Bioinformatic and statistical scripts to analyze the leaf-associated fungal community of wild plant populations (ICPSR doi:10.15454/JQPBOW)

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Part 1: Document Description
Part 2: Study Description
Part 5: Other Study-Related Materials
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Document Description

Citation

Title:

Bioinformatic and statistical scripts to analyze the leaf-associated fungal community of wild plant populations

Identification Number:

doi:10.15454/JQPBOW

Distributor:

Portail Data INRAE

Date of Distribution:

2020-03-09

Version:

3

Bibliographic Citation:

Ma, Yuxin, 2020, "Bioinformatic and statistical scripts to analyze the leaf-associated fungal community of wild plant populations", https://doi.org/10.15454/JQPBOW, Portail Data INRAE, V3

Study Description

Citation

Title:

Bioinformatic and statistical scripts to analyze the leaf-associated fungal community of wild plant populations

Identification Number:

doi:10.15454/JQPBOW

Authoring Entity:

Ma, Yuxin (INRA - Institut National de la Recherche Agronomique)

Distributor:

Portail Data INRAE

Access Authority:

Ma, Yuxin

Depositor:

Ma, Yuxin

Date of Deposit:

2020-03-09

Study Scope

Keywords:

Microorganisms, Omics, Plant Health and Pathology

Abstract:

This dataset contains R-scripts to perform bioinformatic and statistical analysis on leaf-associated fungal communities of wild plant populations (Ma et al. Leaf-associated fungal and viral communities of wild plant populations differ between cultivated and natural ecosystems. Submitted). Raw sequences are available at https://doi.org/10.15454/X23KJF. Metadata and ASV tables are also provided allowing to use statistical analysis scripts without running the bioinformatic steps.

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:

Leaf-associated fungal and viral communities of wild plant populations differ between cultivated and natural ecosystems

Other Study-Related Materials

Label:

1.ITS1_dada2_processing_and_taxonomyassginment_2020.12.Rmd

Text:

R markdown script for sequence processing and taxonomy assignment

Notes:

application/octet-stream

Other Study-Related Materials

Label:

1.ITS2_dada2_processing_and_taxonomyassginment_2020.12.Rmd

Text:

ITS2 data sequence processing and taxonomic assignmemt

Notes:

application/octet-stream

Other Study-Related Materials

Label:

2.generate_physeq_filterASV_its1-2020.12.Rmd

Text:

Rmarkdown

Notes:

application/octet-stream

Other Study-Related Materials

Label:

2.generate_physeq_filterASV_its2-2020.12.Rmd

Text:

Generate phyloseq object its2 (both plant and culture samples)

Notes:

application/octet-stream

Other Study-Related Materials

Label:

3.generate_krona.Rmd

Text:

krona plot of discovered fungi

Notes:

application/octet-stream

Other Study-Related Materials

Label:

4.depth-richness-eveness-diversity-ITS12&ITS2.Rmd

Text:

statistic analysis of fungal richness, diversity, GLMM test, PCoA, PERMANOVA......

Notes:

application/octet-stream

Other Study-Related Materials

Label:

ASV-its1-table-output.txt

Text:

ASV table - its1 (both plant and culture samples)

Notes:

text/plain

Other Study-Related Materials

Label:

ASV-its2-table-output.txt

Text:

ASV table - its2 (both plant and culture samples)

Notes:

text/plain

Other Study-Related Materials

Label:

Funguild-2021-its1.Rmd

Text:

the R markdown script for guild assignation using FUNGuild and statistic analysis

Notes:

application/octet-stream

Other Study-Related Materials

Label:

Input_Funguild_all_its1_2021.txt

Text:

The input file (ITS1) used for guild assignation

Notes:

text/plain

Other Study-Related Materials

Label:

Input_Funguild_all_its2_2021.txt

Text:

The input file (ITS2) used for guild assignation

Notes:

text/plain

Other Study-Related Materials

Label:

its1_rep_seqs.fasta

Text:

its1 ASV sequences with ASV ids

Notes:

text/plain

Other Study-Related Materials

Label:

its2_rep_seqs.fasta

Text:

its2 ASV sequences with ASV ids

Notes:

text/plain

Other Study-Related Materials

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Output_Funguild_all_its1_2021.guilds.txt

Text:

the output file of guild assignation of ITS1 amplicons

Notes:

text/plain

Other Study-Related Materials

Label:

Output_Funguild_all_its2_2021.guilds.txt

Text:

the output file of guild assignation of ITS2 amplicons

Notes:

text/plain

Other Study-Related Materials

Label:

ps.ITS1.RDS

Text:

ITS1 phyloseq object including both plant and culture samples

Notes:

application/gzip

Other Study-Related Materials

Label:

ps.ITS2.RDS

Text:

phyloseq object of ITS2 dataset (both plant and culture samples)

Notes:

application/gzip

Other Study-Related Materials

Label:

sample-its1-table-output.txt

Text:

Metadata of samples - its1 (both plant and culture samples)

Notes:

text/plain

Other Study-Related Materials

Label:

sample-its2-table-output.txt

Text:

Metadata of samples - its2 (both plant and culture samples)

Notes:

text/plain

Other Study-Related Materials

Label:

taxa-its1-table-output.txt

Text:

taxonomic assignment table - its1 (both plant and culture samples)

Notes:

text/plain

Other Study-Related Materials

Label:

taxa-its2-table-output.txt

Text:

taxonomy assignment - its2 (both plant and culture samples)

Notes:

text/plain