cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.p5p6st
title: Occurrence Download

description: A dataset containing 441 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Erica intervallaris Salisb."
 ]
}

 The dataset includes 441 records from 35 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0044307-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9jf7uy
title: Occurrence Download

description: A dataset containing 149907 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Solidago canadensis L."
 ]
}

 The dataset includes 149907 records from 638 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011211-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.er2jvv
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Tragopogon kindingeri Adamovic"
 ]
}

 The dataset includes 5 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0129371-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.x7qp3j
title: Occurrence Download

description: A dataset containing 314 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Helicteres velutina K.Schum."
 ]
}

 The dataset includes 314 records from 39 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0080872-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qyc8c5
title: Occurrence Download

description: A dataset containing 2792 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Plethodon albagula Grobman, 1944",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 1000",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 2792 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0044172-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pcszxf
title: Occurrence Download

description: A dataset containing 1490 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Serrasalmus rhombeus (Linnaeus, 1766)"
 ]
}

 The dataset includes 1490 records from 49 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0137585-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wmvft9
title: Occurrence Download

description: A dataset containing 65 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Bolbitius callistus (Peck) Watling"
 ]
}

 The dataset includes 65 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0198968-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.acw7eu
title: Occurrence Download

description: A dataset containing 198007 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Wikiplantbase #Toscana"
 ]
}

 The dataset includes 198007 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0080875-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zfquwr
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Eriosema bieense Torre"
 ]
}

 The dataset includes 5 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0044167-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nxzkwy
title: Occurrence Download

description: A dataset containing 4686 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Tetropium fuscum (Fabricius, 1787)"
 ]
}

 The dataset includes 4686 records from 106 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0185790-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.axqpce
title: Occurrence Download

description: A dataset containing 7786 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Bufo marinus (Linnaeus, 1758)",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 7786 records from 83 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008001-180131172636756/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3vyqey
title: Occurrence Download

description: A dataset containing 10 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Eriosema betsileense Du Puy & Labat"
 ]
}

 The dataset includes 10 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0044155-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.g69fv8
title: Occurrence Download

description: A dataset containing 2306 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "BasisOfRecord is Observation",
 "BasisOfRecord is Human Observation"
 ]
 },
 {
 "or" : [
 "Continent is Africa",
 "Continent is Asia",
 "Continent is North America",
 "Continent is South America"
 ]
 },
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Streptopelia decaocto (Frivaldszky, 1838)",
 "Year 1950-2020"
 ]
}

 The dataset includes 2306 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0116819-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nnrenc
title: Occurrence Download

description: A dataset containing 24 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "Issue is Coordinate rounded",
 "Issue is Geodetic datum assumed WGS84"
 ]
 },
 "Month is May",
 "TaxonKey is Lasiurus blossevillii (Lesson & Garnot, 1826)"
 ]
}

 The dataset includes 24 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008001-180508205500799/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.10561582
title: MUFFIN : A suite of tools for the analysis of functional sequencing data - Example input data

description: This repository contains the data required to run the example notebooks and to reproduce the figures from the paper : 



MUFFIN : A suite of tools for the analysis of functional sequencing data


Pierre de Langen, Benoit Ballester

bioRxiv 2023.12.11.570597; doi: https://doi.org/10.1101/2023.12.11.570597

 

Source code is located here :

https://github.com/pdelangen/Muffin

 



10k_pbmc_gene/ contains the data for 10k pbmc dataset in standard 10x sparse count table format.

genome_annot/ contains gencode v38 and chromosomes for the human (used for gene set enrichment analyses)

GO_files/ contains gene set information retrieved from the g:ProfileR website.

immune_chip/ contains the data required to re-run the ChIP-seq analyses, it will require to also launch the dl_data.smk to retrieve the data from ENCODE.

tcga_atac/ contains the sample-genomic region ATAC tag count table, as well as the sample metadata and a gene set file of cancer hallmark genes.

muffin_apptainer.img is a singularity/apptainer image file which contains the muffin package.
DOI: 10.15468/dl.tfayb7
title: Occurrence Download

description: A dataset containing 68 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Plethodon kisatchie Highton, 1989",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 1000",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 68 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0044156-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.10708208
title: MUFFIN : A suite of tools for the analysis of functional sequencing data - Example input data

description: This repository contains the data required to run the example notebooks and to reproduce the figures from the paper : 



MUFFIN : A suite of tools for the analysis of functional sequencing data


Pierre de Langen, Benoit Ballester

bioRxiv 2023.12.11.570597; doi: https://doi.org/10.1101/2023.12.11.570597

 

Source code is located here :

https://github.com/pdelangen/Muffin

 



10k_pbmc_gene/ contains the data for 10k pbmc dataset in standard 10x sparse count table format.

genome_annot/ contains gencode v38 and chromosomes for the human (used for gene set enrichment analyses)

GO_files/ contains gene set information retrieved from the g:ProfileR website.

immune_chip/ contains the data required to re-run the ChIP-seq analyses, it will require to also launch the dl_data.smk to retrieve the data from ENCODE.

tcga_atac/ contains the sample-genomic region ATAC tag count table, as well as the sample metadata and a gene set file of cancer hallmark genes.

scATAC/  contains the cell barcode-genomic region ATAC tag count table, as well as the barcode metadata and the 10k pbmc dataset pre-analyzed in h5 AnnData format.
DOI: 10.5281/zenodo.10706745
title: MUFFIN : A suite of tools for the analysis of functional sequencing data - Example input data

description: This repository contains the data required to run the example notebooks and to reproduce the figures from the paper : 



MUFFIN : A suite of tools for the analysis of functional sequencing data


Pierre de Langen, Benoit Ballester

bioRxiv 2023.12.11.570597; doi: https://doi.org/10.1101/2023.12.11.570597

 

Source code is located here :

https://github.com/pdelangen/Muffin

 



10k_pbmc_gene/ contains the data for 10k pbmc dataset in standard 10x sparse count table format.

genome_annot/ contains gencode v38 and chromosomes for the human (used for gene set enrichment analyses)

GO_files/ contains gene set information retrieved from the g:ProfileR website.

immune_chip/ contains the data required to re-run the ChIP-seq analyses, it will require to also launch the dl_data.smk to retrieve the data from ENCODE.

tcga_atac/ contains the sample-genomic region ATAC tag count table, as well as the sample metadata and a gene set file of cancer hallmark genes.

scATAC/  contains the cell barcode-genomic region ATAC tag count table, as well as the barcode metadata and the 10k pbmc dataset pre-analyzed in h5 AnnData format.
DOI: 10.15468/dl.8rzdw2
title: Occurrence Download

description: A dataset containing 52 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Argentina",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Deyeuxia chrysostachya É.Desv."
 ]
}

 The dataset includes 52 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0122987-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.10561580
title: MUFFIN : A suite of tools for the analysis of functional sequencing data - Example input data

description: This repository contains the data required to run the example notebooks and to reproduce the figures from the paper : 



MUFFIN : A suite of tools for the analysis of functional sequencing data


Pierre de Langen, Benoit Ballester

bioRxiv 2023.12.11.570597; doi: https://doi.org/10.1101/2023.12.11.570597

 

Source code is located here :

https://github.com/pdelangen/Muffin

 



10k_pbmc_gene/ contains the data for 10k pbmc dataset in standard 10x sparse count table format.

genome_annot/ contains gencode v38 and chromosomes for the human (used for gene set enrichment analyses)

GO_files/ contains gene set information retrieved from the g:ProfileR website.

immune_chip/ contains the data required to re-run the ChIP-seq analyses, it will require to also launch the dl_data.smk to retrieve the data from ENCODE.

tcga_atac/ contains the sample-genomic region ATAC tag count table, as well as the sample metadata and a gene set file of cancer hallmark genes.

scATAC/  contains the cell barcode-genomic region ATAC tag count table, as well as the barcode metadata and the 10k pbmc dataset pre-analyzed in h5 AnnData format.
DOI: 10.5281/zenodo.10926960
title: MUFFIN : A suite of tools for the analysis of functional sequencing data - Example input data

description: This repository contains the data required to run the example notebooks and to reproduce the figures from the paper : 



MUFFIN : A suite of tools for the analysis of functional sequencing data


Pierre de Langen, Benoit Ballester

bioRxiv 2023.12.11.570597; doi: https://doi.org/10.1101/2023.12.11.570597

 

Source code is located here :

https://github.com/pdelangen/Muffin

 



10k_pbmc_gene/ contains the data for 10k pbmc dataset in standard 10x sparse count table format.

genome_annot/ contains gencode v38 and chromosomes for the human (used for gene set enrichment analyses)

GO_files/ contains gene set information retrieved from the g:ProfileR website.

immune_chip/ contains the data required to re-run the ChIP-seq analyses, it will require to also launch the dl_data.smk to retrieve the data from ENCODE.

tcga_atac/ contains the sample-genomic region ATAC tag count table, as well as the sample metadata and a gene set file of cancer hallmark genes.

scATAC/  contains the cell barcode-genomic region ATAC tag count table, as well as the barcode metadata and the 10k pbmc dataset pre-analyzed in h5 AnnData format.
DOI: 10.5281/zenodo.10950191
title: MUFFIN : A suite of tools for the analysis of functional sequencing data - Example input data

description: This repository contains the data required to run the example notebooks and to reproduce the figures from the paper : 



MUFFIN : A suite of tools for the analysis of functional sequencing data


Pierre de Langen, Benoit Ballester

bioRxiv 2023.12.11.570597; doi: https://doi.org/10.1101/2023.12.11.570597

 

Source code is located here :

https://github.com/pdelangen/Muffin

 



10k_pbmc_gene/ contains the data for 10k pbmc dataset in standard 10x sparse count table format.

genome_annot/ contains gencode v38 and chromosomes for the human (used for gene set enrichment analyses)

GO_files/ contains gene set information retrieved from the g:ProfileR website.

immune_chip/ contains the data required to re-run the ChIP-seq analyses, it will require to also launch the dl_data.smk to retrieve the data from ENCODE.

tcga_atac/ contains the sample-genomic region ATAC tag count table, as well as the sample metadata and a gene set file of cancer hallmark genes.

scATAC/  contains the cell barcode-genomic region ATAC tag count table, as well as the barcode metadata and the 10k pbmc dataset pre-analyzed in h5 AnnData format.
DOI: 10.15468/dl.d5vstb
title: Occurrence Download

description: A dataset containing 467 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Nepal",
 "TaxonKey is Celastraceae"
 ]
}

 The dataset includes 467 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008001-180824113759888/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7gpxa4
title: Occurrence Download

description: A dataset containing 15 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Equilabium selukwense (N.E.Br.) Mwany. & A.J.Paton"
 ]
}

 The dataset includes 15 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0044169-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.esxhnj
title: Occurrence Download

description: A dataset containing 17 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "BasisOfRecord is Human Observation",
 "BasisOfRecord is Material sample",
 "BasisOfRecord is Specimen",
 "BasisOfRecord is Machine Observation"
 ]
 },
 "Geometry POLYGON((-65.83008 -60.19616,-16.34766 -60.67318,-15.11719 -42.81152,-13.71094 -12.89749,-31.28906 10.83331,-43.24219 24.84657,-38.32031 36.87962,-25.83984 65.58572,-36.38672 67.54217,-47.63672 67.54217,-68.68652 67.25506,-69.16992 65.54937,-77.21191 64.68032,-78.00293 63.33241,-77.3877 62.20651,-72.68555 59.04055,-70.13672 53.85253,-76.24512 48.95137,-78.83789 41.83683,-82.44141 37.30028,-95.80078 33.57801,-101.77734 27.21556,-98.10791 18.16673,-94.81201 17.28771,-90.06592 14.96601,-87.60498 15.00846,-85.18799 13.94473,-84.35303 10.2933,-82.33154 8.68964,-81.10107 8.47237,-80.52979 8.6462,-79.29932 9.25394,-78.46436 8.9936,-77.03613 7.4932,-69.60937 2.1089,-50.97656 -14.26438,-68.99414 -40.5138,-72.1582 -51.01375,-68.4668 -54.41893,-65.83008 -60.19616))",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Euthyonidiella arenicola (Pawson & Miller, 1992)"
 ]
}

 The dataset includes 17 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0197410-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dvzyga
title: Occurrence Download

description: A dataset containing 21 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ceratophyus martinezi Lauffer, 1909"
 ]
}

 The dataset includes 21 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008001-181108115102211/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.c7v3kk
title: Occurrence Download

description: A dataset containing 1701428 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "Year 2019-2024"
 ]
}

 The dataset includes 1701428 records from 1021 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0044178-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vgs7bd
title: Occurrence Download

description: A dataset containing 995 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "TaxonKey is Polygonaceae",
 "TaxonKey is Rumex L."
 ]
 },
 "Country is Morocco",
 "BasisOfRecord is Specimen"
 ]
}

 The dataset includes 995 records from 30 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002071-160822134323880/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ii6yoi
title: Occurrence Download

description: A dataset containing 2374 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "TaxonKey is Cucurbita pepo L."
 ]
}

 The dataset includes 2374 records from 65 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020600-191105090559680/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rsax3g
title: Occurrence Download

description: A dataset containing 239 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Coelocaryon botryoides Vermoesen"
 ]
}

 The dataset includes 239 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006993-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.osyvrl
title: Occurrence Download

description: A dataset containing 3549 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Casuarius casuarius (Linnaeus, 1758)"
 ]
}

 The dataset includes 3549 records from 76 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002071-171219132708484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nmwhqj
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Desmodium schubertianum Standl. & L.O.Williams"
 ]
}

 The dataset includes 6 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0171727-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ny9wtq
title: Occurrence Download

description: A dataset containing 3134 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Country is Mexico",
 {
 "or" : [
 "Year 1965-2019",
 "Year 1967-2019"
 ]
 },
 "HasCoordinate is true",
 "TaxonKey is Papaveraceae",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 3134 records from 115 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016379-191105090559680/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hownac
title: Occurrence Download

description: A dataset containing 4312 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ammodramus bairdii (Audubon, 1844)"
 ]
}

 The dataset includes 4312 records from 52 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002072-150221044754056/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.93s4um
title: Occurrence Download

description: A dataset containing 7 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Desmodium schusteri (Schindl.) Standl."
 ]
}

 The dataset includes 7 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0171729-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.