cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15454/nouqy2/a1lfpd
title: cv_MTV_LASSO_simul.Rmd

description: For each script "cv_xx_simul.Rmd", we apply cross-validation on simulated data. The input files are the simulated data and the genetic map (SSR or GBS). Each script generates a "tsv" file (e.g. "MTV_LASSO_results_same_minor_2.tsv") with Pearson's correlation, Spearman's correlation, bias, regression coefficient, etc for all cross-validation folds and responses. All these scripts are run with a bash script which generate one script per QTL number and simulation repetition.
DOI: 10.35078/9tqs6y/vgy7io
title: Limeira B.jpg

description: :unav
DOI: 10.15454/nouqy2/anwpmi
title: SxG.allelic-effects_SSR_add.tab

description: This text file is the design matrix for coding additive allelic effects with the SSR markers. This file has been created in `create_diffX_GP.Rmd`.
DOI: 10.35078/ofbtbf/hzwlri
title: Paulo Roberto A.jpg

description: :unav
DOI: 10.15454/nouqy2/b6em1x
title: cv_EN_JJ.Rmd

description: We downloaded simulated data from Jia and Jannink (2012) and applied our methods on their simulated data. For each following scripts (cv_xx_JJ.Rmd), the input files are the simulated data from Jia and Jannink (2012) analysis. Each script generates a tsv file (e.g. `EN_results_same_minor_20QTL_15.tsv`) with Pearson's correlation, Spearman's correlation, bias, regression coefficient, etc for all cross-validation folds and responses. All these scripts are run with a bash script which generate one script per QTL number and simulation repetition.
DOI: 10.35078/hujihe/kpfb7r
title: Pega D.jpg

description: :unav
DOI: 10.35078/9tqs6y/kecrhl
title: Lopes A.jpg

description: :unav
DOI: 10.15454/nouqy2/banbh9
title: cv_LASSO.GB_RD.Rmd

description: For each following scripts, the input files are the genetic map (SSR or GBS) and the phenotypic (BLUP) data (`SxG_pharch_BLUPs.tsv`). Each script generates a "tsv" file (e.g. `LASSO.GB_results_RDpharch_new_GBS.tsv`) with Pearson's correlation, Spearman's correlation, bias, regression coefficient, etc for all cross-validation folds and responses.
DOI: 10.35078/hujihe/s0mug1
title: Terra de Sal D.jpg

description: :unav
DOI: 10.35078/ofbtbf/cnmmgc
title: Gentil Parrudo A.jpg

description: :unav
DOI: 10.15454/nouqy2/bfoc6j
title: SxG_Doligez-et-al-2013.loc

description: Text file with genotypes in Joinmap format, for the 191 offsprings and the 153 SSR markers mapped on the Syrah x Grenache consensus genetic map. The first column is the marker name, the second one is the segregation type, the third one is the phase, and the remaining columns are genotypic classes at this marker for each offspring. Offsprings are ordered according to "SxG_Doligez-et-al-2013.qua" file.
DOI: 10.35078/9tqs6y/k0wh9l
title: Bonito D.jpg

description: :unav
DOI: 10.15454/nouqy2/c6doqm
title: SxG.allelic-effects.txt

description: This text file is the design matrix for coding additive and dominance allelic effects with the SNP markers. This file has been created in `create_diffX_GP.Rmd`.
DOI: 10.35078/hujihe/bcwdhw
title: Córrego Lagoa Duarte B.jpg

description: :unav
DOI: 10.35078/ofbtbf/mqrmis
title: DICIONARIO_KARDEX_PROGRAMA_CONTROLE_DOENÇA_CHAGAS.pdf

description: Dicionário para interpretação da ficha epidemiologica (Kardex)
DOI: 10.15454/nouqy2/cgrcxn
title: genetic_map_phys-gen_SxG_GBS.tab

description: Table file which combines information with genetic and physical positions of markers and associated linkage groups for the SNP genetic map.
DOI: 10.15454/nouqy2/chimbr
title: prediction_and_selection_quality.Rmd

description: This script takes as input classification results (the table "classification_results_GBS.tsv") and lambda values chosen by cross-validation on simulated data. It links the quality of classification with prediction accuracy or parameter value chosen in cross-validation and generates the Figure S22.
DOI: 10.35078/9tqs6y/7bn4wq
title: Lagedo A.jpg

description: :unav
DOI: 10.35078/hujihe/xdo3xu
title: Constantino Foncino Silva D.jpg

description: :unav
DOI: 10.15454/nouqy2/cl5g6x
title: 0_ReadMe.md

description: This document describes the input files, scripts and output files generated for this publication. This document is in Markdown format. A global overview of the study and associated scripts (mind-map) is available at : https://framindmap.org/c/maps/991026/public.
DOI: 10.15454/nouqy2/cmyud3
title: fit_mrk-selection_RDpharch_SSR.Rmd

description: This script applies marker selection for all traits and Interval Mapping methods with the SSR genetic map in order to study impact of genetic map densification. Results are saved in `res_fit_RD_pharch_SSR.RData` and `QTL.table_RDpharch_SSR.Rdata`.
DOI: 10.35078/hujihe/cplbnj
title: Lagoa do Melado D.jpg

description: :unav
DOI: 10.35078/nuvyw6/xvmxeb
title: Antônio Ferreira da Costa A.jpg

description: :unav
DOI: 10.15454/nouqy2/cu2kap
title: cv_SIM_RD.Rmd

description: For each following scripts, the input files are the genetic map (SSR or GBS) and the phenotypic data (BLUPs or phenotypes) (`SxG_pharch_BLUPs.tsv`). Each script generates a "tsv" file (e.g. `SIM_results_RDpharch_new_GBS.tsv`) with Pearson's correlation, Spearman's correlation, bias, regression coefficient, etc for all cross-validation folds and responses.
DOI: 10.35078/9tqs6y/fwypeh
title: Retiro São José A.jpg

description: :unav
DOI: 10.15454/nouqy2/czgk52
title: cv_spring_diff-h2.Rmd

description: We applied genomic prediction with different methods on simulated data with different heritability values between responses. Scripts are adapted to handle cases where traits were not equivalent. As for default simulation, each script generates a "tsv" file (e.g. "spring_results_same_minor_diff-h2_JJ_GBS_2.tsv") with Pearson's correlation, Spearman's correlation, bias, regression coefficient, etc for all cross-validation folds and responses. All these analyzes are run with a bash script which generate one script per QTL number and simulation repetition.
DOI: 10.15454/nouqy2/d0jjig
title: SxG.gendose.imputed_mean.txt

description: This text file is the design matrix of gene dose from SNP markers, extracted from the filtered vcf (FruitSelGen-grape-VITVI-PN40024-12x-v2-montpellier_SxG_raw-snps_gatk-filter_fimpute_filter-mendel_filter-segreg.vcf) and imputed by the mean allele frequency. This file has been created in `create_diffX_GP.Rmd`.
DOI: 10.35078/9tqs6y/l5ouhb
title: Derrubada A.jpg

description: :unav
DOI: 10.35078/hujihe/saq1nz
title: Lagoa A.jpg

description: :unav
DOI: 10.35078/nuvyw6/vdgstz
title: Vila Peçanha Bairro B.jpg

description: :unav
DOI: 10.15454/nouqy2/djo4t7
title: SxG_Doligez-et-al-2013.map

description: Text file in Joinmap format with the Syrah x Grenache consensus genetic map comprised of 153 SSR markers.
DOI: 10.15454/nouqy2/dlfwu8
title: cv_MTV_LASSO_JJ.Rmd

description: We downloaded simulated data from Jia and Jannink (2012) and applied our methods on their simulated data. For each following scripts (cv_xx_JJ.Rmd), the input files are the simulated data from Jia and Jannink (2012) analysis. Each script generates a "tsv" file (e.g. "MTV_LASSO_results_same_minor_20QTL_15.tsv") with Pearson's correlation, Spearman's correlation, bias, regression coefficient, etc for all cross-validation folds and responses. All these scripts are run with a bash script which generate one script per QTL number and simulation repetition.
DOI: 10.35078/nuvyw6/bjcipo
title: Barra Beija Flor B.jpg

description: :unav
DOI: 10.35078/9tqs6y/yk2ibs
title: Chauba B.jpg

description: :unav
DOI: 10.35078/hujihe/qelqx8
title: Cabeceira Bordão C.jpg

description: :unav
DOI: 10.15454/nouqy2/dq8k7c
title: compare_SSR-GBS_mapping.Rmd

description: Script which load physical and genetic position of markers from the SSR and SNP genetic maps and which compare them. It generates the Figure 1.
DOI: 10.15454/nouqy2/emssxc
title: fit_mrk-selection_RDpharch_GBS.Rmd

description: This script applies marker selection for all traits and methods on experimental data with the SNP genetic map. Results are saved in `res_fit_RD_pharch_GBS_all.RData` and `QTL.table_RDpharch_GBS.Rdata`.
DOI: 10.35078/hujihe/pcb1hm
title: Fátima A.jpg

description: :unav
DOI: 10.35078/nuvyw6/pl8oc8
title: Vila Peçanha Bairro A.jpg

description: :unav
DOI: 10.15454/nouqy2/f29dm9
title: SxG_GBS_genedose.tsv

description: This table is the genotyping file after map construction, with 3961 markers, coded in additive gene-dose. This file can also be found in https://data.inrae.fr/privateurl.xhtml?token=782ff6ff-d79c-4714-b0da-b85c5a4514a5.
DOI: 10.35078/9tqs6y/ldirdf
title: Casa da Mata D.jpg

description: :unav
DOI: 10.15454/nouqy2/fbihap
title: pharch_explo-pheno_lme4_DeltaPsi_WW_2012-2013.Rmd

description: This script exports for each trait a table with BLUP values, as well as model fitting information. BLUPs are fitted from raw phenotypic data that are available at https://data.inrae.fr/privateurl.xhtml?token=383f6606-1c3c-4d90-8607-704cd53de068. There is one script per trait.
DOI: 10.35078/hujihe/pypsek
title: Rosário A.jpg

description: :unav
DOI: 10.35078/nuvyw6/x8eqhb
title: Astolfo Alves da Silva B.jpg

description: :unav
DOI: 10.15454/nouqy2/fvirnr
title: cv_spring_simul.Rmd

description: For each script "cv_xx_simul.Rmd", we apply cross-validation on simulated data. The input files are the simulated data and the genetic map (SSR or GBS). Each script generates a "tsv" file (e.g. "spring_results_same_minor_2.tsv") with Pearson's correlation, Spearman's correlation, bias, regression coefficient, etc for all cross-validation folds and responses. All these scripts are run with a bash script which generate one script per QTL number and simulation repetition.
DOI: 10.15454/nouqy2/fvm3kh
title: analyse_results_real-data_pred-ability.Rmd

description: This script combines genomic prediction results for all predictions based on experimental data. Then it plots results apply diverse statistics and generates the Figure 3, Figure "plot_corP_pharch_comp_meth_mean-resp.png" and Table S14.
DOI: 10.35078/9tqs6y/ch1a0m
title: Coqueiros B.jpg

description: :unav
DOI: 10.35078/nuvyw6/zwnibo
title: Divino do Traíra Pov. A.jpg

description: :unav
DOI: 10.15454/nouqy2/gfzc10
title: cv_MTV_RR_JJ.Rmd

description: We downloaded simulated data from Jia and Jannink (2012) and applied our methods on their simulated data. For each following scripts (cv_xx_JJ.Rmd), the input files are the simulated data from Jia and Jannink (2012) analysis. Each script generates a "tsv" file (e.g. "MTV_RR_results_same_minor_20QTL_15.tsv") with Pearson's correlation, Spearman's correlation, bias, regression coefficient, etc for all cross-validation folds and responses. All these scripts are run with a bash script which generate one script per QTL number and simulation repetition.
DOI: 10.35078/9tqs6y/uwpngn
title: Quilombo C.jpg

description: :unav
DOI: 10.35078/hujihe/mwoa0d
title: José Guido A.jpg

description: :unav
DOI: 10.15454/nouqy2/go4jtj
title: cv_EN_RD.Rmd

description: For each following scripts, the input files are the genetic map (SSR or GBS) and the phenotypic (BLUP) data (`SxG_pharch_BLUPs.tsv`). Each script generates a tsv file (e.g. `EN_results_RDpharch_new_GBS.tsv`) with Pearson's correlation, Spearman's correlation, bias, regression coefficient, etc for all cross-validation folds and responses.
DOI: 10.35078/nuvyw6/lfpjfv
title: Almiro Alves A.jpg

description: :unav
DOI: 10.15454/nouqy2/h06lmx
title: cv_MTV_RR_diff-h2.Rmd

description: We applied genomic prediction with different methods on simulated data with different heritability values between responses. Scripts are adapted to handle cases where traits were not equivalent. As for default simulation, each script generates a "tsv" file (e.g. "MTV_RR_results_same_minor_diff-h2_JJ_GBS_2.tsv") with Pearson's correlation, Spearman's correlation, bias, regression coefficient, etc for all cross-validation folds and responses. All these analyzes are run with a bash script which generate one script per QTL number and simulation repetition.
DOI: 10.35078/hujihe/h9uzft
title: Antônio Leite B.jpg

description: :unav
DOI: 10.35078/9tqs6y/ei3vx3
title: Papula A.jpg

description: :unav
DOI: 10.35078/nuvyw6/wq3aeo
title: José Tobias B.jpg

description: :unav
DOI: 10.15454/nouqy2/hg6jt9
title: cv_MTV_RR_RD.Rmd

description: For each following scripts, the input files are the genetic map (SSR or GBS) and the phenotypic (BLUP) data (`SxG_pharch_BLUPs.tsv`). Each script generates a "tsv" file (e.g. `MTV_RR_results_RDpharch_new_GBS.tsv`) with Pearson's correlation, Spearman's correlation, bias, regression coefficient, etc for all cross-validation folds and responses.
DOI: 10.15454/nouqy2/hrhnoe
title: gather_BLUP_info.Rmd

description: This R script is run when all BLUPs are computed, to combine them into one table `SxG_pharch_BLUPs.tsv`. It generates the Figure S3, Figure S2, Figure S3, Figure S4.
DOI: 10.35078/9tqs6y/3g475c
title: Retiro da Prata B.jpg

description: :unav
DOI: 10.35078/hujihe/3nk3ih
title: Natalino Lisboa da Cruz C.jpg

description: :unav
DOI: 10.35078/nuvyw6/bvfwqv
title: Matadouro Bairro B.jpg

description: :unav
DOI: 10.15454/nouqy2/hyepnf
title: 0_ReadMe.html

description: This document describes the input files, scripts and output files generated for this publication. This document is in html format. A global overview of the study and associated scripts (mind-map) is available at : https://framindmap.org/c/maps/991026/public.
DOI: 10.15454/nouqy2/jb4vrm
title: cv_LASSO_JJ.Rmd

description: We downloaded simulated data from Jia and Jannink (2012) and applied our methods on their simulated data. For each following scripts (cv_xx_JJ.Rmd), the input files are the simulated data from Jia and Jannink (2012) analysis. Each script generates a tsv file (e.g. "LASSO_results_same_minor_20QTL_15.tsv") with Pearson's correlation, Spearman's correlation, bias, regression coefficient, etc for all cross-validation folds and responses. All these scripts are run with a bash script which generate one script per QTL number and simulation repetition.
DOI: 10.35078/9tqs6y/qj2mpr
title: Quilombo A.jpg

description: :unav
DOI: 10.35078/hujihe/6wvibi
title: Xamixuga D.jpg

description: :unav
DOI: 10.35078/nuvyw6/b0xbp7
title: Brandina B.jpg

description: :unav
DOI: 10.15454/nouqy2/jf6snp
title: cv_MTV_RR_simul.Rmd

description: For each script "cv_xx_simul.Rmd", we apply cross-validation on simulated data. The input files are the simulated data and the genetic map (SSR or GBS). Each script generates a "tsv" file (e.g. "RR_results_same_minor_2.tsv") with Pearson's correlation, Spearman's correlation, bias, regression coefficient, etc for all cross-validation folds and responses. All these scripts are run with a bash script which generate one script per QTL number and simulation repetition.
DOI: 10.35078/9tqs6y/snsqjw
title: Cachoeira B.jpg

description: :unav
DOI: 10.15454/nouqy2/jrgwmv
title: Function4GenoClass.R

description: This R script contains diverse R functions useful for the analysis, such that for data simulation, marker selection analysis or cross-validation.
DOI: 10.35078/nuvyw6/g42irm
title: José Elias A.jpg

description: :unav
DOI: 10.15454/nouqy2/jubktl
title: SxG_pharch_BLUPs.tsv

description: Table with fitted genotypic data for all traits (14) and for the progeny (186 offsprings) and the parents (TP-GRE is Grenache and TP-SYR is Syrah). The raw phenotypic data and details about the experiment are available at https://data.inrae.fr/privateurl.xhtml?token=383f6606-1c3c-4d90-8607-704cd53de068. Other BLUPs have been used from this dataset in Coupel-Ledru et al. (2014,2016). The suffix “WW” or “WD” in column names indicates whether the BLUP is calculated for the well-watered or for the water deficit scenario. This table has been generated by "gather_BLUP_info.Rmd", after running mixed-model analysis for all traits.
DOI: 10.35078/hujihe/xcq9dp
title: Lambari B.jpg

description: :unav
DOI: 10.35078/9tqs6y/h6hnqd
title: Sismaria B.jpg

description: :unav
DOI: 10.15454/nouqy2/jyntjm
title: list_genes_vitis_correspondencesV3_1-2.tsv

description: This table is the list of correspondence between v1 and v3 structural annotation, sent by Jérôme Grimplet, done according to Canaguier et al, 2017. This file is nearly the same as "list_genes_vitis_correspondencesV3_1.xlsx" which can be found on URGI website:(https://urgi.versailles.inra.fr/content/download/5723/43038/file/list_genes_vitis_correspondencesV3_1.xlsx), except some white spaces and 2 different values at column 51, rows 20002 and 21844.
DOI: 10.35078/nuvyw6/kdbqum
title: José Lau Martins A.jpg

description: :unav
DOI: 10.15454/nouqy2/kcix8q
title: fit_mrk-selection_simul.Rmd

description: This script takes as input simulated genotypic values, the genetic map and applies marker selection for: i) all methods: SIM, LASSO, EN, LASSO with Stability Selection (LASSO.SS), multivariate group LASSO (MTV_LASSO), with Stability Selection (MTV_LASSO.SS), EN with mFDR (marginal False Discovery Rate), LASSO with mFDR and spring ii) all heritability values (4) and responses (2) from a given set of simulated data iii) all parameters (40 tested) in a given range. A bash script (`bash_mrk_sim.sh`) needs to be run in order to repeat marker selection for other simulated data (e.g. for other configuration and simulation repetitions).
DOI: 10.35078/hujihe/dhbekl
title: Córrego Croeira A.jpg

description: :unav
DOI: 10.15454/nouqy2/kigldp
title: MapGBS_CIM.SSR_MIM.SSR_MIM.GBS.pdf

description: This figure has been generated in "compare_mrk-selection_RD_mapping_IM-methods.Rmd". Position of QTLs found with MIM and CIM along the SNP genetic map LOD-1 QTL confidence intervals are represented by vertical bars, in red when detected by CIM on the SSR map, in pale blue when detected by MIM on the SSR map, in deep blue when detected by MIM on the SNP map. Trait name and percentage of variance explained are indicated next to confidence intervals. Only chromosomes with detected QTLs are drawn.
DOI: 10.35078/9tqs6y/zyblcn
title: Daniel Reiz B.jpg

description: :unav
DOI: 10.35078/nuvyw6/zbqfwc
title: Alair Vieira B.jpg

description: :unav
DOI: 10.15454/nouqy2/l9wrwy
title: launch_cv_RD.sh

description: Bash script for launching genomic prediction with experimental data. The bash script creates a script per method and predictor matrix (genotypic data), the job is then launched on an analysis cluster with the command 'qsub'.
DOI: 10.35078/hujihe/xpvxuu
title: Pereiras D.jpg

description: :unav
DOI: 10.15454/nouqy2/ljqhuq
title: classify_mrk-selection_simul.Rmd

description: This script loads the selected markers, generated in fit_mrk-selection_simul.Rmd and classifies selected markers in TP, FP, TN, FN. It generates the table "classification_results_GBS.tsv", the Figure 2 (ROC curve) and the Figure S11 (partial Area Under the Curve).
DOI: 10.35078/9tqs6y/zxk6ua
title: Cascalho B.jpg

description: :unav
DOI: 10.35078/nuvyw6/fwke88
title: Vila Martins Bairro B.jpg

description: :unav
DOI: 10.15454/nouqy2/lnwnou
title: get_colours.R

description: This R script contains is used to get colours associated with each method for plotting.
DOI: 10.35078/hujihe/mcnuxg
title: Vargem do Pilão A.jpg

description: :unav
DOI: 10.15454/nouqy2/lzlqeo
title: SxG_Doligez2013_ordered-genos-design-mat.tab

description: This text file is the design matrix for coding additive and dominance effects, markers are ordered according to the genetic map. This file has been created in `create_diffX_GP.Rmd`.
DOI: 10.35078/9tqs6y/2e2fwo
title: Palmital A.jpg

description: :unav
DOI: 10.35078/nuvyw6/5zhd7l
title: Francisco Menta A.jpg

description: :unav
DOI: 10.15454/nouqy2/mbjysv
title: compare_mrk-selection_RDpharch_GBS_LD.Rmd

description: This script compares marker selection for all methods. It characterizes markers selected by several methods, for that, it extends marker selection to close markers (i.e. with high linkage disequilibrium) and defines the 25 most reliable QTLs. It generates "most_reliable_QTLs.tsv", the Figure 4, TableS15, Figure S16.
DOI: 10.35078/hujihe/xfmsx0
title: Curtume C.jpg

description: :unav
DOI: 10.15454/nouqy2/msnv2m
title: cv_simul-data_diff-h2_JJ.Rmd

description: This script creates simulated phenotypic values for the Syrah x Grenache progeny. It takes as input `SxG.allelic-effects.txt` with additive and dominance allelic effects. It simulates multivariate phenotypic data (BLUPs) with different heritability values among the two traits (0.1 and 0.5) and for two QTL numbers (20 and 200) using the function _SimulResponse_ from `Function4GenoClass.R`. This script is used with a bash script to create one script per configuration and simulation repetition. The simulated data are saved in *Rdata* format and in table with phenotypic values (y) and true marker effect (B) for both responses and all heritability values (e.g. `same_minor_diff-h2_JJ_GBS_2.tsv` and `same_minor_diff-h2_JJ_GBS_2.Rdata` for same and minor configuration, repetition 2).
DOI: 10.15454/nouqy2/nk8kgm
title: SxG_Doligez-et-al-2013.qua

description: Text file with genotype names and a single fake phenotype in Joinmap format, for running R/qtl.
DOI: 10.35078/9tqs6y/kis52z
title: Contenda B.jpg

description: :unav
DOI: 10.35078/nuvyw6/xt34mz
title: Ornélio de Paula Oliveira B.jpg

description: :unav
DOI: 10.15454/nouqy2/nwpjxe
title: cv_MIM_RD.Rmd

description: For each following scripts, the input files are the genetic map (SSR or GBS) and the phenotypic (BLUP) data (`SxG_pharch_BLUPs.tsv`). Each script generates a "tsv" file (e.g. `MIM_results_RDpharch_new_GBS.tsv`) with Pearson's correlation, Spearman's correlation, bias, regression coefficient, etc for all cross-validation folds and responses.
DOI: 10.35078/hujihe/vp5zmh
title: João da Silva C.jpg

description: :unav
DOI: 10.15454/nouqy2/ocqblu
title: SxG_GBS.qua

description: Text file in R/qtl format for creating the cross object of the SNP map (available at https://data.inrae.fr/privateurl.xhtml?token=782ff6ff-d79c-4714-b0da-b85c5a4514a5).
DOI: 10.35078/9tqs6y/tfhj3f
title: Pedra Branca D.jpg

description: :unav
DOI: 10.35078/nuvyw6/dqgdg7
title: Antônio Menta B.jpg

description: :unav
DOI: 10.15454/nouqy2/oinsqf
title: SxG.allelic-effects_dominance-removed.txt

description: This text file is the design matrix for coding additive allelic effects with the SNP markers. This file has been created in `create_diffX_GP.Rmd`.
DOI: 10.35078/hujihe/4uv7cn
title: São João A.jpg

description: :unav
DOI: 10.15454/nouqy2/pun21u
title: bash_mrk_sim.sh

description: Bash script for launching data simulation and genomic prediction with default parameters, repeated 10 times. The bash script create a script per takes simulation repetition and configuration, the job is then launched on an analysis cluster with the command 'qsub'.
DOI: 10.35078/nuvyw6/jruzpr
title: João Zizico A.jpg

description: :unav
DOI: 10.15454/nouqy2/qijtm9
title: cv_EN_simul.Rmd

description: For each script "cv_xx_simul.Rmd", we apply cross-validation on simulated data. The input files are the simulated data and the genetic map (SSR or GBS). Each script generates a "tsv" file (e.g. "EN_results_same_minor_2.tsv") with Pearson's correlation, Spearman's correlation, bias, regression coefficient, etc for all cross-validation folds and responses. All these scripts are run with a bash script which generate one script per QTL number and simulation repetition.
DOI: 10.35078/9tqs6y/vmisoy
title: Arataca B.jpg

description: :unav
DOI: 10.35078/hujihe/30igqf
title: Água Limpa I. B.jpg

description: :unav
DOI: 10.35078/nuvyw6/mqoqff
title: José Campos B.jpg

description: :unav
DOI: 10.15454/nouqy2/qrukr0
title: compare_maps_SSR-GBS.png

description: Comparison of SSR and SNP consensus genetic maps of a pseudo-F1 V. vinifera population, obtained by plotting genetic positions as a function of physical positions for each chromosome. The position of the SSR marker indicated by a triangle on chromosome 12 was uncertain.
DOI: 10.35078/9tqs6y/fur48w
title: Ribeirão B.jpg

description: :unav
DOI: 10.15454/nouqy2/r1gvbs
title: SxG_GBS.loc

description: Text file in R/qtl format for creating the cross object of the SNP map (available at https://data.inrae.fr/privateurl.xhtml?token=782ff6ff-d79c-4714-b0da-b85c5a4514a5).