Bioinformatic scripts to assess the effect of the cropping system on both community and network α- and β-properties of fungal microbiota (ICPSR doi:10.15454/NSHUAQ)

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Document Description

Citation

Title:

Bioinformatic scripts to assess the effect of the cropping system on both community and network α- and β-properties of fungal microbiota

Identification Number:

doi:10.15454/NSHUAQ

Distributor:

Portail Data INRAE

Date of Distribution:

2019-05-09

Version:

1

Bibliographic Citation:

Pauvert, Charlie; Vallance, Jessica; Delière, Laurent; Buée, Marc; Vacher, Corinne, 2019, "Bioinformatic scripts to assess the effect of the cropping system on both community and network α- and β-properties of fungal microbiota", https://doi.org/10.15454/NSHUAQ, Portail Data INRAE, V1

Study Description

Citation

Title:

Bioinformatic scripts to assess the effect of the cropping system on both community and network α- and β-properties of fungal microbiota

Identification Number:

doi:10.15454/NSHUAQ

Authoring Entity:

Pauvert, Charlie (INRA - Institut National de la Recherche Agronomique)

Vallance, Jessica (INRA - Institut National de la Recherche Agronomique)

Delière, Laurent (INRA - Institut National de la Recherche Agronomique)

Buée, Marc (INRA - Institut National de la Recherche Agronomique)

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

Distributor:

Portail Data INRAE

Access Authority:

Pauvert, Charlie

Access Authority:

Vacher, Corinne

Depositor:

Pauvert, Charlie

Date of Deposit:

2019-04-09

Study Scope

Keywords:

Biodiversity and Ecology, Computer science, Farming Systems and Practices, Microorganisms, Omics, Plant Health and Pathology

Abstract:

These bioinformatics scripts were applied to the sequences available at https://doi.org/10.15454/3DPFNJ. They are based on several softwares, including SparCC (Friedman and Alm 2012) and DADA2 (Callahan et al. 2016). The code corresponds to R and R markdown files. These scripts were used to assess the effect of the cropping system on both community and network α- and β-properties of the foliar fungal microbiota of grapevine (Pauvert et al. Microbial networks inferred from metabarcoding data lack replicability: consequences for next-generation biomonitoring, Submitted).

Kind of Data:

Workflow

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

Other Study-Related Materials

Label:

networks-lack-replicability-code.Rmd

Notes:

text/x-r-markdown

Other Study-Related Materials

Label:

networks-lack-replicability-dada2_R1.R

Notes:

type/x-r-syntax