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May 18, 2021
Chonova, Teofana; Keck, Francois; Bouchez, Agnès; Rimet, Frederic, 2020, "A ready-to-use database for DADA2: Diat.barcode_rbcL_263bp_DADA2 based on Diat.barcode v9", https://doi.org/10.15454/QBLSXP, Portail Data INRAE, V3
This database is an adaptation for DADA2 of Diat.barcode v9. Length of sequences is 263 bp ------------------------- Rimet, Frederic; Chonova, Teofana; Gassiole, Gilles; Gusev, Evgenuy; Kahlert, Maria; Keck, François; Kelly, Martyn; Kulikovskiy, Maxim; Maltsev, Yevhen; Mann, Davi...
Dec 1, 2020
Chonova, Teofana; Vasselon, Valentin; Bouchez, Agnès; Rimet, Frédéric, 2020, "A ready-to-use database for mothur: Diat.barcode_rbcL_263bp_mothur based on Diat.barcode v9", https://doi.org/10.15454/SOMFSU, Portail Data INRAE, V2
Ready to use database adapted from Diat.barcode v9 for MOTHUR
Jul 30, 2019 - Omics Dataverse
Pauvert, Charlie; Vallance, Jessica; Delière, Laurent; Buée, Marc; Vacher, Corinne, 2019, "Amplicon Sequence Variant (ASV) table obtained by metabarcoding foliar fungal communities in conventional and organic vineyards", https://doi.org/10.15454/WOICSE, Portail Data INRAE, V1, UNF:6:PSwFBpb4Vxgr5rwUlkcPUQ== [fileUNF]
This Amplicon Sequence Variant (ASV) table was obtained by metabarcoding foliar fungal communities in conventional and organic vineyards. This table was generated after the application of the bioinformatics scripts (at https://doi.org/10.15454/NSHUAQ) to the sequences available a...
Apr 23, 2021
Plaza Onate, Florian; Ghozlane, Amine; Almeida, Mathieu, 2021, "An updated catalog of genes and species of the pig gut microbiota", https://doi.org/10.15454/OPAULL, Portail Data INRAE, V1, UNF:6:Ggdc9+Ypa5HI+KYp/YYwqw== [fileUNF]
Dataset overview We built an updated catalog of 9.3M genes found in the pig gut microbiota. Co-abundant genes were binned in 1523 Metagenomic Species Pan-genomes (MSPs) for which we provide taxonomic labels and a phylogenetic tree. In addition, we reconstituted 7059 Metagenome-As...
Aug 18, 2020 - Genes specific to phytoparasitic nematodes INRAE/EMBRAPA
Danchin, Etienne; Grynberg, Priscila; Togawa, Roberto, 2020, "Annotated list of species used in this study", https://doi.org/10.15454/IIAQOW, Portail Data INRAE, V1
Annotated list of the 63 species used in the Orthofinder comparative analysis of nematodes (61 species) and two tardigrade species as out-groups. Description: Lines 1-64, definition of columns - Abbrev Species: abbreviated species name. Species identifiers used in all the Orthofi...
Dec 7, 2020 - Omics Dataverse
Fort, Tania; Pauvert, Charlie; Zanne, Amy; Ovaskainen, Otso; Caignard, Thomas; Barret, Matthieu; Compant, Stéphane; Hampe, Arndt; Delzon, Sylvain; Vacher, Corinne, 2020, "Bioinformatic and statistical scripts for "Fort et al. 2020. Maternal effects shape seed fungal communities in Quercus petraea, New Phytologist"", https://doi.org/10.15454/0CNFWS, Portail Data INRAE, V3, UNF:6:+ROFl+GYxv+1vFHcrzj8MA== [fileUNF]
This dataset contains R-scripts to analyse the diversity and composition of seed fungal communities (Fort et al. 2020. Maternal effects shape seed fungal communities in Quercus petraea. New Phytologist, https://doi.org/10.1111/nph.17153). The bioinformatic script was applied to r...
Feb 3, 2021
Vacher, Corinne, 2021, "Bioinformatic scripts to analyze metabarcoding data of fungal communities associated with two grapevine varieties (Vitis vinifera ‘Regent’ and ‘Cabernet-Sauvignon’)", https://doi.org/10.15454/KMAU1G, Portail Data INRAE, V1, UNF:6:O96E7S960CaSgbyN7MInuA== [fileUNF]
This archive provides the bioinformatic scripts used to analyze a metabarcoding dataset (available at https://www.ncbi.nlm.nih.gov/bioproject/678415) representing foliar fungal communities associated with two grapevine varieties (Vitis vinifera ‘Regent’ and ‘Cabernet-Sauvignon’)...
May 9, 2019 - Omics Dataverse
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
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 w...
Feb 7, 2019
Flori, Laurence, 2019, "Data associated to the paper "A genomic map of climate adaptation in Mediterranean cattle breeds" (Flori et al., Molecular Ecology, Epub 2018 Dec 29. doi: 10.1111/mec.15004)", https://doi.org/10.15454/PWKBFB, Portail Data INRAE, V1
This dataset consists of genotypes of 640 animals for 39921 variants (SNPs). Animals belong to 21 Mediterranean cattle populations. The compressed archive contains two files (in plink format): i) a genotyping data file named "MED_set.ped" (640 rows, 79848 columns) that contains,...
Apr 19, 2018
Laloe, Denis, 2018, "Data associated to the paper "Genetic diversity and relationships among six local cattle populations in semi-arid areas assessed by a bovine medium-density data" (Boushaba et al, 2018)", https://doi.org/10.15454/HCFRWQ, Portail Data INRAE, V1
This data file consists of genotypes of 732 animals for 41183 markers. The animals belong to 23 populations. The file is a "csv" file where the field separator is ";". First line is a header. First column is the population identification the animal belongs to; following colums is...
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