cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.vzpk3v
title: Occurrence Download

description: A dataset containing 119 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cicer montbretii Jaub. & Spach"
 ]
}

 The dataset includes 119 records from 26 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0137811-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8xa7ov
title: Occurrence Download

description: A dataset containing 11144 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Accipiter virgatus (Temminck, 1822)",
 "HasCoordinate is TRUE"
 ]
}

 The dataset includes 11144 records from 34 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003735-190813142620410/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.23cz8b
title: Occurrence Download

description: A dataset containing 104 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "TaxonKey is Phyllomedusa bahiana Lutz, 1925"
 ]
}

 The dataset includes 104 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020991-231002084531237/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3f6pax
title: Occurrence Download

description: A dataset containing 32374 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Year 1968-2018",
 "Geometry POLYGON ((-12.3046875 54.97761367069628, -4.21875 62.431074232920906, 4.21875 62.75472592723178, 11.6015625 68.00757101804004, 16.875 70.8446726342528, 26.015625 71.74643171904148, 33.75 69.41124235697256, 29.179687499999996 68.39918004344189, 30.234375 66.93006025862448, 29.53125 65.2198939361321, 31.289062500000004 63.23362741232569, 28.4765625 59.88893689676585, 28.828124999999996 56.559482483762245, 32.34375 54.77534585936447, 35.15625 51.83577752045248, 41.484375 49.61070993807422, 36.9140625 21.289374355860424, -16.5234375 21.616579336740603, -10.1953125 44.84029065139799, -12.3046875 54.97761367069628))",
 "HasCoordinate is true",
 "TaxonKey is Natrix natrix (Linnaeus, 1758)"
 ]
}

 The dataset includes 32374 records from 168 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004430-180131172636756/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sxclce
title: Occurrence Download

description: A dataset containing 12 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Mollinedia eugeniifolia Perkins"
 ]
}

 The dataset includes 12 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027431-191105090559680/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/fxhkdq
title: Observations naturalistes indépendantes d'origine privée partagées sur la base de données Kollect Nouvelle-Aquitaine-Observations faunistiques de David GENOUD

description: Observations faunistiques de David GENOUD
DOI: 10.15468/dl.o50hci
title: Occurrence Download

description: A dataset containing 130 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pouteria psammophila (Mart.) Radlk."
 ]
}

 The dataset includes 130 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004431-150410134957023/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.t5yc2s
title: Occurrence Download

description: A dataset containing 29 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cicer kermanense Bornm."
 ]
}

 The dataset includes 29 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0137801-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qaq2s7
title: Occurrence Download

description: A dataset containing 1951 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Blattella germanica (Linnaeus, 1767)"
 ]
}

 The dataset includes 1951 records from 113 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019283-191105090559680/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fdcuqc
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Observation, Human Observation, Specimen)",
 "Geometry POLYGON((-98.5 18.83,-97.33 18.83,-97.33 20.67,-98.5 20.67,-98.5 18.83))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Miconia hemenostigma Naudin"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0198441-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mulkah
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Sesleria italica (Pamp.) Ujhelyi"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004431-160311141623029/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yrn47d
title: Occurrence Download

description: A dataset containing 494 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is Argentina",
 "DatasetKey is one of (iNaturalist Research-grade Observations, Avistajes de espcies de valor especial en áreas protegidas del noreste de Argentina, VERTEBRADOS DE VALOR ESPECIAL EN ÁREAS PROTEGIDAS DE LA ARGENTINA, EOD – eBird Observation Dataset)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "StateProvince is Misiones",
 "TaxonKey is Fungi"
 ]
}

 The dataset includes 494 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0031935-231002084531237/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.d65egz
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Rhodiola rosea subsp. integrifolia (Raf.) H.Hara"
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013610-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rd9b8r
title: Occurrence Download

description: A dataset containing 45 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Malaysia",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Scrophulariaceae"
 ]
}

 The dataset includes 45 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0198442-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.potsh7
title: Occurrence Download

description: A dataset containing 32 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Bomarea bredemeyerana Herb."
 ]
}

 The dataset includes 32 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004431-170627171947987/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.f4u4rx
title: Occurrence Download

description: A dataset containing 10514 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is North America",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Papilio multicaudata Kirby, 1884"
 ]
}

 The dataset includes 10514 records from 67 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021003-231002084531237/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yq3ubh
title: Occurrence Download

description: A dataset listing the 228356 species recorded in GBIF matching the query:
{
 "Country" : [
 "is Canada"
 ]
}

 The dataset's 228356 records were derived from 2069 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017908-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.k7mscf
title: Occurrence Download

description: A dataset containing 108 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Chenopodium desiccatum A.Nelson",
 "Geometry POLYGON((-111 36, -99 36, -99 45, -111 45, -111 36))"
 ]
}

 The dataset includes 108 records from 25 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022033-250402121839773/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15032578
title: Murine datasets and computational analysis: Prdm16_pos antigen-presenting cells

description: Prdm16-dependent antigen-presenting cells induce tolerance to gut antigens

This repository contains all code and computational analysis for the murine datasets associated with the above paper. Items are organized as follows:



2024-04-26/ contains Delta+7kb mouse model raw sequencing data.

2024-06-21/ contains Rorc(t)_DeltaCD11c mouse model raw sequencing data.

2024-10-16/ contains Multiome (RNA+ATAC) raw sequencing data.

2022AkagbosuEtAl/ contains the Multiome public dataset from PMID 36070798 that is integrated alongside our similar data. (Generated by downloading from GEO repository GSE174405 and initial processing through CellRanger with default parameters).

2014-11-26/ contains bulk RNA sequencing data in bigWig format, as input for the Broad IGV tool, to ultimately generate Figure 1b.

Delta7kB_Murine_Analysis/ contains all code in R to process finalized datasets, ultimately generating Figures 2a-c, and ExtData Fig 4a-e.

Cd11c_Murine_Analysis/ contains all code in R to process finalized datasets, ultimately generating Figure 2d.

Multiome_Murine_Analysis/ contains all code in R to process finalized datasets, ultimately generating Figure 2e, ExtData Fig 4f-g, and ExtData Fig 5a-h. 

OUTPUT/ contains final RDS files as output by each workflow, to use as input for each Analysis script. A reader may choose to skip the majority of the above workflow, and only download these files to immediately generate the Figures and/or further explore the data.


In general, a reader can follow the A_import scripts to create initial Seurat objects, B_integrate scripts to integrate separate sequencing runs, C_annotate scripts to assign finalized cell types, and D_analysis scripts to generate all plots. Each workflow ostensibly only requires establishing certain library dependencies, as well as filepaths for INPUT and OUTPUT directories.

Please note, several of the Integration scripts are particularly computationally intensive.  These were successfully run by allocating 512 Gb of memory within our university’s supercomputing environment.

As emphasized within code annotations, this entire workflow is run with R 4.3.2 and Seurat 5.1.0— our computation makes use of that FindClusters implementation, a shared nearest neighbor modularity optimization based clustering algorithm (Seurat 5.2 is not compatible). We specify the Leiden algorithm at these steps, which differs from the default Louvain algorithm, which offers certain computational advantages (see PMID 30914743). While results with Louvain would likely reach the same biological conclusions, the final clusters and annotations we provide here are only useful with Leiden implementation. Finally, we are grateful to our institution’s supercomputer admins, who helped establish a virtual environment with R-Reticulate, which allows for calling the Leiden algorithm (implemented in Python). Readers will similarly need to establish this dependency based on their local environment.
DOI: 10.5281/zenodo.15032579
title: Murine datasets and computational analysis: Prdm16_pos antigen-presenting cells

description: Prdm16-dependent antigen-presenting cells induce tolerance to gut antigens

This repository contains all code and computational analysis for the murine datasets associated with the above paper. Items are organized as follows:



2024-04-26/ contains Delta+7kb mouse model raw sequencing data.

2024-06-21/ contains Rorc(t)_DeltaCD11c mouse model raw sequencing data.

2024-10-16/ contains Multiome (RNA+ATAC) raw sequencing data.

2022AkagbosuEtAl/ contains the Multiome public dataset from PMID 36070798 that is integrated alongside our similar data. (Generated by downloading from GEO repository GSE174405 and initial processing through CellRanger with default parameters).

Delta7kB_Murine_Analysis/ contains all code in R to process finalized datasets, ultimately generating Figures 2a-c, and ExtData Fig 4a-e.

Cd11c_Murine_Analysis/ contains all code in R to process finalized datasets, ultimately generating Figure 2d.

Multiome_Murine_Analysis/ contains all code in R to process finalized datasets, ultimately generating Figure 2e, ExtData Fig 4f-g, and ExtData Fig 5a-h. 

OUTPUT/ contains final RDS files as output by each workflow, to use as input for each Analysis script. A reader may choose to skip the majority of the above workflow, and only download these files to immediately generate the Figures and/or further explore the data.


In general, a reader can follow the A_import scripts to create initial Seurat objects, B_integrate scripts to integrate separate sequencing runs, C_annotate scripts to assign finalized cell types, and D_analysis scripts to generate all plots. Each workflow ostensibly only requires establishing certain library dependencies, as well as filepaths for INPUT and OUTPUT directories.

Please note, several of the Integration scripts are particularly computationally intensive.  These were successfully run by allocating 512 Gb of memory within our university’s supercomputing environment.

As emphasized within code annotations, this entire workflow is run with R 4.3.2 and Seurat 5.1.0— our computation makes use of that FindClusters implementation, a shared nearest neighbor modularity optimization based clustering algorithm (Seurat 5.2 is not compatible). We specify the Leiden algorithm at these steps, which differs from the default Louvain algorithm, which offers certain computational advantages (see PMID 30914743). While results with Louvain would likely reach the same biological conclusions, the final clusters and annotations we provide here are only useful with Leiden implementation. Finally, we are grateful to our institution’s supercomputer admins, who helped establish a virtual environment with R-Reticulate, which allows for calling the Leiden algorithm (implemented in Python). Readers will similarly need to establish this dependency based on their local environment.
DOI: 10.5281/zenodo.15212000
title: Murine datasets and computational analysis: Prdm16_pos antigen-presenting cells

description: Prdm16-dependent antigen-presenting cells induce tolerance to gut antigens

This repository contains all code and computational analysis for the murine datasets associated with the above paper. Items are organized as follows:



2024-04-26/ contains Delta+7kb mouse model raw sequencing data.

2024-06-21/ contains Rorc(t)_DeltaCD11c mouse model raw sequencing data.

2024-10-16/ contains Multiome (RNA+ATAC) raw sequencing data.

2022AkagbosuEtAl/ contains the Multiome public dataset from PMID 36070798 that is integrated alongside our similar data. (Generated by downloading from GEO repository GSE174405 and initial processing through CellRanger with default parameters).

2014-11-26/ contains bulk RNA sequencing data in bigWig format, as input for the Broad IGV tool, to ultimately generate Figure 1b.

Delta7kB_Murine_Analysis/ contains all code in R to process finalized datasets, ultimately generating Figures 2a-c, and ExtData Fig 4a-e.

Cd11c_Murine_Analysis/ contains all code in R to process finalized datasets, ultimately generating Figure 2d.

Multiome_Murine_Analysis/ contains all code in R to process finalized datasets, ultimately generating Figure 2e, ExtData Fig 4f-g, and ExtData Fig 5a-h. 

OUTPUT/ contains final RDS files as output by each workflow, to use as input for each Analysis script. A reader may choose to skip the majority of the above workflow, and only download these files to immediately generate the Figures and/or further explore the data.


In general, a reader can follow the A_import scripts to create initial Seurat objects, B_integrate scripts to integrate separate sequencing runs, C_annotate scripts to assign finalized cell types, and D_analysis scripts to generate all plots. Each workflow ostensibly only requires establishing certain library dependencies, as well as filepaths for INPUT and OUTPUT directories.

Please note, several of the Integration scripts are particularly computationally intensive.  These were successfully run by allocating 512 Gb of memory within our university’s supercomputing environment.

As emphasized within code annotations, this entire workflow is run with R 4.3.2 and Seurat 5.1.0— our computation makes use of that FindClusters implementation, a shared nearest neighbor modularity optimization based clustering algorithm (Seurat 5.2 is not compatible). We specify the Leiden algorithm at these steps, which differs from the default Louvain algorithm, which offers certain computational advantages (see PMID 30914743). While results with Louvain would likely reach the same biological conclusions, the final clusters and annotations we provide here are only useful with Leiden implementation. Finally, we are grateful to our institution’s supercomputer admins, who helped establish a virtual environment with R-Reticulate, which allows for calling the Leiden algorithm (implemented in Python). Readers will similarly need to establish this dependency based on their local environment.
DOI: 10.25549/pcra-c14-57149
title: Redemption tidings, vol. 38, nos. 1-52, 5 Jan. - 28 Dec. 1962

description: [description english/roman)] Issued weekly. "A full gospel magazine" -- subtitle.
DOI: 10.15468/dl.555q45
title: Occurrence Download

description: A dataset containing 126 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Theloderma asperum (Boulenger, 1886)"
 ]
}

 The dataset includes 126 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0307889-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ouocbg
title: Occurrence Download

description: A dataset containing 911989 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "BasisOfRecord is Observation",
 "BasisOfRecord is Specimen",
 "BasisOfRecord is Human Observation"
 ]
 },
 {
 "or" : [
 "PublishingOrg is e2e717bf-551a-4917-bdc9-4fa0f342c530",
 "PublishingOrg is 95f1c5d0-8996-11d9-a962-b8a03c50a862",
 "PublishingOrg is 28eb1a3f-1c15-4a95-931a-4af90ecb574d"
 ]
 },
 "Issue is Coordinate rounded",
 "Year 1980-2018",
 {
 "or" : [
 "DatasetKey is Hawk Migration Association of North America - HawkCount",
 "DatasetKey is iNaturalist Research-grade Observations",
 "DatasetKey is EOD – eBird Observation Dataset"
 ]
 },
 "HasCoordinate is true",
 "TaxonKey is Accipiter cooperii (Bonaparte, 1828)",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 911989 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002152-180920211646547/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/pcra-c14-57217
title: Redemption tidings, vol. 38, nos. 1-52, 5 Jan. - 28 Dec. 1962

description: [description english/roman)] Issued weekly. "A full gospel magazine" -- subtitle.
DOI: 10.6084/m9.figshare.25658928
title: Electrostatic-Induced Ion Confined Partitioning in Graphene Nanolaminate Membrane for Breaking Anion-Cation Co-Transport to Enhance Desalination

description: This dataset contains the raw data source for the figure plots shown in the main manuscript entitled "Electrostatic-Induced Ion Confined Partitioning in Graphene Nanolaminate Membrane for Breaking Anion-Cation Co-Transport to Enhance Desalination"
DOI: 10.15468/dl.7w2wr9
title: Occurrence Download

description: A dataset containing 85 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Raphiocarpus begoniifolius (H.Lév.) B.L.Burtt"
 ]
}

 The dataset includes 85 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0100762-230530130749713/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.25658928.v3
title: Electrostatic-Induced Ion Confined Partitioning in Graphene Nanolaminate Membrane for Breaking Anion-Cation Co-Transport to Enhance Desalination

description: This dataset contains the raw data source for the figure plots shown in the main manuscript entitled "Electrostatic-Induced Ion Confined Partitioning in Graphene Nanolaminate Membrane for Breaking Anion-Cation Co-Transport to Enhance Desalination"
DOI: 10.15468/dl.3h6c4e
title: Occurrence Download

description: A dataset containing 536 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-6.98757 37.44448,-5.30019 37.44448,-5.30019 38.19230,-6.98757 38.19230,-6.98757 37.44448))",
 "HasCoordinate is true",
 "TaxonKey is Juniperus oxycedrus L.",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 536 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0075173-200221144449610/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3qyyu3
title: Occurrence Download

description: A dataset containing 19761 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Xanthotis macleayanus (E.P.Ramsay, 1875)"
 ]
}

 The dataset includes 19761 records from 28 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0380461-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/pcra-c14-59449
title: Redemption tidings, vol. 39, nos. 1-52, 4 Jan. - 27 Dec. 1963

description: [description english/roman)] Issued weekly. "A full gospel magazine" -- subtitle.