate a phyloseq object

Notes:

type/x-r-syntax

Other Study-Related Materials

Label:

run_learn-biocontrol-fwd-reseq_dada2v.1.8.R

Text:

Bioinformatic script used to generate the fungal ASV table corresponding to 20-days old grapevine leaves

Notes:

type/x-r-syntax

Other Study-Related Materials

Label:

run_learn-biocontrol-fwd-sources_dada2v.1.8.R

Text:

Bioinformatic script used to generate the raw fungal ASV table corresponding to environmental microbial sources (senescing leaves, bark, ground cover)

Notes:

type/x-r-syntax

Other Study-Related Materials

Label:

sources-ASV_phyloseq_LearnBiocontrol.RDS

Text:

Fungal ASV table (phyloseq format) corresponding to environmental microbial sources (senescing leaves, bark, ground cover)

Notes:

application/gzip