cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.swnrj6
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Costa Rica",
 "TaxonKey is Klarobelia anomala (R.E.Fr.) Chatrou"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006895-240425142415019/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kf7kp8
title: Occurrence Download

description: A dataset containing 217 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Papaver rupifragum Boiss. & Reut."
 ]
}

 The dataset includes 217 records from 44 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0228893-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7sfd9d
title: Occurrence Download

description: A dataset containing 254 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ichthyothere rufa Gardner"
 ]
}

 The dataset includes 254 records from 43 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0252011-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mmh943
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Tacca leontopetaloides (L.) Kuntze",
 "HasCoordinate is true",
 "Country is Japan",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0208012-220831081235567/datasets/export for details.
DOI: 10.15468/dl.2wgxfp
title: Occurrence Download

description: A dataset containing 74 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Kalanchoe rosei Raym.-Hamet & H.Perrier"
 ]
}

 The dataset includes 74 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000625-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xn9xnm
title: Occurrence Download

description: A dataset containing 1000000 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is VectorBase (Bioinformatics Resource for Invertebrate Vectors of Human Pathogens)"
 ]
}

 The dataset includes 1000000 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0208034-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.25659150.v6
title: Replication Package

description: This package contains pre-survey, focus group, questionnaire answers used in "Process Smells in Practice: An Evaluative Case Study".
DOI: 10.15468/dl.n74zjy
title: Occurrence Download

description: A dataset containing 43532 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Cyclocephala Dejean, 1821"
 ]
}

 The dataset includes 43532 records from 132 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000633-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ya2vfa
title: Occurrence Download

description: A dataset containing 5347 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Spain",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Month is one of (February, January, March, April, May, June, July, August, September, October, November, December)",
 "OccurrenceStatus is Present",
 "StateProvince is one of (Comunidad Autnoma de Andaluca, Comunidad Autonoma de Aragon, Comunidad Autonoma de Cantabria, Asturias, Galicia, Comunidad Valenciana, Comunidad de Madrid, CASTILLA-LEON, Castilla La Mancha, Murcia, Pais Vasco, Navarra Comunidad Foral de, La Rioja, Islas Baleares, Cataluña, Extramadura)",
 "TaxonKey is Oriolus oriolus (Linnaeus, 1758)",
 "Year 2018-2022"
 ]
}

 The dataset includes 5347 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0200499-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.11058998
title: Oliveira et al. 2024 Processed Data

description: This is the collection of processed data for the manuscript "Epigenetic heritability of cell plasticity drives cancer drug resistance through one-to-many genotype to phenotype mapping", the accompanyng code is hosted on GitHub at this link, this data is sufficient to regenerate all the figures.

There are 3 cohorts of organoids analyzed in the paper (more details in the manuscript): MSI, MSS batch 1 and MSS batch 2. All the subdirectories are divided accordingly The directory is structured in 6 main branches:



archetype_params: this folder contains results of the archetypal analysis decomposition for RNA and ATAC of each cohort, they are either in tabular format or as MIDAA objects (more info here) 

archr_objects: this folder contains the zipped archR projects for each of the cohort, beware that archR projects have absolute paths, so you might have to change the internal links to make them work, I know the authors of archR are trying to put the possibilities of relative paths. In case you know of a better way to share archR objects please let me know.

barcode_tables: this stores the barcode quantification tables for each cohort: in the MSI and MSS batch 2 case both floating and cellular barcodes are together in the same table (novaseq...etc), while for MSS batch 1 they are dividend into cell and floating tables

copy_number_data: This folder contains the segmentation and the absolute copy number values obtained from lpWGS for each organoid line and treatment combination, and scDNA-seq results for MSI and MSS batch 2 for Parental and CENPE+MPS1 inh 

other_data: this folder contains various processed data. 

congas_fit_final.rds: contains the final fit of CONGAS  on MSS batch1 multiomemedicc_input_congas_final_tree.new: this contains the tree inferred by MEDICC2 on CONGAS outputpalette_MSI.rds: this contains the color palette for MSI organoidpalette_enriched_100.rds: this contains the color paletter for MSS organoid

AKT_mutect2.ann.all_plugins.VEP.tsv: this contains the mutect calls for SNVs in the AKT Trametinib resistant vs Parental Population of MSS batch 1 deep WGSAZD_TRAM_vs_AKT_blood.cnvs.txt: this contains the ASCAT inferred CNV in the AKT Trametinib resistant vs Parental Population of MSS batch 1 deep WGS


seurat_objects: This folder contains the seurat objects for scRNA-seq data
DOI: 10.5281/zenodo.11058999
title: Oliveira et al. 2024 Processed Data

description: This is the collection of processed data for the manuscript "Epigenetic heritability of cell plasticity drives cancer drug resistance through one-to-many genotype to phenotype mapping", the accompanyng code is hosted on GitHub at this link, this data is sufficient to regenerate all the figures.

There are 3 cohorts of organoids analyzed in the paper (more details in the manuscript): MSI, MSS batch 1 and MSS batch 2. All the subdirectories are divided accordingly The directory is structured in 6 main branches:



archetype_params: this folder contains results of the archetypal analysis decomposition for RNA and ATAC of each cohort, they are either in tabular format or as MIDAA objects (more info here) 

archr_objects: this folder contains the zipped archR projects for each of the cohort, beware that archR projects have absolute paths, so you might have to change the internal links to make them work, I know the authors of archR are trying to put the possibilities of relative paths. In case you know of a better way to share archR objects please let me know.

barcode_tables: this stores the barcode quantification tables for each cohort: in the MSI and MSS batch 2 case both floating and cellular barcodes are together in the same table (novaseq...etc), while for MSS batch 1 they are dividend into cell and floating tables

copy_number_data: This folder contains the segmentation and the absolute copy number values obtained from lpWGS for each organoid line and treatment combination, and scDNA-seq results for MSI and MSS batch 2 for Parental and CENPE+MPS1 inh 

other_data: this folder contains various processed data. 

congas_fit_final.rds: contains the final fit of CONGAS  on MSS batch1 multiomemedicc_input_congas_final_tree.new: this contains the tree inferred by MEDICC2 on CONGAS outputpalette_MSI.rds: this contains the color palette for MSI organoidpalette_enriched_100.rds: this contains the color paletter for MSS organoid

AKT_mutect2.ann.all_plugins.VEP.tsv: this contains the mutect calls for SNVs in the AKT Trametinib resistant vs Parental Population of MSS batch 1 deep WGSAZD_TRAM_vs_AKT_blood.cnvs.txt: this contains the ASCAT inferred CNV in the AKT Trametinib resistant vs Parental Population of MSS batch 1 deep WGS


seurat_objects: This folder contains the seurat objects for scRNA-seq data
DOI: 10.15468/dl.3en3f7
title: Occurrence Download

description: A dataset containing 9739141 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Continent is South America",
 "Country is Ecuador"
 ]
}

 The dataset includes 9739141 records from 116 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006878-240425142415019/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hhcwqr
title: Occurrence Download

description: A dataset containing 756 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Hydrobates pelagicus (Linnaeus, 1758)",
 "DatasetKey is Observation.org, Nature data from around the World",
 "Country is one of (Germany, France, Spain, Portugal, Denmark, Austria, Italy, Switzerland, Greece, Poland, Hungary, Slovenia, Sweden, Norway, Slovakia, Montenegro, Croatia, North Macedonia, Serbia, Iceland, Ireland, United Kingdom of Great Britain and Northern Ireland, Albania, Bosnia and Herzegovina, Bulgaria, Belgium, Netherlands)"
 ]
}

 The dataset includes 756 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0177227-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xhaga6
title: Occurrence Download

description: A dataset containing 1015 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Kalanchoe rotundifolia (Haw.) Haw."
 ]
}

 The dataset includes 1015 records from 48 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000627-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.k4pkby
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Viscaria vulgaris Röhl.",
 "HasCoordinate is true",
 "Country is Japan",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0200489-220831081235567/datasets/export for details.
DOI: 10.15468/dl.k2nwwh
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is China",
 "TaxonKey is Ovis ammon (Linnaeus, 1758)",
 "Year 1923-2023"
 ]
}

 The dataset includes 6 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0283460-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8yc7cv
title: Occurrence Download

description: A dataset containing 10 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Viola utchinensis Koidz.",
 "HasCoordinate is true",
 "Country is Japan",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 10 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0200503-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zrh287
title: Occurrence Download

description: A dataset containing 572 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Acorus tatarinowii Schott"
 ]
}

 The dataset includes 572 records from 25 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006896-240425142415019/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6j4grp
title: Occurrence Download

description: A dataset containing 393 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Bombycilla cedrorum Vieillot, 1808",
 "Year is 2018"
 ]
}

 The dataset includes 393 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0238489-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8m9sp6
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Lepidium meyenii Walp.",
 "HasCoordinate is true",
 "Country is Japan",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0200513-220831081235567/datasets/export for details.
DOI: 10.15468/dl.zmq6w4
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Agathidium katsuragiae Hoshina, 1998",
 "HasCoordinate is true",
 "Country is Japan",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0219625-220831081235567/datasets/export for details.
DOI: 10.15468/dl.8mr2gk
title: Occurrence Download

description: A dataset containing 30 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Brazil",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Culex vomerifer Komp, 1932"
 ]
}

 The dataset includes 30 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0261430-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.11060764
title: Universal Rapid Weather Prediction Model (Sonagi Model) Forecast Result

description: Universal Rapid Weather Prediction Model (Sonagi Model) Forecast Result / 15 Days / Created By Jihyeon Yoon(somehowme@gmail.com, flyingtext@nate.com)
DOI: 10.5281/zenodo.11060765
title: Universal Rapid Weather Prediction Model (Sonagi Model) Forecast Result

description: Universal Rapid Weather Prediction Model (Sonagi Model) Forecast Result / 15 Days / Created By Jihyeon Yoon(somehowme@gmail.com, flyingtext@nate.com)
DOI: 10.15468/dl.mmnpvt
title: Occurrence Download

description: A dataset containing 4673 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is one of (Trypanophora Kollar, 1844, Asota plaginota Butler, 1875, Eterusia Hope, 1841, Marasmia poeyalis (Boisduval, 1833), Omiodes diemenalis (Guenée, 1854))"
 ]
}

 The dataset includes 4673 records from 49 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0234157-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.htbh8q
title: Occurrence Download

description: A dataset containing 21 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((0.29944 43.08197,0.48592 43.08197,0.48592 43.22548,0.29944 43.22548,0.29944 43.08197))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Vipera aspis (Linnaeus, 1758)"
 ]
}

 The dataset includes 21 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0251994-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.r9dqe4
title: Occurrence Download

description: A dataset containing 698 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "TaxonKey is Corylus yunnanensis (Franch.) A.Camus"
 ]
}

 The dataset includes 698 records from 22 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0046850-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8hh9yd
title: Occurrence Download

description: A dataset containing 45 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cryptocarya acutifolia H.W.Li",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 45 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0261483-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nkq7gc
title: Occurrence Download

description: A dataset containing 403784 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Platalea leucorodia Linnaeus, 1758",
 "DatasetKey is Observation.org, Nature data from around the World",
 "Country is one of (Germany, France, Spain, Portugal, Denmark, Austria, Italy, Switzerland, Greece, Poland, Hungary, Slovenia, Sweden, Norway, Slovakia, Montenegro, Croatia, North Macedonia, Serbia, Iceland, Ireland, United Kingdom of Great Britain and Northern Ireland, Albania, Bosnia and Herzegovina, Bulgaria, Belgium, Netherlands)"
 ]
}

 The dataset includes 403784 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0177245-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fu4hfs
title: Occurrence Download

description: A dataset containing 2772 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ficus fistulosa Reinw. ex Blume",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 2772 records from 66 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0261485-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7znbn4
title: Occurrence Download

description: A dataset containing 290 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Puffinus yelkouan (Acerbi, 1827)",
 "DatasetKey is Observation.org, Nature data from around the World",
 "Country is one of (Germany, France, Spain, Portugal, Denmark, Austria, Italy, Switzerland, Greece, Poland, Hungary, Slovenia, Sweden, Norway, Slovakia, Montenegro, Croatia, North Macedonia, Serbia, Iceland, Ireland, United Kingdom of Great Britain and Northern Ireland, Albania, Bosnia and Herzegovina, Bulgaria, Belgium, Netherlands)"
 ]
}

 The dataset includes 290 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0177237-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.b5uahx
title: Occurrence Download

description: A dataset containing 35 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Kalanchoe peteri Werderm."
 ]
}

 The dataset includes 35 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000611-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9wjyzz
title: Occurrence Download

description: A dataset containing 577 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Colombia",
 "TaxonKey is Nasuella olivacea (Gray, 1865)"
 ]
}

 The dataset includes 577 records from 53 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0177233-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cwgzz4
title: Occurrence Download

description: A dataset containing 34 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is China",
 "TaxonKey is Milvus migrans lineatus (J.E.Gray, 1831)",
 "Year 1923-2023"
 ]
}

 The dataset includes 34 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0283462-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7f43wu
title: Occurrence Download

description: A dataset containing 63 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Justicia dusenii (Lindau) Wassh. & L.B.Sm."
 ]
}

 The dataset includes 63 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0039705-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.