cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15454/dbtalb/h5qelr
title: coef pasim.tab

description: Coefficients de dilatation utilisés pour étendre la surface des modes d'exploitation dominants de la PP à toute la surface en PP de l'UPC. Coefficients de correction utilisés pour passer des surfaces en prairies permanentes simulées par le modèle PaSim dans la région, à la surface régionale réelle en PP issue des statistiques publiques. Ratio used to extend the land use of dominant grassland management systems to the whole permanent grassland area of the PCU. Ratio used to correct regional simulated permanent grassland areas in order to be compatible with national statistics.
DOI: 10.15454/dbtalb/n2ehks
title: coef stics ratio de correction.tab

description: Coefficients de correction utilisés pour passer des surfaces des cultures simulées par le modèle STICS dans la région, à la surface régionale réelle des cultures issue des statistiques publiques. Ratio used to correct regional simulated crop land use in order to be compatible with national statistics.
DOI: 10.15454/dbtalb/o5d1oe
title: coef stics dilat.tab

description: Coefficients de dilatation utilisés pour étendre la surface des séquences de culture dominantes à toute la surface cultivée de l'UPC. Ratio used to extend the land use of dominant crop rotations to all the PCU cropland.
DOI: 10.15454/dbtalb/ojul03
title: tableau_de_passage.tab

description: Output of Tableau de passage script.R
DOI: 10.15454/dbtalb/twx5qo
title: tableau_transversal_ligne_base.csv

description: input of Tableau de passage script.R
DOI: 10.15454/dc9pyl/muuf6l
title: Plastic rigid lid consumers' arguments_13_12_19.owl

description: Data associated to the table in owl format
DOI: 10.15454/dc9pyl/pnholn
title: Plastic rigid lid consumers' arguments_13_12_19.csv

description: Data associated to the table in csv format
DOI: 10.15454/dd9j5t/a3k3x6
title: 4.fboot.R

description: R-code to test the robustness of species clusterings. Plot the figures S6 of the paper submitted to Ecology. If "record.ON
DOI: 10.15454/dd9j5t/aof4rt
title: 1.format.R

description: R-code to format the Cedar Creek data. If "record.ON
DOI: 10.15454/dd9j5t/atyujx
title: 3.ftest.R

description: R-code to test the relative weight of each species, assemblage or year on the species clustering. If "record.ON
DOI: 10.15454/dd9j5t/dgnrq7
title: 2.fclust.R

description: R-code to compute the properties of experimental plots (interaction effect, composition effect and relative yield). Plot all the figures of the paper submitted to Ecology, except the figures S6. If "record.ON
DOI: 10.15454/dd9j5t/tfpuyl
title: functClust_0.1.6.tar.gz

description: Copy of the R-package also available at the R-CRAN repository.
DOI: 10.15454/dd9j5t/vnryzy
title: io.R

description: R-code used in the R-files "1.format.R", "2.fclust.R", "3.ftest.R" and "4.fboot.R". Load it using the code : source("io.R").
DOI: 10.15454/df0brl/0pzqdb
title: affil_summary.html

description: :unav
DOI: 10.15454/df0brl/0vvyn6
title: Multi-aff.Rmd

description: :unav
DOI: 10.15454/df0brl/2jgtwy
title: denombrements_levains.tab

description: :unav
DOI: 10.15454/df0brl/3mjtgd
title: demulti-aff_correc_ITS1.tab

description: :unav
DOI: 10.15454/df0brl/4gaubf
title: UniteCompleted_LVG.fasta.nos

description: :unav
DOI: 10.15454/df0brl/4ggpsx
title: multi.tab

description: :unav
DOI: 10.15454/df0brl/4rfzhg
title: dada2_ITS1_sgeerr.txt

description: :unav
DOI: 10.15454/df0brl/6q64tp
title: correc_species_names.R

description: :unav
DOI: 10.15454/df0brl/6svuy2
title: affil.biom

description: :unav
DOI: 10.15454/df0brl/8ig4mh
title: ITS1.fasta

description: :unav
DOI: 10.15454/df0brl/8xasfx
title: itsx.log

description: :unav
DOI: 10.15454/df0brl/8xpikg
title: functions_diversite.R

description: :unav
DOI: 10.15454/df0brl/9d5wrw
title: silva_138_16S_pintail100.fasta

description: :unav
DOI: 10.15454/df0brl/a264v1
title: demulti-sortie_ITS1.tab

description: :unav
DOI: 10.15454/df0brl/ade9yc
title: prepa_data_standard.R

description: :unav
DOI: 10.15454/df0brl/agb1yu
title: seqtab.biom

description: :unav
DOI: 10.15454/df0brl/araz9q
title: Echantillons_MiSeq.tab

description: :unav
DOI: 10.15454/df0brl/b9dane
title: affiliation.log

description: :unav
DOI: 10.15454/df0brl/bfutv0
title: Readme.md

description: :unav
DOI: 10.15454/df0brl/bycwxd
title: affil.biom

description: :unav
DOI: 10.15454/df0brl/cjmpbe
title: affiliation.log

description: :unav
DOI: 10.15454/df0brl/daa1um
title: communes-departement-region.tab

description: :unav
DOI: 10.15454/df0brl/ds7nwf
title: Figures_StatTests.Rmd

description: :unav
DOI: 10.15454/df0brl/dtaw1q
title: silva_138_16S_pintail100.fasta.properties

description: :unav
DOI: 10.15454/df0brl/eescpx
title: tsv_to_biom.log

description: :unav
DOI: 10.15454/df0brl/egmt97
title: demulti-aff_correc_16S.tab

description: :unav
DOI: 10.15454/df0brl/fdinqi
title: quality_R2.pdf

description: :unav
DOI: 10.15454/df0brl/ff4l7u
title: UniteCompleted_LVG.fasta.ndb

description: :unav
DOI: 10.15454/df0brl/g0guy1
title: biom_to_tsv.log

description: :unav
DOI: 10.15454/df0brl/g5i56b
title: seqtab.biom

description: :unav
DOI: 10.15454/df0brl/gdguqn
title: demulti-aff_ITS1.tab

description: :unav
DOI: 10.15454/df0brl/gjsv8y
title: seqtab_tobiom.tab

description: :unav
DOI: 10.15454/df0brl/gzrbmf
title: dada2_LVG.R

description: :unav
DOI: 10.15454/df0brl/ho4ld7
title: dada2_ASV.fasta

description: :unav
DOI: 10.15454/df0brl/ibebb2
title: denombr_gluten.csv

description: :unav
DOI: 10.15454/df0brl/ipve85
title: silva_138_16S_pintail100.fasta.nhr

description: :unav
DOI: 10.15454/df0brl/j4xh2d
title: UniteCompleted_LVG.fasta.not

description: :unav
DOI: 10.15454/df0brl/jgeu43
title: track_reads.csv

description: :unav
DOI: 10.15454/df0brl/kcresj
title: dada2.tab

description: :unav
DOI: 10.15454/df0brl/lbx7uc
title: demulti-aff_16S.tab

description: :unav
DOI: 10.15454/df0brl/ll9qxt
title: UniteCompleted_LVG.fasta.nin

description: :unav
DOI: 10.15454/df0brl/m6surz
title: dada2_ASV.fasta

description: :unav
DOI: 10.15454/df0brl/m86gj3
title: silva_138_16S_pintail100.fasta.nin

description: :unav
DOI: 10.15454/df0brl/mkumu9
title: track_reads.csv

description: :unav
DOI: 10.15454/df0brl/mvkw78
title: corresp_names_bact.tab

description: :unav
DOI: 10.15454/df0brl/ndo8oe
title: UniteCompleted_LVG.fasta.ntf

description: :unav
DOI: 10.15454/df0brl/ngpxhl
title: demulti-sortie_16S.tab

description: :unav
DOI: 10.15454/df0brl/njzehw
title: UniteCompleted_LVG.fasta.nsq

description: :unav
DOI: 10.25345/c5nk3687v
title: MassIVE MSV000089358 - GNPS Visualisation Test Attempt 1
title: This is the first numbered attempt at figuring out why GNPS visualisation is failing. This .mzML file comes from MSV000089085 and can be visualised, hence it's use here. Unlike previous datasets, this dataset's files were transferred to GNPS using WinSCP
DOI: 10.15454/df0brl/noyasq
title: pratiques_boulang_full.csv

description: :unav
DOI: 10.15454/df0brl/nw92ko
title: UniteCompleted_LVG.fasta.nto

description: :unav
DOI: 10.15454/df0brl/oy14bv
title: functions_graphs.R

description: :unav
DOI: 10.15454/df0brl/oz0v3a
title: config.sh

description: :unav
DOI: 10.15454/df0brl/pbtlkp
title: multi.tab

description: :unav
DOI: 10.15454/df0brl/pewvln
title: quality_R2.pdf

description: :unav
DOI: 10.15454/df0brl/qwjcbr
title: tsv_to_biom.log

description: :unav
DOI: 10.15454/df0brl/qzou1u
title: corresp_names_lev.tab

description: :unav
DOI: 10.15454/df0brl/rg9kon
title: itsx_summary.html

description: :unav
DOI: 10.15454/df0brl/rnyl9k
title: UniteCompleted_LVG.fasta

description: :unav
DOI: 10.15454/df0brl/rqjrg5
title: ITS1.biom

description: :unav
DOI: 10.15454/df0brl/rr5ogc
title: run.sh

description: :unav
DOI: 10.15454/df0brl/rthzca
title: silva_138_16S_pintail100.tax

description: :unav
DOI: 10.15454/df0brl/sfg8gv
title: silva_138_16S_pintail100.fasta.nsq

description: :unav
DOI: 10.15454/df0brl/slrg0r
title: function_demulti-aff.R

description: :unav
DOI: 10.15454/df0brl/tbrdna
title: quality_R1.pdf

description: :unav
DOI: 10.15454/df0brl/tgirzn
title: quality_R1.pdf

description: :unav
DOI: 10.15454/df0brl/tif67o
title: dada2_16S_sgeerr.txt

description: :unav
DOI: 10.15454/df0brl/u9uucc
title: track_reads.html

description: :unav
DOI: 10.15454/df0brl/urfbif
title: track_reads.html

description: :unav
DOI: 10.15454/df0brl/v5uw2e
title: Readme.md

description: :unav
DOI: 10.15454/df0brl/vfxqge
title: biom_to_tsv.log

description: :unav
DOI: 10.15454/df0brl/vnbspn
title: dada2_16S_sgelog.txt

description: :unav
DOI: 10.15454/df0brl/vse0w5
title: UniteCompleted_LVG.fasta.nog

description: :unav
DOI: 10.15454/df0brl/wetost
title: dada2.tab

description: :unav
DOI: 10.15454/df0brl/xi9o7g
title: dada2_ITS1_sgelog.txt

description: :unav
DOI: 10.15454/df0brl/yakyig
title: affil_summary.html

description: :unav
DOI: 10.15454/df0brl/ys43lv
title: seqtab_tobiom.tab

description: :unav
DOI: 10.15454/df0brl/zdsyeo
title: UniteCompleted_LVG.fasta.nhr

description: :unav
DOI: 10.15454/dgsnrg/0b4dfk
title: With_Rain.R

description: :unav
DOI: 10.15454/dgsnrg/0ueedh
title: With_Rain_1_125bars.R

description: :unav
DOI: 10.15454/dgsnrg/0wrwgb
title: With_Rain_2_018bars.R

description: :unav
DOI: 10.15454/dgsnrg/17vapo
title: With_Rain_1_025bars_BeforeRain.R

description: :unav
DOI: 10.15454/dgsnrg/1chzkc
title: With_Rain_1_025bars.R

description: :unav
DOI: 10.15454/dgsnrg/1exidd
title: With_Rain_2_14bars_BeforeRain.R

description: :unav
DOI: 10.15454/dgsnrg/1fnkql
title: With_Rain_2_04bars.R

description: :unav
DOI: 10.15454/dgsnrg/1h6omd
title: With_Rain_1_14bars.R

description: :unav
DOI: 10.15454/dgsnrg/1jv5po
title: With_Rain_4_125bars.R

description: :unav
DOI: 10.15454/dgsnrg/36wy1u
title: Without_Rain_2.R

description: :unav
DOI: 10.15454/dgsnrg/4lnijx
title: With_Rain_1_086bars.R

description: :unav
DOI: 10.15454/dgsnrg/4q2zw1
title: Without_Rain_2.R

description: :unav
DOI: 10.15454/dgsnrg/5ewsi0
title: With_Rain_2.R

description: :unav
DOI: 10.15454/dgsnrg/5jndsm
title: With_Rain_1_025bars.R

description: :unav
DOI: 10.15454/dgsnrg/5pdp7p
title: Sed_Exut_February.R

description: :unav
DOI: 10.15454/dgsnrg/6akrkz
title: With_Rain_1_04bars.R

description: :unav
DOI: 10.15454/dgsnrg/6spk58
title: With_Rain_4_125bars.R

description: :unav
DOI: 10.15454/dgsnrg/74xcge
title: With_Rain_1_06bars.R

description: :unav
DOI: 10.15454/dgsnrg/89ws4d
title: Without_Rain_1.R

description: :unav
DOI: 10.15454/dgsnrg/8cj4hk
title: With_Rain_4.R

description: :unav
DOI: 10.15454/dgsnrg/8gt7aa
title: With_Rain_2_14bars.R

description: :unav
DOI: 10.15454/dgsnrg/8kyzg7
title: With_Rain_3_125bars.R

description: :unav
DOI: 10.15454/dgsnrg/9tra67
title: With_Rain_3.R

description: :unav
DOI: 10.15454/dgsnrg/9yhsp5
title: With_Rain_4_125bars.R

description: :unav
DOI: 10.15454/dgsnrg/agutid
title: With_Rain_4.R

description: :unav
DOI: 10.15454/dgsnrg/amvfux
title: With_Rain_3_125bars.R

description: :unav
DOI: 10.15454/dgsnrg/apmv68
title: With_Rain_1_018bars.R

description: :unav
DOI: 10.15454/dgsnrg/b56ash
title: Without_Rain_3.R

description: :unav
DOI: 10.15454/dgsnrg/b80kns
title: With_Rain_1_086bars_DuringRain.R

description: :unav
DOI: 10.15454/dgsnrg/bey88h
title: With_Rain_1_125bars.R

description: :unav
DOI: 10.15454/dgsnrg/bi4zgz
title: Without_Rain.R

description: :unav
DOI: 10.15454/dgsnrg/buawq8
title: With_Rain_3_125bars.R

description: :unav
DOI: 10.15454/dgsnrg/busjzg
title: With_Rain_2_018bars.R

description: :unav
DOI: 10.15454/dgsnrg/bv4ius
title: Without_Rain.R

description: :unav
DOI: 10.15454/dgsnrg/cacn7f
title: With_Rain_2_P018.R

description: :unav
DOI: 10.15454/dgsnrg/cdoxoh
title: With_Rain_1_025bars.R

description: :unav
DOI: 10.15454/dgsnrg/chff4d
title: With_Rain_2_04bars.R

description: :unav
DOI: 10.15454/dgsnrg/cmlss3
title: With_Rain_3.R

description: :unav
DOI: 10.15454/dgsnrg/d5ynoa
title: With_Rain_3.R

description: :unav
DOI: 10.15454/dgsnrg/drq0k9
title: With_Rain_1_04bars.R

description: :unav
DOI: 10.15454/dgsnrg/drrvk3
title: With_Rain_4_P125.R

description: :unav
DOI: 10.15454/dgsnrg/e0srb1
title: With_Rain_2_125bars.R

description: :unav
DOI: 10.15454/dgsnrg/ebuyww
title: With_Rain_1_06bars.R

description: :unav
DOI: 10.15454/dgsnrg/ecwlwx
title: With_Rain_4.R

description: :unav
DOI: 10.15454/dgsnrg/ejxmkh
title: With_Rain_2_14bars.R

description: :unav
DOI: 10.15454/dgsnrg/em6arj
title: Without_Rain.R

description: :unav
DOI: 10.15454/dgsnrg/epbvey
title: Without_Rain_3.R

description: :unav
DOI: 10.15454/dgsnrg/ewgfkz
title: Without_Rain_2.R

description: :unav
DOI: 10.15454/dgsnrg/fssko2
title: With_Rain_2_P086.R

description: :unav
DOI: 10.15454/dgsnrg/fu76mo
title: Without_Rain_1.R

description: :unav
DOI: 10.15454/dgsnrg/g49xuu
title: With_Rain_1_086bars.R

description: :unav
DOI: 10.15454/dgsnrg/gk30su
title: With_Rain_1_04bars.R

description: :unav
DOI: 10.15454/dgsnrg/gywlhg
title: With_Rain_1.R

description: :unav
DOI: 10.15454/dgsnrg/h9sz7u
title: With_Rain_1_025bars_DuringRain.R

description: :unav
DOI: 10.15454/dgsnrg/hm8tdz
title: With_Rain_1_06bars.R

description: :unav
DOI: 10.15454/dgsnrg/hmqiek
title: With_Rain_1_P125.R

description: :unav
DOI: 10.15454/dgsnrg/i6bptj
title: With_Rain_1_14bars_DuringRain.R

description: :unav
DOI: 10.15454/dgsnrg/ihdsfh
title: With_Rain_1_14bars_BeforeRain.R

description: :unav
DOI: 10.15454/dgsnrg/ijlqg0
title: With_Rain_1_018bars.R

description: :unav
DOI: 10.15454/dgsnrg/ilofpu
title: With_Rain_2_06bars.R

description: :unav
DOI: 10.15454/dgsnrg/jmxxm8
title: With_Rain_4.R

description: :unav
DOI: 10.15454/dgsnrg/k4wtzq
title: Without_Rain_2.R

description: :unav
DOI: 10.15454/dgsnrg/kkqs0c
title: With_Rain_1_086bars.R

description: :unav
DOI: 10.15454/dgsnrg/kkwcxh
title: With_Rain_2_06bars.R

description: :unav
DOI: 10.15454/dgsnrg/klolkp
title: With_Rain_1_14bars.R

description: :unav
DOI: 10.15454/dgsnrg/ksfa8r
title: Without_Rain_2.R

description: :unav
DOI: 10.15454/dgsnrg/kv1sys
title: Without_Rain_3.R

description: :unav
DOI: 10.15454/dgsnrg/kwl2ct
title: .Rhistory

description: :unav
DOI: 10.15454/dgsnrg/l5ihpe
title: With_Rain_1_086bars_BeforeRain.R

description: :unav
DOI: 10.15454/dgsnrg/lavgwq
title: With_Rain_2_P04.R

description: :unav
DOI: 10.15454/dgsnrg/ljra96
title: With_Rain_1_P06.R

description: :unav
DOI: 10.15454/dgsnrg/loykcy
title: Without_Rain.R

description: :unav
DOI: 10.15454/dgsnrg/lsb9s2
title: With_Rain_1_018bars.R

description: :unav
DOI: 10.15454/dgsnrg/lyqwti
title: With_Rain_2_086bars.R

description: :unav
DOI: 10.15454/dgsnrg/lz6pz9
title: With_Rain_1_086bars.R

description: :unav
DOI: 10.15454/dgsnrg/mapcn1
title: Sed_Exut_November.R

description: :unav
DOI: 10.15454/dgsnrg/mmbkcf
title: README.txt

description: :unav
DOI: 10.15454/dgsnrg/mozewt
title: Without_Rain_2.R

description: :unav
DOI: 10.15454/dgsnrg/mzffyy
title: With_Rain_2_14bars.R

description: :unav
DOI: 10.15454/dgsnrg/ndmblr
title: Run4.R

description: :unav
DOI: 10.15454/dgsnrg/npto4j
title: Without_Rain_2.R

description: :unav
DOI: 10.15454/dgsnrg/nv7loh
title: With_Rain_2.R

description: :unav
DOI: 10.15454/dgsnrg/p5gm2b
title: Without_Rain_1.R

description: :unav
DOI: 10.15454/dgsnrg/p9l61j
title: With_Rain_1_P04.R

description: :unav
DOI: 10.15454/dgsnrg/q6n3cu
title: With_Rain_2_086bars.R

description: :unav
DOI: 10.15454/dgsnrg/qccxhf
title: Without_Rain_1.R

description: :unav
DOI: 10.15454/dgsnrg/qcf3md
title: Without_Rain_1.R

description: :unav
DOI: 10.15454/dgsnrg/qdjie7
title: Without_Rain.R

description: :unav
DOI: 10.15454/dgsnrg/qkp9rj
title: With_Rain_2_06bars.R

description: :unav
DOI: 10.15454/dgsnrg/qvovif
title: With_Rain_3.R

description: :unav
DOI: 10.15454/dgsnrg/rpkykj
title: With_Rain_2_125bars.R

description: :unav
DOI: 10.15454/dgsnrg/sproyo
title: With_Rain_1.R

description: :unav
DOI: 10.15454/dgsnrg/stntvs
title: With_Rain_2_086bars.R

description: :unav
DOI: 10.15454/dgsnrg/tfxkfy
title: With_Rain_3_P125.R

description: :unav
DOI: 10.15454/dgsnrg/tldf6k
title: With_Rain_1_14bars.R

description: :unav
DOI: 10.15454/dgsnrg/tzhpvj
title: With_Rain_1_086bars.R

description: :unav
DOI: 10.15454/dgsnrg/uqvg3c
title: With_Rain_2.R

description: :unav
DOI: 10.15454/dgsnrg/v0dili
title: With_Rain_2_P125.R

description: :unav
DOI: 10.15454/dgsnrg/vcbtvr
title: Without_Rain_1.R

description: :unav
DOI: 10.15454/dgsnrg/vezevi
title: Without_Rain_2.R

description: :unav
DOI: 10.15454/dgsnrg/vp9cb1
title: With_Rain_1_P086.R

description: :unav
DOI: 10.15454/dgsnrg/vsh8ha
title: With_Rain_2.R

description: :unav
DOI: 10.15454/dgsnrg/w9ehzo
title: With_Rain_2_P06.R

description: :unav
DOI: 10.15454/dgsnrg/wofdma
title: Without_Rain_1.R

description: :unav
DOI: 10.15454/dgsnrg/xehzsn
title: With_Rain_2_125bars.R

description: :unav
DOI: 10.15454/dgsnrg/xhjzgv
title: With_Rain_1_086bars.R

description: :unav
DOI: 10.15454/dgsnrg/xnsnqe
title: Without_Rain_1.R

description: :unav
DOI: 10.15454/dgsnrg/xosuy0
title: With_Rain_1.R

description: :unav
DOI: 10.15454/dgsnrg/xr0uhb
title: Without_Rain_3.R

description: :unav
DOI: 10.15454/dgsnrg/xuolnm
title: With_Rain_1_125bars.R

description: :unav
DOI: 10.15454/dgsnrg/ytrn5g
title: With_Rain_2_04bars.R

description: :unav
DOI: 10.15454/dgsnrg/yzyura
title: With_Rain_1.R

description: :unav
DOI: 10.15454/dgsnrg/zjrxac
title: With_Rain_1_P018.R

description: :unav
DOI: 10.15454/dgsnrg/zkv99s
title: With_Rain_2_018bars.R

description: :unav
DOI: 10.15454/di74ps/2vdbcf
title: Mat.Supp.5.2_gel_TD_PCR.pdf

description: :unav
DOI: 10.15454/di74ps/3gp2it
title: Mat.Supp.6_Mocks_MA_variability_triplicates_raw_results.png

description: :unav
DOI: 10.15454/di74ps/cs60ey
title: Mat.Supp.1_protocole_echantillonnage_general_DROM.pdf

description: :unav
DOI: 10.15454/di74ps/dp5j7y
title: Mat.Supp.7.1_new_barcodes_16S_Nano_2021.fasta

description: :unav
DOI: 10.15454/di74ps/id4x9j
title: Mat.Supp.5.1_gel_PCR_gradient.pdf

description: :unav
DOI: 10.15454/di74ps/kscmyv
title: Mat.Supp.7.2_new_barcodes_23S_Nano_2021.fasta

description: :unav
DOI: 10.15454/di74ps/ninfml
title: Mat.Supp.3_Schema_protocole_GenElute_TCC.pdf

description: :unav
DOI: 10.15454/di74ps/pkjbg5
title: Mat.Supp.5.3_Plan_detaille_plaque_NanoMiSeq_PGTB.ods

description: :unav
DOI: 10.15454/di74ps/xbjyqq
title: Mat.Supp.4_Schema_protocoles_MN_nucleospin_soil.pdf

description: :unav
DOI: 10.15454/di74ps/yqsila
title: Mat.Supp.2_protocole_PGTB_sequencage.pdf

description: :unav
DOI: 10.15454/dk0b4k/ncn66r
title: L. salivarius_manufacturing_conditions_v1.xlsx

description: Manufacturing conditions and associated literature references
DOI: 10.15454/dkxvac/jdhrhd
title: Submit_Synteny_Brassicaea_V2.xlsx

description: Submission file of Brassicaea botanic family (8 proto-chromosomes) in PlantSyntenyViewer
DOI: 10.15454/dldjvf/0uswoh
title: genesWithBothTypesOfDomains.minc_v3.txt

description: List of genes (ID) with both TE-related domains and non-TE related domains. Produced by get_genes_list_from_hmmer_output.py
DOI: 10.15454/dldjvf/24syvk
title: hmmprofDB.pfam32_GyDB2.hmm

description: hmm profiles database made from the concatenation of pfam32 and GyDB2. Used to identify protein coding genes with TE related domains.
DOI: 10.15454/dldjvf/2ldvzf
title: readme.txt

description: :unav
DOI: 10.15454/dldjvf/3k4msg
title: hmmprofDB.pfam32_GyDB2.hmm

description: hmm profiles database made from the concatenation of pfam32 and GyDB2. Used to identify protein coding genes with TE related domains.
DOI: 10.15454/dldjvf/91ex8g
title: get_genes_domains_from_hmmer3_output.py

description: In-house python (&gt;=3) scripts which take as input HMMER3 output (tabular format) and extract the best HMM profiles chain for each protein. Requires the following libraries: sys, os, csv, re, pandas
DOI: 10.15454/dldjvf/cnsmwy
title: TEs_with_genes_inside.more95pctOfGeneSize.tab

description: :unav
DOI: 10.15454/dldjvf/dkuqah
title: meloidogyne_incognita.v3.2015.faa

description: M. incognita proteome stem from https://doi.org/10.1371/journal.pgen.1006777
DOI: 10.15454/dldjvf/dm6gmz
title: TEs_with_genes_inside.more95pctOfGeneSize.genesWithAtLeastOneTErelatedDomain.tab

description: :unav
DOI: 10.15454/dldjvf/fmztmn
title: genesWithBothTypesOfDomains.minc_v3.txt

description: List of genes (ID) with both TE-related domains and non-TE related domains. Produced by get_genes_list_from_hmmer_output.py
DOI: 10.15454/dldjvf/gz0piv
title: genesWithOnlyTErelatedDomains.minc_v3.txt

description: List of genes with only TE-related domains. Produced by get_genes_list_from_hmmer_output.py
DOI: 10.15454/dldjvf/hoza7i
title: genesWithoutTErelatedDomains.minc_v3.txt

description: List of genes with no TE-related domains. Produced by get_genes_list_from_hmmer_output.py
DOI: 10.15454/dldjvf/jha6rz
title: minc_v3.genes.sorted.expressionLevels.tab

description: M. incognita genes coordinates and expression level (median log10(FPKM+1)) per life stage (egg (W), juvenile 2 (J2), juvenile 3 (J3), female (Fem)). *_expressCat columns represent each gene expression ranking. Last column says if the gene is substantially expressed or not (expression level category is medium plus, high or very high in at least one developmental stage.Stem from M. incognita transcriptome https://doi.org/10.1371/journal.pgen.1006777.
DOI: 10.15454/dldjvf/k4a0oi
title: genes_analysis_workflow.Rmd

description: gene analysis workflow used to evaluate genes expression and to find genes potentially involved in the TEs transposition machinery.
DOI: 10.15454/dldjvf/nmzo7g
title: get_genes_list_from_hmmer_output.py

description: In-house python (&gt;=3) scripts which create gene list from get_genes_domains_from_hmmer3_output.py output. Requires the following libraries: sys, os
DOI: 10.15454/dldjvf/shw0z1
title: get_genes_list_from_hmmer_output.py

description: In-house python (&gt;=3) scripts which create gene list from get_genes_domains_from_hmmer3_output.py output. Requires the following libraries: sys, os
DOI: 10.15454/dldjvf/suh4jw
title: genesWithoutTErelatedDomains.minc_v3.txt

description: List of genes with no TE-related domains. Produced by get_genes_list_from_hmmer_output.py
DOI: 10.15454/dldjvf/tjwdw4
title: genesWithOnlyTErelatedDomains.minc_v3.txt

description: List of genes with only TE-related domains. Produced by get_genes_list_from_hmmer_output.py
DOI: 10.15454/dldjvf/vfxxxo
title: minc_v3.genes.sorted.bed

description: M. incognita genes annotation (bed format). Stem from https://doi.org/10.1371/journal.pgen.1006777
DOI: 10.15454/dldjvf/weamsz
title: genes_with_TE_related_domains.txt

description: Concatenation of the genes ID list contained in genesWithBothTypesOfDomains.minc_v3.txt and genesWithOnlyTErelatedDomains.minc_v3.txt
DOI: 10.15454/dldjvf/wq6lnv
title: meloidogyne_incognita.v3.2015.faa

description: M. incognita proteome stem from https://doi.org/10.1371/journal.pgen.1006777
DOI: 10.15454/dldjvf/y3c2x5
title: median_FPKM.txt

description: data from a previously published life-stage specific RNA-seq analysis of M. incognita transcriptome during tomato plant infection (Blanc-Mathieu et al. 2017). This analysis encompassed four different life stages: (i) eggs, (ii) pre-parasitic second stage juveniles (J2), (iii) a mix of late parasitic J2, third stage (J3) and fourth stage (J4) juveniles and (iv) adult females, all sequenced in triplicates. The median expression (log 10 FPKM) value over the 3 replicates was kept as a representative value in each life stage.
DOI: 10.15454/dldjvf/yxtcxo
title: minc_v3.TEannotations.19-07-19.filtered_classiffiedOnly.minLen250.minId85.minConsCov33.blastVsCons.noOverlap.bed

description: M. incognita 'canonical' TE annotation from Kozlowski D. 2020a. Transposable Elements prediction and annotation in the M. incognita genome. Portail Data INRAE [Internet]. Available from: https://doi.org/10.15454/EPTDOS
DOI: 10.15454/dldjvf/z9gasf
title: genes_analysis_workflow.Rmd

description: gene analysis workflow used to evaluate genes expression and to find genes potentially involved in the TEs transposition machinery.
DOI: 10.15454/dldjvf/zfn0k5
title: minc_v3.genes.sorted.expressionLevels.tab

description: :unav