cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.35078/ofbtbf/iychu0
title: Daniel Dias B.jpg

description: :unav
DOI: 10.15454/ngbspc/au8dvh
title: Genecatalog_CAZy.tab

description: :unav
DOI: 10.15454/ngbspc/bowlwn
title: Genecatalog_eggNog_full_lineage.tsv

description: :unav
DOI: 10.35078/9tqs6y/xr9cfo
title: Vista Alegre A.jpg

description: :unav
DOI: 10.35078/hujihe/u3pl8i
title: Jenipapo A.jpg

description: :unav
DOI: 10.35078/ofbtbf/tnn4nb
title: Sebastião Paula B.jpg

description: :unav
DOI: 10.15454/ngbspc/bphsrh
title: Genecatalog_count_KO_sample.tab

description: :unav
DOI: 10.35078/9tqs6y/6rcex5
title: Santa Cruz Faz. A.jpg

description: :unav
DOI: 10.15454/ngbspc/bz1fgz
title: Genecatalog_KO.tab

description: :unav
DOI: 10.35078/hujihe/tazdkn
title: Mosquito D.jpg

description: :unav
DOI: 10.15454/ngbspc/cvvysq
title: Genecatalog_Nmapped_reads.tsv.gz

description: :unav
DOI: 10.35078/ofbtbf/yopobv
title: Domingos Viamão Sítio B.jpg

description: :unav
DOI: 10.15454/ngbspc/d4fadu
title: Genecatalog.nr_euk.kaiju.html

description: :unav
DOI: 10.35078/9tqs6y/sca1xl
title: Casa da Mata A.jpg

description: :unav
DOI: 10.15454/ngbspc/ent36v
title: MAG_genome_completeness.tab

description: :unav
DOI: 10.35078/hujihe/fzn6h7
title: Viana D.jpg

description: :unav
DOI: 10.15454/ngbspc/f765i5
title: MAG_sequences.tar.gz

description: :unav
DOI: 10.35078/9tqs6y/ceo9vy
title: Cachoeira I. B.jpg

description: :unav
DOI: 10.35078/ofbtbf/esfx9h
title: Joaquim Pedro da Silva A.jpg

description: :unav
DOI: 10.15454/ngbspc/hzcw2s
title: ATLAS_assembly_report.html

description: ATLAS report
DOI: 10.35078/9tqs6y/d5ytsd
title: Macuco B.jpg

description: :unav
DOI: 10.35078/hujihe/yombyf
title: Mocó B.jpg

description: :unav
DOI: 10.15454/ngbspc/ief4ru
title: Genecatalog_median_coverage.tsv.gz

description: :unav
DOI: 10.35078/9tqs6y/u0tcfh
title: Lapinha B.jpg

description: :unav
DOI: 10.35078/ofbtbf/ucgj9s
title: Córrego Fundo A.jpg

description: :unav
DOI: 10.15454/ngbspc/ipmnbt
title: ATLAS_QC_report.html

description: ATLAS report
DOI: 10.35078/hujihe/fzgda9
title: Itapecuru A.jpg

description: :unav
DOI: 10.15454/ngbspc/jvy8xf
title: Genecatalog_with-note.fna.gz

description: :unav
DOI: 10.35078/ofbtbf/hegggw
title: Cachoeira Grande II A.jpg

description: :unav
DOI: 10.15454/ngbspc/kluxv2
title: notebook.Rmd

description: complete rmarkdown analysis report
DOI: 10.35078/9tqs6y/cia73r
title: Curtume B.jpg

description: :unav
DOI: 10.35078/hujihe/ezonoq
title: Canta Galo A.jpg

description: :unav
DOI: 10.15454/ngbspc/lj5cbg
title: MAG_median_coverage_genomes.tsv

description: :unav
DOI: 10.35078/ofbtbf/axpebk
title: Jorge Silva B.jpg

description: :unav
DOI: 10.15454/ngbspc/lj8bcx
title: ATLAS_config.yaml

description: ATLAS config file
DOI: 10.35078/9tqs6y/9b7oi0
title: Bento Raimundo B.jpg

description: :unav
DOI: 10.35078/hujihe/g7o1vy
title: Barra do Córrego Machado D.jpg

description: :unav
DOI: 10.15454/ngbspc/mfnibv
title: MAG_taxonomy.tab

description: :unav
DOI: 10.15454/ngbspc/pap7n5
title: raw-samples.nr_euk.kaiju.html

description: :unav
DOI: 10.15454/ngbspc/rkqiz1
title: Genecatalog.get_lineage.py

description: :unav
DOI: 10.35078/hujihe/5rbxk3
title: Lapinha C.jpg

description: :unav
DOI: 10.35078/ofbtbf/l2saoo
title: Antônio Vieira B.jpg

description: :unav
DOI: 10.15454/ngbspc/rttovx
title: MAG_raw_counts_genomes.tab

description: :unav
DOI: 10.35078/9tqs6y/ycq8ej
title: Capoeirão A.jpg

description: :unav
DOI: 10.35078/hujihe/dhtd26
title: Chapada C.jpg

description: :unav
DOI: 10.35078/ofbtbf/d1y4hz
title: São Geraldo Bairro B.jpg

description: :unav
DOI: 10.15454/ngbspc/s5oemi
title: MAG_count_CAZy.tab

description: :unav
DOI: 10.15454/ngbspc/tsttoa
title: Genecatalog_core.fna

description: :unav
DOI: 10.35078/ofbtbf/c5xyzq
title: Cachoeira Grande II B.jpg

description: :unav
DOI: 10.15454/ngbspc/ulpulh
title: Ecaomic_dominant_phylotypes_nonrariefied.rds

description: phyloseq object
DOI: 10.35078/9tqs6y/4nrxol
title: Arataca II. A.jpg

description: :unav
DOI: 10.35078/hujihe/5ond31
title: Juscelino Viana B.jpg

description: :unav
DOI: 10.15454/ngbspc/zq3jgq
title: ATLAS_dag.pdf

description: snakemake DAG
DOI: 10.35078/9tqs6y/zegkv7
title: Vista Alegre B.jpg

description: :unav
DOI: 10.35078/ofbtbf/glpuzf
title: Neném Leão A.jpg

description: :unav
DOI: 10.15454/nhhrsr/s2a2dw
title: rpg_complete_2019_d63.zip

description: :unav
DOI: 10.35078/hujihe/cyu2vy
title: Pôrto do Rosário A.jpg

description: :unav
DOI: 10.35078/9tqs6y/0gjjsg
title: Pimenta A.jpg

description: :unav
DOI: 10.35078/ofbtbf/xgxbmq
title: Cabeceira São Matias Grande A.jpg

description: :unav
DOI: 10.35078/hujihe/ockyhm
title: Tocoiós C.jpg

description: :unav
DOI: 10.35078/9tqs6y/gp7bnp
title: Estiva A.jpg

description: :unav
DOI: 10.35078/hujihe/ayinzi
title: Malhadão A.jpg

description: :unav
DOI: 10.35078/ofbtbf/xqxf3z
title: Vargem do Bode A.jpg

description: :unav
DOI: 10.35078/9tqs6y/i2byn9
title: Ribeirão A.jpg

description: :unav
DOI: 10.35078/ofbtbf/cfglfe
title: São Pedro Taperão Pov. B.jpg

description: :unav
DOI: 10.35078/hujihe/fmykyr
title: Pôrto do Rosário C.jpg

description: :unav
DOI: 10.35078/9tqs6y/0k5j1l
title: Córrego Rafael B.jpg

description: :unav
DOI: 10.35078/ofbtbf/6cyt0k
title: Álvaro Teodoro A.jpg

description: :unav
DOI: 10.35078/9tqs6y/4mvpwg
title: Machado B.jpg

description: :unav
DOI: 10.35078/hujihe/ahmg7k
title: Curtume A.jpg

description: :unav
DOI: 10.35078/hujihe/ujgef6
title: Olhos D'água III. D.jpg

description: :unav
DOI: 10.35078/ofbtbf/nrdbn6
title: Bento Vieira Sítio B.jpg

description: :unav
DOI: 10.35078/9tqs6y/9ravsq
title: Ranca Toco B.jpg

description: :unav
DOI: 10.35078/hujihe/dk1jri
title: Vinícius Gomes A.jpg

description: :unav
DOI: 10.35078/ofbtbf/wf4h9t
title: Sebastião Paula A.jpg

description: :unav
DOI: 10.35078/9tqs6y/8egkix
title: Córrego Rafael A.jpg

description: :unav
DOI: 10.35078/ofbtbf/phiaaj
title: Nacip Raydan Cid. B.jpg

description: :unav
DOI: 10.35078/hujihe/ojppts
title: José Maria Miranda C.jpg

description: :unav
DOI: 10.35078/9tqs6y/hnyi1x
title: Vargem do Bom Sucesso B.jpg

description: :unav
DOI: 10.35078/ofbtbf/ihxn3n
title: Santos Nogueira A.jpg

description: :unav
DOI: 10.35078/hujihe/ujvuoq
title: Matinada A.jpg

description: :unav
DOI: 10.35078/9tqs6y/nuguc7
title: Fazenda Velha B.jpg

description: :unav
DOI: 10.35078/ofbtbf/sxjbif
title: Jandira B.jpg

description: :unav
DOI: 10.35078/hujihe/p5h6mj
title: Funil A.jpg

description: :unav
DOI: 10.35078/9tqs6y/8is3io
title: Pinho B.jpg

description: :unav
DOI: 10.35078/ofbtbf/v30ugk
title: Avelino Cardoso A.jpg

description: :unav
DOI: 10.35078/hujihe/9ldp9i
title: Manoel Lopes Leite B.jpg

description: :unav
DOI: 10.35078/ofbtbf/wgoszm
title: São Geraldo Bairro A.jpg

description: :unav
DOI: 10.35078/9tqs6y/9xwt4c
title: Gororós D.jpg

description: :unav
DOI: 10.35078/hujihe/j3s4zj
title: Cabeceira Córrego João Gomes A.jpg

description: :unav
DOI: 10.35078/9tqs6y/w1w8cx
title: Engenho A.jpg

description: :unav
DOI: 10.35078/ofbtbf/mxjcoe
title: Bananal Bom Jardim B.jpg

description: :unav
DOI: 10.35078/hujihe/ibe0tp
title: Barreiro Faz. B.jpg

description: :unav
DOI: 10.35078/9tqs6y/tyintq
title: Purgatório A.jpg

description: :unav
DOI: 10.25345/c51v5bh9j
title: MassIVE MSV000089355 - Cover_Crop_Root_Exudates_GC-MS
title: 19 cover crops species root exudates were characterized by GC-MS for chemical characterization of the root exudate profiles across different agricultural crops grown hydroponically.
DOI: 10.35078/hujihe/n46jqb
title: Córrego do Pedro D.jpg

description: :unav
DOI: 10.35078/ofbtbf/j41bfw
title: Avelino Cardoso Sítio A.jpg

description: :unav
DOI: 10.35078/9tqs6y/bjtin6
title: Cachoeira A.jpg

description: :unav
DOI: 10.35078/ofbtbf/xhatti
title: Álvaro Teodoro B.jpg

description: :unav
DOI: 10.35078/hujihe/9wu0ub
title: Vargem da Páscoa I. B.jpg

description: :unav
DOI: 10.35078/9tqs6y/ibi1ec
title: Angu Cru A.jpg

description: :unav
DOI: 10.35078/ofbtbf/ofze80
title: Bananal Bom Jardim A.jpg

description: :unav
DOI: 10.35078/hujihe/axkd9q
title: Água Limpa I. D.jpg

description: :unav
DOI: 10.35078/ofbtbf/kkwouz
title: Vargem Grande B.jpg

description: :unav
DOI: 10.35078/9tqs6y/89wmcf
title: Pedra Branca C.jpg

description: :unav
DOI: 10.35078/hujihe/fgol9r
title: Santa Polônia C.jpg

description: :unav
DOI: 10.35078/ofbtbf/e5lhf7
title: Juarez Francisco Souto B.jpg

description: :unav
DOI: 10.35078/hujihe/t7acdz
title: Joaquim Rodrigues C.jpg

description: :unav
DOI: 10.35078/ofbtbf/rgpxfe
title: Cachoeira Grande I A.jpg

description: :unav
DOI: 10.35078/9tqs6y/m9iswd
title: Carambola A.jpg

description: :unav
DOI: 10.35078/hujihe/kaxtk0
title: Nunes C.jpg

description: :unav
DOI: 10.35078/ofbtbf/f8lcki
title: Manoel Pereira A.jpg

description: :unav
DOI: 10.35078/9tqs6y/ru7kuh
title: Cedro A.jpg

description: :unav
DOI: 10.35078/hujihe/ns8qfg
title: Chapadão II. B.jpg

description: :unav
DOI: 10.35078/ofbtbf/c3p8ub
title: São Matias A.jpg

description: :unav
DOI: 10.35078/9tqs6y/auwbid
title: Saca Pó B.jpg

description: :unav
DOI: 10.35078/hujihe/rdocra
title: Patrimônio A.jpg

description: :unav
DOI: 10.35078/ofbtbf/ohkyt1
title: Manoel Pereira B.jpg

description: :unav
DOI: 10.35078/hujihe/a5bshi
title: Chapadão I. D.jpg

description: :unav
DOI: 10.35078/9tqs6y/xss86n
title: G. da Folheta B.jpg

description: :unav
DOI: 10.35078/ofbtbf/j1ujza
title: Aurélio Madeira A.jpg

description: :unav
DOI: 10.35078/9tqs6y/abhcth
title: Chambá C.jpg

description: :unav
DOI: 10.35078/hujihe/focubv
title: Barra do Córrego São João I. A.jpg

description: :unav
DOI: 10.35078/ofbtbf/xdewrc
title: Avelino Cardoso B.jpg

description: :unav
DOI: 10.35078/hujihe/36qoi4
title: Itapicuru B.jpg

description: :unav
DOI: 10.35078/ofbtbf/g5ivu7
title: Domingos Viamão B.jpg

description: :unav
DOI: 10.35078/9tqs6y/vi6yih
title: Derrubada B.jpg

description: :unav
DOI: 10.35078/hujihe/nd4yrl
title: Vargem do Fernando C.jpg

description: :unav
DOI: 10.35078/ofbtbf/szktk5
title: Rosinha B.jpg

description: :unav
DOI: 10.35078/9tqs6y/cq4591
title: Angu Cru B.jpg

description: :unav
DOI: 10.35078/hujihe/rxhtso
title: Sucuruí A.jpg

description: :unav
DOI: 10.35078/ofbtbf/ixsraj
title: Santos Nogueira B.jpg

description: :unav
DOI: 10.15454/nm3wet/7iydpx
title: Plastic not closed consumers' arguments_17_04_20.csv

description: Data associated to the table in csv format
DOI: 10.35078/9tqs6y/bmbexq
title: Ranca Toco C.jpg

description: :unav
DOI: 10.35078/hujihe/stbxhb
title: Clemente Lima C.jpg

description: :unav
DOI: 10.15454/nm3wet/b5dtwd
title: Plastic not closed consumers' arguments_13_12_19.csv

description: Data associated to the table in csv format
DOI: 10.35078/ofbtbf/xbepwh
title: Jandira A.jpg

description: :unav
DOI: 10.15454/nm3wet/maiz3w
title: Plastic not closed consumers' arguments_13_12_19.owl

description: Data associated to the table in owl format
DOI: 10.35078/9tqs6y/t54cre
title: Cachoeira II. B.jpg

description: :unav
DOI: 10.15454/nnj75s/yofx3y
title: Laboratory_data_MerinoMartin_et_al_SBB_2020.tab

description: :unav
DOI: 10.35078/hujihe/fblkoz
title: Geraldo Leite A.jpg

description: :unav
DOI: 10.35078/ofbtbf/rstl4g
title: Avelino Cardoso Sítio B.jpg

description: :unav
DOI: 10.15454/no7azk/fjksii
title: rpg_complete_2018_d88.zip

description: :unav
DOI: 10.35078/9tqs6y/j5esbk
title: Bonito C.jpg

description: :unav
DOI: 10.35078/hujihe/pdttjb
title: Vargem do Fernando D.jpg

description: :unav
DOI: 10.35078/ofbtbf/dcsnvd
title: Neném Leão B.jpg

description: :unav
DOI: 10.15454/not2lh/1gklhp
title: res_up_J2vsW_biological_process_raw.xls

description: All differentially represented Biological Process GO terms in genes upregulated
DOI: 10.35078/hujihe/udmktj
title: Itapicuru A.jpg

description: :unav
DOI: 10.15454/not2lh/2kd60w
title: res_up_J2vsW_molecular_function_raw.xls

description: All differentially represented Molecular Function GO terms in genes upregulated
DOI: 10.35078/9tqs6y/exmbct
title: Galvão Faz. A.jpg

description: :unav
DOI: 10.35078/ofbtbf/ulpodn
title: Jorge Silva A.jpg

description: :unav
DOI: 10.15454/not2lh/9lcq98
title: res_up_J2vsW_biological_process_overrep.xls

description: Overrepresented Biological Process GO terms in genes upregulated
DOI: 10.15454/not2lh/ochabh
title: res_up_J2vsW_molecular_function_overrep.xls

description: Overrepresented Molecular Function GO terms in genes upregulated
DOI: 10.35078/9tqs6y/8jrfqm
title: Gaia A.jpg

description: :unav
DOI: 10.35078/hujihe/vrhqlu
title: Igrejinha Faz. C.jpg

description: :unav
DOI: 10.35078/ofbtbf/tksko3
title: Córrego Fundo B.jpg

description: :unav
DOI: 10.15454/not2lh/qiwup8
title: res_up_J2vsW_cellular_component_overrep.xls

description: Overrepresented Cellular Component GO terms in genes upregulated
DOI: 10.35078/hujihe/wtt3co
title: Funil C.jpg

description: :unav
DOI: 10.35078/ofbtbf/abu3nn
title: Daniel Dias A.jpg

description: :unav
DOI: 10.15454/not2lh/qqzv0u
title: res_up_J2vsW_cellular_component_raw.xls

description: All differentially represented Cellular Component GO terms in genes upregulated
DOI: 10.35078/9tqs6y/rezpvm
title: Sapê B.jpg

description: :unav
DOI: 10.35078/ofbtbf/gze6w0
title: Aurélio Madeira B.jpg

description: :unav
DOI: 10.15454/not2lh/vxipj1
title: res_up_J2vsW_biological_process_underrep.xls

description: Under-represented Biological Process GO terms in genes upregulated
DOI: 10.35078/hujihe/t09vrk
title: João da Serra B.jpg

description: :unav
DOI: 10.15454/not2lh/xlkhql
title: res_up_J2vsW_cellular_component_underrep.xls

description: Under-represented Cellular Component GO terms in genes upregulated
DOI: 10.15454/not2lh/xmpx2s
title: res_up_J2vsW_molecular_function_underrep.xls

description: Under-represent Molecular function GO terms in genes upregulated
DOI: 10.35078/9tqs6y/ewilr6
title: Chambá B.jpg

description: :unav
DOI: 10.35078/ofbtbf/kw5b0v
title: São Matias B.jpg

description: :unav
DOI: 10.15454/nouqy2/1qr8zr
title: cv_MTV_LASSO_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_LASSO_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: 10.35078/9tqs6y/qbukr1
title: Romana C.jpg

description: :unav
DOI: 10.35078/hujihe/4amsuh
title: Bela Vista Faz. B.jpg

description: :unav
DOI: 10.15454/nouqy2/1rinkn
title: compare_mrk-selection_RD_mapping_IM-methods.Rmd

description: This script compares QTLs from Coupel-Ledru et al., (2014,2016) with SIM and MIM QTLs, for both genetic maps (SSR and SNP). It generates the Figure "MapGBS_CIM.SSR_MIM.SSR_MIM.GBS.pdf" (position of QTLs from MIM SNP and CIM SSR along the genetic map), Figure "boxplot_perc.var_CIM_MIM_common-QTLs.png" (percentage of variance explained for all selected markers in all traits according to method selection).
DOI: 10.35078/ofbtbf/aqw4pv
title: Vargem do Bode B.jpg

description: :unav
DOI: 10.3217/d37gw-fkx65
title: Supplementary Data to Publication: Additive Manufacturing of an Fe-Cr-Co permanent magnet alloy with a novel approach of in-situ alloying

description: This data set serves as supplementary data for a publication with the title "Additive Manufacturing of an Fe-Cr-Co permanent magnet alloy with a novel approach of in-situ alloying" to be published in the European Journal of Materials (Taylor&Francis).
DOI: 10.35078/9tqs6y/fae3jf
title: Paiol A.jpg

description: :unav
DOI: 10.15454/nouqy2/2n5bkh
title: cv_SIM_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. "SIM_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/hujihe/vzmynm
title: Salitre D.jpg

description: :unav
DOI: 10.15454/nouqy2/45p9ll
title: cv_MTV_LASSO_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_LASSO_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/ofbtbf/9ywmy8
title: Nacip Raydan Cid. A.jpg

description: :unav
DOI: 10.15454/nouqy2/4fhak4
title: cv_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. "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/ckfo29
title: Pitanga B.jpg

description: :unav
DOI: 10.35078/hujihe/7cxkma
title: José Maria Miranda B.jpg

description: :unav
DOI: 10.15454/nouqy2/56wgta
title: cv_MTV_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. "MTV_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/ofbtbf/mwx6jk
title: Juarez Francisco Souto A.jpg

description: :unav
DOI: 10.15454/nouqy2/5tgvjw
title: cv_EN_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. "EN_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: 10.35078/9tqs6y/ocjrws
title: Córrego Branco B.jpg

description: :unav
DOI: 10.35078/hujihe/i8ffzb
title: Geraldo Leite D.jpg

description: :unav
DOI: 10.15454/nouqy2/6h4jqz
title: boxplot_perc.var_CIM_MIM_common-QTLs.png

description: This figure has been generated in `compare_mrk-selection_RD_mapping_IM-methods.Rmd`. Distribution of percentage of variance explained by CIM SSR QTLs, according to other methods detecting them Categories on x-axis: CIM SSR only: QTLs detected only by Coupel-Ledru et al. (2014, 2016); CIM SSR & MIM SSR or MIM SNP: QTLs detected by Coupel-Ledru et al. (2014, 2016) and MIM SSR or MIM SNP in the present study; all: QTLs detected by all three methods. Percentage of variance are those for the CIM SSR QTL from Coupel-Ledru et al. (2014, 2016).
DOI: 10.35078/ofbtbf/uofgog
title: Cachoeira Grande I B.jpg

description: :unav
DOI: 10.15454/nouqy2/6okqtv
title: cv_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/luq7uv
title: Paineira A.jpg

description: :unav
DOI: 10.35078/ofbtbf/on8v9c
title: Gentil Parrudo B.jpg

description: :unav
DOI: 10.15454/nouqy2/7p62bx
title: cv_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. "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/hujihe/zqojrv
title: Itapicuri de Cima B.jpg

description: :unav
DOI: 10.15454/nouqy2/8kptcn
title: plot_corP_pharch_comp_xdata_mean-resp.png

description: Mean predictive ability across traits according to input matrix data Mean Pearson’s correlation between predicted and observed genotypic values (BLUPs of phenotypic data) for different design matrix as input for 10 methods. Results were averaged across the 14 traits x 10 CV-replicates x 5 CV-folds. For IM methods, input data are in R/qtl format. For spring, only the smallest design matrix were tested because of the high computationnal cost. Input matrices tested: * SSR add: design matrix with multi-allelic SSR markers with additive effects. * SSR dom: design matrix with multi-allelic SSR markers with additive and dominance effects. * SNP raw: gene dose from all markers in the filtered vcf (17,298 markers). * SNP gene-dose: gene dose recoded from the multi-allelic SNP markers, imputed with Lep-MAP3. * SNP add: design matrix with multi-allelic SNP markers with additive effects, imputed with Lep-MAP3. * SNP add dom: design matrix with multi-allelic SNP markers with additive and dominance effects, imputed with Lep-MAP3
DOI: 10.35078/9tqs6y/mdct2n
title: Paulo XIXI B.jpg

description: :unav
DOI: 10.35078/ofbtbf/gso1ok
title: Juquinha Batista B.jpg

description: :unav
DOI: 10.15454/nouqy2/8l3zyv
title: cv_LASSO_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_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/ntezyf
title: Campestre B.jpg

description: :unav
DOI: 10.15454/nouqy2/9apbj3
title: cv_LASSO.GB_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. "LASSO.GB_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/ofbtbf/gkxcno
title: Bento Vieira Sítio A.jpg

description: :unav
DOI: 10.15454/nouqy2/9frgzi
title: genetic_map_phys-gen_SxG_SSR.tab

description: Table which combines information with genetic and physical position of markers for the SSR genetic map. This file has been created in "create_diffX_GP.Rmd". The physical positions of SSR markers absent from the latest URGI JBrowse were retrieved by aligning their forward primer with BLAST (Altchul et al, 1990) on the PN40024 12X.v2 reference sequence (Canaguier et al, 2017) using default parameter values, except for Expect threshold which was set to 1 or 10. Physical positions were still missing for six SSRs and one was uncertain (high Expect value).
DOI: 10.35078/9tqs6y/dfxkmu
title: Córrego do Feijão D.jpg

description: :unav
DOI: 10.35078/hujihe/rqcxmi
title: Cabeceira Córrego Dundia A.jpg

description: :unav