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config.yml
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default:
production: TRUE
app_url: "https://shinypro.synapse.org/users/nkauer/dccvalidator-test/"
parent: "syn20400157"
path_to_markdown: "inst/using-the-dccvalidator-app-amp-ad.Rmd"
study_table: "syn11363298"
samples_table: "syn21578908"
annotations_table: "syn10242922"
annotations_link: "https://shinypro.synapse.org/users/nsanati/annotationUI/"
templates_link: "https://www.synapse.org/#!Synapse:syn18512044"
docs_tab:
include_tab: TRUE
include_upload_widget: TRUE
tab_name: "Upload Study Documentation"
path_to_docs_markdown: "inst/study-documentation-amp-ad.Rmd"
teams:
- "273957"
include_biospecimen_type: FALSE
templates:
manifest_template: "syn20820080"
individual_templates:
human: "syn12973254"
mouse or other animal model: "syn12973253"
biospecimen_templates:
mouse or other animal model: "syn12973252"
human: "syn12973252"
drosophila: "syn20673251"
assay_templates:
rnaSeq: "sysbio.metadataTemplates-assay.rnaSeq"
species_list:
- "mouse or other animal model"
- "human"
- "drosophila"
complete_columns:
manifest:
- "parent"
- "path"
individual:
- "individualID"
biospecimen:
- "individualID"
- "specimenID"
assay:
- "specimenID"
contact_email: "nicole.kauer@synapse.org"
dev:
production: FALSE
testing:
samples_table: "syn22089767"
include_biospecimen_type: TRUE
templates:
manifest_template: "syn20820080"
individual_templates:
human: "syn12973254"
mouse or other animal model: "syn12973253"
biospecimen_templates:
mouse or other animal model:
in vitro: "syn25955510"
other: "syn12973252"
human: "syn12973252"
drosophila: "syn20673251"
assay_templates:
rnaSeq: "syn12973256"
proteomics: "sysbio.metadataTemplates-assay.proteomics"
complete_columns:
manifest:
- "parent"
individual:
- "individualID"
biospecimen:
- "individualID"
- "specimenID"
assay:
- "specimenID"
amp-ad:
app_url: "https://shinypro.synapse.org/users/nkauer/dccvalidator-ad/"
parent: "syn21643404"
annotations_table: "syn21459391"
annotations_link: "https://shinypro.synapse.org/users/kwoo/amp-ad-metadata-dictionary/"
teams:
- "3405451"
docs_tab:
include_tab: TRUE
include_upload_widget: FALSE
tab_name: "Study Documentation"
path_to_docs_markdown: "inst/study-documentation-amp-ad.Rmd"
species_list:
- "human"
- "drosophila"
- "MODEL-AD mouse model"
- "other mouse or animal model"
include_biospecimen_type: TRUE
templates:
individual_templates:
human: "syn12973254"
other mouse or animal model: "syn12973253"
MODEL-AD mouse model: "syn21084071"
biospecimen_templates:
human:
in vivo, postmortem, other: "syn12973252"
in vitro: "syn25955510"
other mouse or animal model:
in vivo, postmortem, other: "syn12973252"
in vitro: "syn25955510"
MODEL-AD mouse model:
in vivo, postmortem, other: "syn12973252"
in vitro: "syn25955510"
drosophila: "syn20673251"
assay_templates:
ATACseq: "syn22024364"
autorad: "syn22087295"
immunoassay: "syn22117582"
proteomics: "syn12973255"
single cell RNAseq: "syn21018360"
wholeGenomeSeq: "syn21018358"
wholeExomeSeq: "syn21078272"
NanoString: "syn21082744"
snpArray: "syn21372586"
STARRSeq: "syn26125115"
TMT quantitation: "syn21433357"
methylationArray: "syn22036881"
MRI: "syn22087332"
PET: "syn22087299"
16SrRNAseq: "syn24184375"
metabolomics: "syn24216748"
HI-C: "syn25671270"
ChIPSeq: "syn22907810"
bisulfiteSeq: "syn25830897"
complete_columns:
manifest:
- "consortium"
- "study"
- "grant"
- "fileFormat"
- "parent"
- "path"
individual:
- "individualID"
biospecimen:
- "individualID"
- "specimenID"
assay:
- "specimenID"
contact_email: "AMPAD_SageAdmin@synapse.org"
pec:
app_url: "https://shinypro.synapse.org/users/kmontgomery/apps_w_oauth/dccvalidator/"
parent: "syn21763123"
path_to_markdown: "inst/using-the-dccvalidator-pec.Rmd"
study_table: "syn20968992"
samples_table: "syn22175287"
annotations_table: "syn20981788"
annotations_link: "https://www.synapse.org/#!Synapse:syn20729790"
templates_link: "https://www.synapse.org/#!Synapse:syn20729790"
docs_tab:
include_tab: TRUE
include_upload_widget: FALSE
tab_name: "Study Documentation"
path_to_docs_markdown: "inst/study-documentation-pec.Rmd"
teams:
- "3323356"
include_biospecimen_type: TRUE
templates:
manifest_template: "syn20782058"
individual_templates:
human: "syn20781820"
animal: "syn21053116"
biospecimen_templates:
human:
in vivo, postmortem, other: "syn20768131"
in vitro: "syn26011297"
other mouse or animal model:
in vivo, postmortem, other: "syn20768131"
in vitro: "syn26011297"
assay_templates:
ATACSeq: "syn20768526"
bisulfiteSeq: "syn23017098"
ChIPSeq: "syn21861858"
HI-C: "syn21680758"
immunoassay: "syn25805392"
methylationArray: "syn25805391"
rnaSeq: "syn20768650"
snpArray: "syn21680759"
STARRSeq: "syn26011215"
TMT quantitation: "syn21680761"
wholeGenomeSeq: "syn20980993"
species_list:
- "human"
- "animal model"
complete_columns:
manifest:
- "consortium"
- "study"
- "grant"
- "fileFormat"
- "parent"
- "path"
individual:
- "individualID"
- "individualIdSource"
- "species"
- "reportedGender"
- "postmortem"
- "primaryDiagnosis"
biospecimen:
- "individualID"
- "specimenID"
- "organ"
- "tissue"
- "nucleicAcidSource"
assay:
- "specimenID"
contact_email: "PEC_SageAdmin@synapse.org"
veoibd:
app_url: "https://shinypro.synapse.org/users/nkauer/dccvalidator-veoibd/"
parent: "syn25556537"
path_to_markdown: "inst/using-the-dccvalidator-veoibd.Rmd"
study_table: "syn25557724"
samples_table: "syn25557826"
annotations_table: "syn25558026"
annotations_link: "https://www.synapse.org/#!Synapse:syn20729790"
templates_link: "https://www.synapse.org/#!Synapse:syn20729790"
docs_tab:
include_tab: TRUE
include_upload_widget: FALSE
tab_name: "Study Documentation"
path_to_docs_markdown: "inst/study-documentation-pec.Rmd"
teams:
- "3382930"
- "3425042"
templates:
manifest_template: "syn20782058"
individual_templates:
human: "syn20781820"
animal: "syn21053116"
biospecimen_templates:
animal model: "syn20768131"
human: "syn20768131"
assay_templates:
wholeGenomeSeq: "syn20980993"
rnaSeq: "syn20768650"
ATACSeq: "syn20768526"
TMT quantitation: "syn21680761"
HI-C: "syn21680758"
snpArray: "syn21680759"
ChIPSeq: "syn21861858"
bisulfiteSeq: "syn23017098"
species_list:
- "human"
- "animal model"
complete_columns:
manifest:
- "consortium"
- "study"
- "grant"
- "fileFormat"
- "parent"
- "path"
individual:
- "individualID"
- "individualIdSource"
- "species"
- "reportedGender"
- "postmortem"
- "primaryDiagnosis"
biospecimen:
- "individualID"
- "specimenID"
- "organ"
- "tissue"
- "nucleicAcidSource"
assay:
- "specimenID"
contact_email: "cmolitor@synapse.org"
1kD:
parent: "syn27605292"
path_to_markdown: "inst/using-the-dccvalidator-1kD.Rmd"
study_table: "syn27610007"
samples_table: "syn27817789"
annotations_table: "syn27806892"
annotations_link: "https://www.synapse.org/#!Synapse:syn27817580"
templates_link: "https://www.synapse.org/#!Synapse:syn27817580"
docs_tab:
include_tab: FALSE
include_upload_widget: FALSE
tab_name: "Study Documentation"
path_to_docs_markdown: "inst/study-documentation-1kD.Rmd"
teams:
- "3433360" # 1kD_admin
- "3436722" # 1kD_Connectome
- "3436721" # 1kD_InfantNaturalStatistics
- "3436720" # 1kD_BRAINRISE
- "3436718" # 1kD_KHULA
- "3436509" # 1kD_MicrobiomeBrainDevelopment
- "3436717" # 1kD_M4EFaD_LABS
- "3436716" # 1kD_Assembloids
- "3436713" # 1kD_DyadicSociometrics_NTU
- "3466183" # 1kD_DyadicSociometrics_Cambridge
- "3436714" # 1kD_First1000Daysdatabase
- "3458847" # 1kD_M4EFaD_BMT team
- "3464137" # 1kD_Computer Vision Analysis of PCI
- "3460645" # 1kD_M4EFaD_Auckland
include_biospecimen_type: FALSE
templates:
manifest_template: "syn27832372"
individual_templates:
human: "syn29358381"
biospecimen_templates:
human: "syn29358373"
complete_columns:
manifest:
- "path"
- "parent"
- "fileFormat"
- "project"
- "study"
- "resourceType"
- "timepoint"
- "age_in_days"
individual:
- "project"
- "study"
- "individualID"
- "householdID"
- "person"
- "sex"
- "noOfChildren"
- "noOfAdults"
- "spokenLanguage"
biospecimen:
- "project"
- "study"
- "person"
- "individualID"
- "specimenID"
- "specimenType"
- "samplingAge"
- "samplingAgeUnits"
- "ageStartingSolidFood"
- "ageStartingSolidFoodUnits"
- "breastfed"
- "formulafed"
- "formulaName"
- "antibioticUse"
- "antibioticName"
contact_email: "1kD_SageAdmin@synapse.org"