cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.26716621
title: Additional file 13 of Comprehensive analysis of the REST transcription factor regulatory networks in IDH mutant and IDH wild-type glioma cell lines and tumors

description: Additional file 13. Number of cytosines within REST or KAISO motifs within REST ChIP-seq peaks assigned to REST-repressed or -activated targets. The peaks were categorized according to whether they had detected binding motifs of both REST and KAISO, or just one of them.
DOI: 10.6084/m9.figshare.26716621.v1
title: Additional file 13 of Comprehensive analysis of the REST transcription factor regulatory networks in IDH mutant and IDH wild-type glioma cell lines and tumors

description: Additional file 13. Number of cytosines within REST or KAISO motifs within REST ChIP-seq peaks assigned to REST-repressed or -activated targets. The peaks were categorized according to whether they had detected binding motifs of both REST and KAISO, or just one of them.
DOI: 10.6084/m9.figshare.26716624
title: Additional file 14 of Comprehensive analysis of the REST transcription factor regulatory networks in IDH mutant and IDH wild-type glioma cell lines and tumors

description: Additional file 14. Number of sites where individual REST or KAISO motifs were detected within REST ChIP-seq peaks derived from the cell lines. Sites discovered as differentially methylated among glioma tumor groups were matched to individual REST or KAISO motifs and then to peaks that were paired with REST-repressed or -activated targets. The number of all detected sites of REST or KAISO motifs and the number of differentially methylated sites were significantly different (Chi2 = 34.763, df = 14, p-value = 0.001593). Asterisk indicates differences in DNA methylation larger than expected by chance (*). ND - no data.
DOI: 10.6084/m9.figshare.26716624.v1
title: Additional file 14 of Comprehensive analysis of the REST transcription factor regulatory networks in IDH mutant and IDH wild-type glioma cell lines and tumors

description: Additional file 14. Number of sites where individual REST or KAISO motifs were detected within REST ChIP-seq peaks derived from the cell lines. Sites discovered as differentially methylated among glioma tumor groups were matched to individual REST or KAISO motifs and then to peaks that were paired with REST-repressed or -activated targets. The number of all detected sites of REST or KAISO motifs and the number of differentially methylated sites were significantly different (Chi2 = 34.763, df = 14, p-value = 0.001593). Asterisk indicates differences in DNA methylation larger than expected by chance (*). ND - no data.
DOI: 10.6084/m9.figshare.26716627
title: Additional file 15 of Comprehensive analysis of the REST transcription factor regulatory networks in IDH mutant and IDH wild-type glioma cell lines and tumors

description: Additional file 15. List of REST repressed or REST activated genes containing differentially methylated sites in REST or KAISO motifs within the associated REST ChiP-seq peaks.
DOI: 10.6084/m9.figshare.26716627.v1
title: Additional file 15 of Comprehensive analysis of the REST transcription factor regulatory networks in IDH mutant and IDH wild-type glioma cell lines and tumors

description: Additional file 15. List of REST repressed or REST activated genes containing differentially methylated sites in REST or KAISO motifs within the associated REST ChiP-seq peaks.
DOI: 10.6084/m9.figshare.25763107
title: Additional file 2 of Novel genome-wide DNA methylation profiling reveals distinct epigenetic landscape, prognostic model and cellular composition of early-stage lung adenocarcinoma

description: Supplementary Material 2
DOI: 10.6084/m9.figshare.25763107.v1
title: Additional file 2 of Novel genome-wide DNA methylation profiling reveals distinct epigenetic landscape, prognostic model and cellular composition of early-stage lung adenocarcinoma

description: Supplementary Material 2
DOI: 10.6084/m9.figshare.25763118
title: Additional file 2 of Identification and characterization of whole blood gene expression and splicing quantitative trait loci during early to mid-lactation of dairy cattle

description: Supplementary Material 2
DOI: 10.6084/m9.figshare.25763118.v1
title: Additional file 2 of Identification and characterization of whole blood gene expression and splicing quantitative trait loci during early to mid-lactation of dairy cattle

description: Supplementary Material 2
DOI: 10.5281/zenodo.13338592
title: Conceptual Assessment Questions with Experts - OntoTurnover

description: Objective: To describe the questions and alternatives used in the conceptual evaluation with experts carried out in the OntoTurnover engineering process.
DOI: 10.5281/zenodo.13338593
title: Conceptual Assessment Questions with Experts - OntoTurnover

description: Objective: To describe the questions and alternatives used in the conceptual evaluation with experts carried out in the OntoTurnover engineering process.
DOI: 10.6084/m9.figshare.26716726
title: Additional file 4 of Elucidating the callus-to-shoot-forming mechanism in Capsicum annuum ‘Dempsey’ through comparative transcriptome analyses

description: Supplementary Material 4: Data S1 Annotation and differential expression data for C. annuum ‘Dempsey’ with four other species for comparison. Data S2 DiVenn 2.0 differential expression data for the callus transcriptomes of C. annuum ‘Dempsey’ and four other species. Data S3 DiVenn 2.0 differential expression data for the shoot transcriptomes of C. annuum ‘Dempsey’ and four other species. Data S4 Phytohormone-related gene expression in K-means clusters 1, 3, and 5 of C. annuum ‘Dempsey’ and four other species.
DOI: 10.6084/m9.figshare.26716726.v1
title: Additional file 4 of Elucidating the callus-to-shoot-forming mechanism in Capsicum annuum ‘Dempsey’ through comparative transcriptome analyses

description: Supplementary Material 4: Data S1 Annotation and differential expression data for C. annuum ‘Dempsey’ with four other species for comparison. Data S2 DiVenn 2.0 differential expression data for the callus transcriptomes of C. annuum ‘Dempsey’ and four other species. Data S3 DiVenn 2.0 differential expression data for the shoot transcriptomes of C. annuum ‘Dempsey’ and four other species. Data S4 Phytohormone-related gene expression in K-means clusters 1, 3, and 5 of C. annuum ‘Dempsey’ and four other species.
DOI: 10.6084/m9.figshare.26776966
title: CPB larval preweights Dec. 2021

description: Larval preweights for CPB performance experiment Dec 2021, used to calculate larval weight change in 'Larval_performance_Sept2021.R' code
DOI: 10.6084/m9.figshare.26776966.v1
title: CPB larval preweights Dec. 2021

description: Larval preweights for CPB performance experiment Dec 2021, used to calculate larval weight change in 'Larval_performance_Sept2021.R' code
DOI: 10.6084/m9.figshare.26716837
title: Additional file 9 of Short-term exposure to antibiotics begets long-term disturbance in gut microbial metabolism and molecular ecological networks

description: Additional file 9: Table S1. Dissimilarity comparison of microbial diversities between antibiotic group and control.
DOI: 10.6084/m9.figshare.26716837.v1
title: Additional file 9 of Short-term exposure to antibiotics begets long-term disturbance in gut microbial metabolism and molecular ecological networks

description: Additional file 9: Table S1. Dissimilarity comparison of microbial diversities between antibiotic group and control.
DOI: 10.6084/m9.figshare.26716840
title: Additional file 10 of Short-term exposure to antibiotics begets long-term disturbance in gut microbial metabolism and molecular ecological networks

description: Additional file 10: Table S2. Parameters of empirical networks.
DOI: 10.6084/m9.figshare.26716840.v1
title: Additional file 10 of Short-term exposure to antibiotics begets long-term disturbance in gut microbial metabolism and molecular ecological networks

description: Additional file 10: Table S2. Parameters of empirical networks.
DOI: 10.15468/dl.kce3ag
title: Occurrence Download

description: A dataset containing 115935 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is ZFMK Ichthyology collection"
 ]
}

 The dataset includes 115935 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0059043-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.lwwgaf
title: Occurrence Download

description: A dataset containing 46 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cuculus micropterus Gould, 1838",
 "Country is Bhutan"
 ]
}

 The dataset includes 46 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015608-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qlx1gv
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "DatasetKey is Atlas de las Aves de México: Fase II",
 "TaxonKey is Colinus virginianus nigripectus Nelson, 1897"
 ]
}

 The dataset includes 4 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001918-180730143533302/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ydofbl
title: Occurrence Download

description: A dataset containing 329502 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Country is United States of America",
 {
 "or" : [
 "Issue is Coordinate reprojected",
 "Issue is Coordinate rounded",
 "Issue is Recorded date mismatch",
 "Issue is Recorded date invalid"
 ]
 },
 "TaxonKey is Reptilia"
 ]
}

 The dataset includes 329502 records from 119 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015610-180131172636756/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9xmnsi
title: Occurrence Download

description: A dataset containing 5693 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "Country is Mexico",
 "Country is United States of America"
 ]
 },
 "TaxonKey is Senecio flaccidus Less."
 ]
}

 The dataset includes 5693 records from 77 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001918-190307172214381/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.extwrx
title: Occurrence Download

description: A dataset containing 272 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "TaxonKey is Nymphaea mexicana Zucc."
 ]
 },
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 272 records from 50 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015610-180508205500799/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bvjjym
title: Occurrence Download

description: A dataset containing 87 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Chloris chloridea (J.Presl) Hitchc."
 ]
}

 The dataset includes 87 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001918-190621201848488/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.umoz02
title: Occurrence Download

description: A dataset containing 17 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Colombia",
 "TaxonKey is Aotus zonalis Goldman, 1914"
 ]
}

 The dataset includes 17 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015610-181003121212138/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mdsw93
title: Occurrence Download

description: A dataset containing 6199 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "Country is Mexico",
 "Country is United States of America"
 ]
 },
 "HasCoordinate is true",
 "TaxonKey is Agkistrodon contortrix (Linnaeus, 1766)",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 6199 records from 40 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017762-200221144449610/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nnkzvj
title: Occurrence Download

description: A dataset containing 359 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Penelope albipennis Taczanowski, 1878"
 ]
}

 The dataset includes 359 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015610-181108115102211/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6vhtt3
title: Occurrence Download

description: A dataset containing 48 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Combretum goldieanum F.Muell."
 ]
}

 The dataset includes 48 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015666-200127171203522/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.irs4oy
title: Occurrence Download

description: A dataset containing 37308 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "BasisOfRecord is Observation",
 "BasisOfRecord is Machine Observation",
 "BasisOfRecord is Human Observation",
 "BasisOfRecord is Material sample",
 "BasisOfRecord is Literature Occurrence",
 "BasisOfRecord is Specimen",
 "BasisOfRecord is Living Specimen",
 "BasisOfRecord is Unknown evidence"
 ]
 },
 "Country is Mexico",
 "Year 2000-2019",
 "HasCoordinate is true",
 "TaxonKey is Streptopelia decaocto (Frivaldszky, 1838)",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 37308 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015611-190415153152247/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xdqc4p
title: Occurrence Download

description: A dataset containing 284 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Coriolopsis floccosa (Jungh.) Ryvarden"
 ]
}

 The dataset includes 284 records from 30 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023486-200221144449610/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fjlmms
title: Occurrence Download

description: A dataset containing 30 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Leucopternis occidentalis Salvin, 1876"
 ]
}

 The dataset includes 30 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015610-171219132708484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.uc8uj3
title: Occurrence Download

description: A dataset containing 11 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Heteromys teleus Anderson & Jarrín-V., 2002"
 ]
}

 The dataset includes 11 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015612-181108115102211/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.upevxn
title: Occurrence Download

description: A dataset containing 6210 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Abundances and biological traits of the juveniles salmon sampled in the survey of Salmon abundance Indices in the Nivelle river (France)"
 ]
}

 The dataset includes 6210 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023498-200221144449610/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.10342364
title: Beyond benchmarking: towards predictive models of dataset-specific single-cell RNA-seq pipeline performance

description: This repository includes:

clusters.zip

.Once unzipped, the top-level directory is named clusters/.

Within this directory, there are 86 sub-directories, one for each of the scRNA-seq datasets used in the paper. These sub-directories are named with the corresponding EBI Single Cell Atlas IDs.

Each sub-directory contains CSV files containing clustering results for each of the pipelines run on that dataset.
*_unscaled.csv 

CSV files containing raw performance metrics (CH, DB, SIL, GSEA) computed on each pipeline and dataset combination
*CorrectedImputed.csv and gseaScaledImputed.csv

CSV files containing performance metrics corrected for the number of clusters and missing values imputed in the case of CH, SIL, and DB. For GSEA, only scaling and imputation was performed.
pipelineParams.csv and datasetFeatures.csv

CSV files containing parameters used for each of the pipelines run, and dataset summary statistics for each of the scRNA-seq datasets.
DOI: 10.15468/dl.4ujjwn
title: Occurrence Download

description: A dataset containing 215144 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Coturnix coturnix (Linnaeus, 1758)",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 215144 records from 341 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015612-190415153152247/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qnwpok
title: Occurrence Download

description: A dataset containing 5496 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Abondances et caractéristiques biologiques des juvéniles de saumons échantillonnés lors des indices d'abondance du saumon dans la rivière Nivelle (France)"
 ]
}

 The dataset includes 5496 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023487-200221144449610/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.10342363
title: Beyond benchmarking and towards predictive models of dataset-specific single-cell RNA-seq pipeline performance

description: This repository includes:



clusters.zip



.Once unzipped, the top-level directory is named clusters/.



Within this directory, there are 86 sub-directories, one for each of the scRNA-seq datasets used in the paper. These sub-directories are named with the corresponding EBI Single Cell Atlas IDs.



Each sub-directory contains CSV files containing clustering results for each of the pipelines run on that dataset.







*_unscaled.csv 



CSV files containing raw performance metrics (CH, DB, SIL, GSEA) computed on each pipeline and dataset combination



*CorrectedImputed.csv and gseaScaledImputed.csv



CSV files containing performance metrics corrected for the number of clusters and missing values imputed in the case of CH, SIL, and DB. For GSEA, only scaling and imputation was performed.



pipelineParams.csv and datasetFeatures.csv



CSV files containing parameters used for each of the pipelines run, and dataset summary statistics for each of the scRNA-seq datasets.




Files with the prefix "large_samples" correspond to data associated with the 6 scRNA-seq datasets containing >100k cells. The large_samples_clusters.zip file contains the same structure as cluster.zip, but with 6 sub-directories.
DOI: 10.5281/zenodo.11403435
title: Beyond benchmarking and towards predictive models of dataset-specific single-cell RNA-seq pipeline performance

description: This repository includes:



clusters.zip



.Once unzipped, the top-level directory is named clusters/.



Within this directory, there are 86 sub-directories, one for each of the scRNA-seq datasets used in the paper. These sub-directories are named with the corresponding EBI Single Cell Atlas IDs.



Each sub-directory contains CSV files containing clustering results for each of the pipelines run on that dataset.







*_unscaled.csv 



CSV files containing raw performance metrics (CH, DB, SIL, GSEA) computed on each pipeline and dataset combination



*CorrectedImputed.csv and gseaScaledImputed.csv



CSV files containing performance metrics corrected for the number of clusters and missing values imputed in the case of CH, SIL, and DB. For GSEA, only scaling and imputation was performed.



pipelineParams.csv and datasetFeatures.csv



CSV files containing parameters used for each of the pipelines run, and dataset summary statistics for each of the scRNA-seq datasets.




Files with the prefix "large_samples" correspond to data associated with the 6 scRNA-seq datasets containing >100k cells. The large_samples_clusters.zip file contains the same structure as cluster.zip, but with 6 sub-directories.
DOI: 10.15468/dl.koa0er
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "or" : [
 "DatasetKey is Penguins of Antarctica"
 ]
}

 The dataset includes 5 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017142-180508205500799/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.paabv7
title: Occurrence Download

description: A dataset containing 57860 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is French Polynesia",
 "TaxonKey is Tracheophyta"
 ]
}

 The dataset includes 57860 records from 64 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015613-180131172636756/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3rjcbs
title: Occurrence Download

description: A dataset containing 80 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Zimbabwe",
 "TaxonKey is Prunus africana (Hook.fil.) Kalkman"
 ]
}

 The dataset includes 80 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009356-200221144449610/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zkqt2v
title: Occurrence Download

description: A dataset containing 314880 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Vaccinium myrtillus L.",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 314880 records from 415 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015614-181003121212138/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.