cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.18182843
title: Supplementary Data for: MASA – a computational tool to predict transcription factor activity from ATAC-seq

description: 1. Reference Data (Configuration)

This dataset contains the genomic background files and nucleotide codes required for the MASA (with HOMER motif enrichment option) software/pipeline. The data covers Human (hg19) and Mouse (mm10) reference genomes.

Extract these files into your MASA configuration directory to enable analysis on specific genome builds.



hg19_nuccode_v1.0.tar.gz : Nucleotide code mapping files for Human genome (hg19).

mm10_nuccode_v1.0.tar.gz: Nucleotide code mapping files for Mouse genome (mm10).

hg19_files_v1.0.tar.xz: Motif DB for Human (hg19).

mm10_files_v1.0.tar.xz: Motif DB for Mouse (mm10).


2. Vignette & Reproduction Data (Fed vs Fasted)

These files allow users to reproduce the analysis presented in the MASA manuscript and vignette.



bg_files_fed_fasted.tar.gz : Final Output Directory. Contains the complete MASA results for the Fed vs Fasted comparison, except the nuccode files.

bam_merged.tar.gz : Merged BAM files combining replicates for each condition.

bam_replicates.tar.gz : Raw alignment files (BAM) for individual replicates (3 Fed, 3 Fasted). (Note: Large file)

tag_directories.tar.gz : Intermediate tag directories generated by HOMER during the MASA pipeline execution.

macs2.tar.gz : MACS2 peak calling results (narrowPeak files) generated from the merged BAM files for each condition (Fed and Fasted).
description: Instructions for Reproducing the Vignette Directory Structure:

To run the MASA vignette using these datasets, please extract all downloaded archives (.tar.gz) and organize the files into the following directory structure:





BAM and Tag Directories: Create a directory named /YOUR_PROJECT_NAME/bam_merged. Place all extracted  files (from bam_merged.tar.gz and bam_replicates.tar.gz) and the extracted Tag Directories (from tag_directories.tar.gz) into this folder. The name of the bam replicates (.bam and .bai should be renammed feloowing this example fed_1.bam and fed_1.bai.




Peak Files: Create a directory named /YOUR_PROJECT_NAME/macs2. Place all extracted peak files (from macs2.tar.gz) into this folder.




Nucleotide Codes: Place the extracted nucleotide code files (e.g., contents of mm10_nuccode_v1.0) directly inside the MASA result directory bg_files_fed_fasted (this directory is referred to as bg_dir in the vignette code).


Motif Database: Important: Do not forget to download the Motif Database archive (mm10_files / hg19_files). MASA requires access to this database to perform the analysis.


Note: Ensure all archives are fully unzipped before running the analysis.
DOI: 10.5281/zenodo.18182842
title: Supplementary Data for: MASA – a computational tool to predict transcription factor activity from ATAC-seq

description: 1. Reference Data (Configuration)

This dataset contains the genomic background files and nucleotide codes required for the MASA (with HOMER motif enrichment option) software/pipeline. The data covers Human (hg19) and Mouse (mm10) reference genomes.

Extract these files into your MASA configuration directory to enable analysis on specific genome builds.



hg19_nuccode_v1.0.tar.gz : Nucleotide code mapping files for Human genome (hg19).

mm10_nuccode_v1.0.tar.gz: Nucleotide code mapping files for Mouse genome (mm10).

hg19_files_v1.0.tar.xz: Motif DB for Human (hg19).

mm10_files_v1.0.tar.xz: Motif DB for Mouse (mm10).


2. Vignette & Reproduction Data (Fed vs Fasted)

These files allow users to reproduce the analysis presented in the MASA manuscript and vignette.



bg_files_fed_fasted.tar.gz : Final Output Directory. Contains the complete MASA results for the Fed vs Fasted comparison, except the nuccode files.

bam_merged.tar.gz : Merged BAM files combining replicates for each condition.

bam_replicates.tar.gz : Raw alignment files (BAM) for individual replicates (3 Fed, 3 Fasted). (Note: Large file)

tag_directories.tar.gz : Intermediate tag directories generated by HOMER during the MASA pipeline execution.

macs2.tar.gz : MACS2 peak calling results (narrowPeak files) generated from the merged BAM files for each condition (Fed and Fasted).
description: Instructions for Reproducing the Vignette Directory Structure:

To run the MASA vignette using these datasets, please extract all downloaded archives (.tar.gz) and organize the files into the following directory structure:





BAM and Tag Directories: Create a directory named /YOUR_PROJECT_NAME/bam_merged. Place all extracted  files (from bam_merged.tar.gz and bam_replicates.tar.gz) and the extracted Tag Directories (from tag_directories.tar.gz) into this folder. The name of the bam replicates (.bam and .bai should be renammed feloowing this example fed_1.bam and fed_1.bai.




Peak Files: Create a directory named /YOUR_PROJECT_NAME/macs2. Place all extracted peak files (from macs2.tar.gz) into this folder.




Nucleotide Codes: Place the extracted nucleotide code files (e.g., contents of mm10_nuccode_v1.0) directly inside the MASA result directory bg_files_fed_fasted (this directory is referred to as bg_dir in the vignette code).


Motif Database: Important: Do not forget to download the Motif Database archive (mm10_files / hg19_files). MASA requires access to this database to perform the analysis.


Note: Ensure all archives are fully unzipped before running the analysis.
DOI: 10.5281/zenodo.18523242
title: Datasets for "A Design Space-Based Network for Efficient and Accurate Fish Recognition in Aquaculture"

description: This dataset serves as supplementary material for the manuscript titled "A Design Space-Based Network for Efficient and Accurate FishRecognition in Aquaculture", submitted to the journal Ecological Informatics.

Content:This repository contains the experimental data used in the study.

Usage:Please refer to the associated GitHub repository for code and usage instructions: https://github.com/X1a0hu/A-Design-Space-Based-Network-for-Efficient-and-Accurate-Fish-Recognition-in-Aquaculture
DOI: 10.5281/zenodo.18523241
title: Datasets for "A Design Space-Based Network for Efficient and Accurate Fish Recognition in Aquaculture"

description: This dataset serves as supplementary material for the manuscript titled "A Design Space-Based Network for Efficient and Accurate FishRecognition in Aquaculture", submitted to the journal Ecological Informatics.

Content:This repository contains the experimental data used in the study.

Usage:Please refer to the associated GitHub repository for code and usage instructions: https://github.com/X1a0hu/A-Design-Space-Based-Network-for-Efficient-and-Accurate-Fish-Recognition-in-Aquaculture
DOI: 10.15468/dl.y7pftu
title: Occurrence Download

description: A dataset containing 326 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cymodocea rotundata",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 326 records from 31 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001229-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qytzvv
title: Occurrence Download

description: A dataset containing 2154 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Pereskia aculeata"
 ]
}

 The dataset includes 2154 records from 162 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001230-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2zy3sc
title: Occurrence Download

description: A dataset containing 170 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Halodule pinifolia",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 170 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001231-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9nyy8z
title: Occurrence Download

description: A dataset containing 1232536 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Vanellus chilensis",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 1232536 records from 593 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001184-260208012135463/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.28888299
title: Additional file 2 of DNA methylation associated with the serum alanine aminotransferase concentration: evidence from Chinese monozygotic twins

description: Additional file 2.
DOI: 10.6084/m9.figshare.28888299.v1
title: Additional file 2 of DNA methylation associated with the serum alanine aminotransferase concentration: evidence from Chinese monozygotic twins

description: Additional file 2.
DOI: 10.6084/m9.figshare.28888303
title: Additional file 1 of Integrative DNA methylome and transcriptome analysis identify potential genes on the influence of dilated cardiomyopathy-associated heart failure

description: Additional file1 (XLSX 9 KB)
DOI: 10.6084/m9.figshare.28888303.v1
title: Additional file 1 of Integrative DNA methylome and transcriptome analysis identify potential genes on the influence of dilated cardiomyopathy-associated heart failure

description: Additional file1 (XLSX 9 KB)
DOI: 10.15468/dl.qa8pbs
title: Occurrence Download

description: A dataset containing 50 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Amritodus atkinsoni"
 ]
}

 The dataset includes 50 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026513-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2bubxf
title: Occurrence Download

description: A dataset containing 309 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Bupleurum komarovianum"
 ]
}

 The dataset includes 309 records from 31 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026515-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4ptfs3
title: Occurrence Download

description: A dataset containing 32 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cytisus multiflorus",
 "Country is United States of America",
 "HasCoordinate is true"
 ]
}

 The dataset includes 32 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026512-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.uth5mn
title: Occurrence Download

description: A dataset containing 100 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Tinca tinca",
 "Country is Canada",
 "HasCoordinate is true"
 ]
}

 The dataset includes 100 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026516-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3xf85e
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Tinca tinca",
 "Country is Chile",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026517-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.enju94
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Tinca tinca",
 "Country is India",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026518-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hbpc2w
title: Occurrence Download

description: A dataset containing 301 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "TaxonKey is Castanopsis echinocarpa"
 ]
}

 The dataset includes 301 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026521-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sdpdg3
title: Occurrence Download

description: A dataset containing 434 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Byblis filifolia"
 ]
}

 The dataset includes 434 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026520-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gxb7bx
title: Occurrence Download

description: A dataset containing 1349 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Phaulopsis imbricata",
 "HasCoordinate is true",
 "Geometry POLYGON ((-17.66889 -35.11691, 51.34702 -35.11691, 51.34702 37.62, -17.66889 37.62, -17.66889 -35.11691))"
 ]
}

 The dataset includes 1349 records from 62 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026519-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.d3vmb2
title: Occurrence Download

description: A dataset containing 26 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Melanoides tuberculata",
 "Country is Jamaica",
 "HasCoordinate is true"
 ]
}

 The dataset includes 26 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026523-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cwxn5h
title: Occurrence Download

description: A dataset containing 173 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Melanoides tuberculata",
 "Country is Mexico",
 "HasCoordinate is true"
 ]
}

 The dataset includes 173 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026524-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tahjv4
title: Occurrence Download

description: A dataset containing 1008 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cytisus proliferus",
 "Country is New Zealand",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1008 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026528-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.td78bc
title: Occurrence Download

description: A dataset containing 731 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Byblis liniflora"
 ]
}

 The dataset includes 731 records from 34 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026527-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8x6vg4
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "BasisOfRecord is one of (Human Observation, Machine Observation, Occurrence evidence, Observation)",
 "TaxonKey is one of (Ardea herodias)",
 "Country is one of (Afghanistan, Armenia, Azerbaijan, Bahrain, Bangladesh, Bhutan, Brunei Darussalam, Cambodia, China, Cyprus, Georgia, Hong Kong, India, Indonesia, Iran (Islamic Republic of), Iraq, Israel, Japan, Jordan, Kazakhstan, Korea (Democratic People’s Republic of), Korea, Republic of, Kuwait, Kyrgyzstan, Lao People’s Democratic Republic, Lebanon, Macao, Malaysia, Maldives, Mongolia, Myanmar, Nepal, Oman, Pakistan, Palestine, State of, Philippines, Qatar, Saudi Arabia, Singapore, Sri Lanka, Syrian Arab Republic, Tajikistan, Thailand, Timor-Leste, Türkiye, Turkmenistan, United Arab Emirates, Uzbekistan, Viet Nam, Yemen)"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026530-250717081556266/datasets/export for details.
DOI: 10.15468/dl.4tekfu
title: Occurrence Download

description: A dataset containing 35 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Melanoides tuberculata",
 "Country is Peru",
 "HasCoordinate is true"
 ]
}

 The dataset includes 35 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026525-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.v88wgb
title: Occurrence Download

description: A dataset containing 22 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Tinca tinca",
 "Country is Ireland",
 "HasCoordinate is true"
 ]
}

 The dataset includes 22 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026533-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fbk752
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Tinca tinca",
 "Country is Israel",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026534-250717081556266/datasets/export for details.
DOI: 10.15468/dl.ynzqrd
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Tinca tinca",
 "Country is Japan",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026535-250717081556266/datasets/export for details.
DOI: 10.15468/dl.tjr9xc
title: Occurrence Download

description: A dataset containing 258 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Byblis gigantea"
 ]
}

 The dataset includes 258 records from 44 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026536-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.49wrc6
title: Occurrence Download

description: A dataset containing 69 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Melanoides tuberculata",
 "Country is Trinidad and Tobago",
 "HasCoordinate is true"
 ]
}

 The dataset includes 69 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026539-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cwyt75
title: Occurrence Download

description: A dataset containing 2388 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Thunbergia alata",
 "HasCoordinate is true",
 "Geometry POLYGON ((-17.66889 -35.11691, 51.34702 -35.11691, 51.34702 37.62, -17.66889 37.62, -17.66889 -35.11691))"
 ]
}

 The dataset includes 2388 records from 62 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026538-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kvjuxe
title: Occurrence Download

description: A dataset containing 246500 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Buddleja davidii"
 ]
}

 The dataset includes 246500 records from 1714 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026449-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.p8kmp9
title: Occurrence Download

description: A dataset containing 1301 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Sciurus carolinensis",
 "HasCoordinate is true",
 "Country is Italy"
 ]
}

 The dataset includes 1301 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000456-251009101135966/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.13140/rg.2.1.2053.9765
title: Hoff, M., Deluzarche, F., 2016. Daphne laureola L. dans l’Herbier de l’Université de Strasbourg (STR) : 5 p. Herbier de l’Université de Strasbourg.
DOI: 10.25824/redu/uo6w2i
title: Perfil dos cuidadores e crianças, escala de sobrecarga e narrativas abertas

description: O presente conjunto de dados reúne informações obtidas em pesquisa voltada à compreensão da sobrecarga e das necessidades de informação de cuidadores de crianças e adolescentes com epilepsia. Sua finalidade é oferecer subsídios para análises quantitativas e qualitativas que possam contribuir para a produção de conhecimento científico e para o planejamento de estratégias de apoio aos cuidadores e às famílias. Os dados quantitativos consiste em dados relacionado ao perfil sociodemografico dos cuidadores e crianças com epilepsia, scores obtidos da escala de sobrecarga Burden Interview. Os dados qualitativos corresponde a três perguntas abertas respondidas de forma dissertativa que exploram percepções, dificuldades, necessidades de informação e experiências vividas pelos cuidadores no cotidiano do cuidador. A natureza dos dados é mista, integrando informações quantitativas (variáveis categóricas e contínuas provenientes dos perfis e da escala de sobrecarga) e qualitativas (respostas abertas com relatos e percepções dos participantes). Essa combinação possibilita análises multimétodos, abrangendo tanto a caracterização estatística do fenômeno quanto a compreensão em profundidade das vivências subjetivas.
DOI: 10.15468/dl.8n62v9
title: Occurrence Download

description: A dataset containing 298772 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Briza media L.",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 298772 records from 679 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0289937-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.