R scripts used to infer microbial networks from metabarcoding data and validate them using text-mining (ICPSR doi:10.15454/5WD6P6)

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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:

R scripts used to infer microbial networks from metabarcoding data and validate them using text-mining

Identification Number:

doi:10.15454/5WD6P6

Distributor:

Portail Data INRAE

Date of Distribution:

2020-02-18

Version:

1

Bibliographic Citation:

Vacher, Corinne, 2020, "R scripts used to infer microbial networks from metabarcoding data and validate them using text-mining", https://doi.org/10.15454/5WD6P6, Portail Data INRAE, V1, UNF:6:LNjhKptvEnA9T2eqRWfBNQ== [fileUNF]

Study Description

Citation

Title:

R scripts used to infer microbial networks from metabarcoding data and validate them using text-mining

Identification Number:

doi:10.15454/5WD6P6

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, Farming Systems and Practices, Microorganisms, Omics, Plant Health and Pathology

Abstract:

R scripts and datafiles used to infer microbial association networks from metabarcoding data of grapevine foliar samples infected or not by powdery mildew (Erysiphe necator). R script used to search for microbial associations in the Scopus database.

Kind of Data:

Dataset

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--f98283

File: disease.tab

  • Number of cases: 1872

  • No. of variables per record: 8

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

Notes:

UNF:6:YhNhP0OvsKWGb7vuuHzrVQ==

File Description--f98285

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==

File Description--f98286

File: vigor.tab

  • Number of cases: 39

  • No. of variables per record: 4

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

Notes:

UNF:6:ukTDZ/fG7CyAj4aRerGm7Q==

Variable Description

List of Variables:

Variables

BlockType

f98283 Location:

Variable Format: character

Notes: UNF:6:2/cjGnc7wv4IBVEL5C3HPQ==

Replicate

f98283 Location:

Summary Statistics: Mean 2.487179487179486; StDev 1.1296717968606134; Max. 4.0; Valid 1872.0; Min. 1.0

Variable Format: numeric

Notes: UNF:6:IBVi8Gjb8QRj08o8lVVnRA==

Plant

f98283 Location:

Variable Format: character

Notes: UNF:6:KS1Zp+PLH1d8ts9z3NFBDQ==

Disease

f98283 Location:

Variable Format: character

Notes: UNF:6:nhzpFW1cB5GZPW5DHROvJg==

ArmOrientation

f98283 Location:

Variable Format: character

Notes: UNF:6:zKIxCg+j1rI4E12Ja53A+A==

LeafPosition

f98283 Location:

Variable Format: character

Notes: UNF:6:IAWYhKJcVZIs73Sk10KZnA==

LeafReplicate

f98283 Location:

Summary Statistics: Mean 1.5; Max. 2.0; StDev 0.5001336005367865; Min. 1.0; Valid 1872.0

Variable Format: numeric

Notes: UNF:6:yKp75YWsQ/3u0xDTIrC34g==

Evaluation

f98283 Location:

Summary Statistics: Min. 0.0; Mean 9.842414529914528; StDev 15.225307918790342; Max. 90.0; Valid 1872.0;

Variable Format: numeric

Notes: UNF:6:GiM0N40tazc8PI7UkkNZ3w==

Label

f98285 Location:

Variable Format: character

Notes: UNF:6:zOVXBLLG4JlW5OxlIuyQGw==

Sample

f98285 Location:

Variable Format: character

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

Treatment

f98285 Location:

Variable Format: character

Notes: UNF:6:Ybta81EmfhZuYA7ilQ7t+Q==

Date

f98285 Location:

Variable Format: character

Notes: UNF:6:dm1xWrWeerdBzUKqNJ3SJQ==

Replicate

f98285 Location:

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

Variable Format: numeric

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

LeafAge

f98285 Location:

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

Variable Format: numeric

Notes: UNF:6:W4Dv2EDFvfvpjFYoKQNYEg==

SLA

f98285 Location:

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

Variable Format: numeric

Notes: UNF:6:hgYZwkKOx5ftXSUkLpBc1Q==

LeafWaterContent

f98285 Location:

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

Variable Format: numeric

Notes: UNF:6:VZwA36XA6lIP2WE1ZPi5Kg==

MeanTempSinceFlush

f98285 Location:

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

Variable Format: numeric

Notes: UNF:6:puizFc6e3pvOUL9ZmERQDw==

VarTempSinceFlush

f98285 Location:

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

Variable Format: numeric

Notes: UNF:6:gsndJHX+FjPJuJNpr7vRPQ==

MeanVPDSinceFlush

f98285 Location:

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

Variable Format: numeric

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

VarVPDSinceFlush

f98285 Location:

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

Variable Format: numeric

Notes: UNF:6:eUM0eDGDzU963WSOwq6c3w==

RainyDaysSinceFlush

f98285 Location:

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

Variable Format: numeric

Notes: UNF:6:quf0TN5HxHGPk9FD149QnA==

Run

f98285 Location:

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

Variable Format: numeric

Notes: UNF:6:GKNJtguhumNRBGhBpRgU5Q==

Source

f98285 Location:

Variable Format: character

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

AbsoluteABD

f98285 Location:

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

Variable Format: numeric

Notes: UNF:6:6ABOnxoSEFYrdn5Z4ODUGQ==

LeafID

f98285 Location:

Variable Format: character

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

LeafState

f98285 Location:

Variable Format: character

Notes: UNF:6:Oq4hGy0UEAL9koipb2MBbw==

Zone

f98285 Location:

Variable Format: character

Notes: UNF:6:ByiiJRKz8/ZaJ5yXNHi2DQ==

D_inoc

f98285 Location:

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

Variable Format: numeric

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

PM

f98285 Location:

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

Variable Format: numeric

Notes: UNF:6:rgCgxSB0m0AFWpyCEsCS/Q==

Zone

f98286 Location:

Variable Format: character

Notes: UNF:6:QSNbzepWTY+DyuLLkhmBjQ==

Cep

f98286 Location:

Variable Format: character

Notes: UNF:6:ZonMI4zWQmDw69ODlmsXzg==

Ramx

f98286 Location:

Summary Statistics: Mean 7.871794871794871; Min. 3.0; StDev 2.451417282646351; Max. 14.0; Valid 39.0

Variable Format: numeric

Notes: UNF:6:6qR6Ra5Fyd/x4/T/gHuuww==

Feui.ramx

f98286 Location:

Summary Statistics: Valid 39.0; Min. 11.0; Mean 22.897435897435898; Max. 31.0; StDev 4.666763060504357

Variable Format: numeric

Notes: UNF:6:C4N7I5+g0i3Twxn8it0gzg==

Other Study-Related Materials

Label:

aln.tsv

Text:

Yeast strains used in the co-culture experiments

Notes:

text/tsv

Other Study-Related Materials

Label:

analysis-learn-biocontrol.Rmd

Text:

R script for community data analysis and network inference

Notes:

application/octet-stream

Other Study-Related Materials

Label:

ASV_phyloseq_LearnBiocontrol.RDS

Text:

Fungal ASV table (phyloseq format) obtained for 20-days old grapevine leaves (infected or not by powdery mildew)

Notes:

application/gzip

Other Study-Related Materials

Label:

dists.csv

Text:

Distance between sampled leaves and environmental microbial sources (senescing leaves, bark, ground)

Notes:

text/csv

Other Study-Related Materials

Label:

get_top_taxa_avgRA.R

Text:

R function used to generate the table of the most abundant taxa

Notes:

type/x-r-syntax

Other Study-Related Materials

Label:

sources-ASV_phyloseq_LearnBiocontrol.RDS

Text:

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

Notes:

application/gzip

Other Study-Related Materials

Label:

text_mining_in_pathobiome.R

Text:

R script used to search for fungal associations in the Scopus database

Notes:

type/x-r-syntax