cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.17527449
title: Cell-free DNA methylome and fragmentome analysis for relapse monitoring of Ewing Sarcoma - figure generation

description: This repository holds code behind the manuscript "Cell-free DNA methylome and fragmentome analysis for relapse monitoring of Ewing Sarcoma" by Richardson, Safrastyan, Karimpour et al. This contains the code and data required to regenerate all the figures in the paper. 

The code is structured as follows:



input: Inputs required to generate the figures. Some will be generated by `final_markdowns` scripts.

final_markdowns: Scripts to generate the figures in the paper, given all the inputs in `input`. These are separate RMarkdown files, and should be self-contained, and are able to be ran directly based on the files within `input`. They should be ideally run in order, or at the very least before the final Table generation/export. 

`Rlib_info` in `final_markdowns` contains commonly used R packages and their versions
description: This work was funded by the CRUK National Biomarker Centre (CTRNBC-2022/100001), The Christie Charitable Trust and the Children's Cancer Research Fund (DIVE/2023). Support was received from the Manchester Experimental Cancer Medicines Centre and the National Institute for Health and Care Research (NIHR) Manchester Biomedical Research Centre (BRC) (NIHR203308).
DOI: 10.5281/zenodo.17527450
title: Cell-free DNA methylome and fragmentome analysis for relapse monitoring of Ewing Sarcoma - figure generation

description: This repository holds code behind the manuscript "Cell-free DNA methylome and fragmentome analysis for relapse monitoring of Ewing Sarcoma" by Richardson, Safrastyan, Karimpour et al. This contains the code and data required to regenerate all the figures in the paper. 

The code is structured as follows:



input: Inputs required to generate the figures. Some will be generated by `final_markdowns` scripts.

final_markdowns: Scripts to generate the figures in the paper, given all the inputs in `input`. These are separate RMarkdown files, and should be self-contained, and are able to be ran directly based on the files within `input`. They should be ideally run in order, or at the very least before the final Table generation/export. 

`Rlib_info` in `final_markdowns` contains commonly used R packages and their versions
description: This work was funded by the CRUK National Biomarker Centre (CTRNBC-2022/100001), The Christie Charitable Trust and the Children's Cancer Research Fund (DIVE/2023). Support was received from the Manchester Experimental Cancer Medicines Centre and the National Institute for Health and Care Research (NIHR) Manchester Biomedical Research Centre (BRC) (NIHR203308).
DOI: 10.15468/dl.eb6pzf
title: Occurrence Download

description: A dataset containing 1472 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Croatia",
 "OccurrenceStatus is Present",
 "TaxonKey is Ciconia nigra"
 ]
}

 The dataset includes 1472 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002438-260119153935675/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sq2guq
title: Occurrence Download

description: A dataset containing 839 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Callitris oblonga",
 "Year 2014-2025"
 ]
}

 The dataset includes 839 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002439-260119153935675/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hj2qhp
title: Occurrence Download

description: A dataset containing 214025 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is Netherlands",
 "OccurrenceStatus is Present",
 "TaxonKey is Oenanthe oenanthe"
 ]
}

 The dataset includes 214025 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002387-260119153935675/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17558723
title: Supplementary data for: "Plant fucosyltransferase FUT11 distorts the sugar acceptor to catalyze via a transient oxocarbenium intermediate mechanism"

description: This dataset comprises computational data associated with the research article titled "Plant fucosyltransferase FUT11 distorts the sugar acceptor to catalyze via a transient oxocarbenium intermediate mechanism".
DOI: 10.5281/zenodo.17558724
title: Supplementary data for: "Plant fucosyltransferase FUT11 distorts the sugar acceptor to catalyze via a transient oxocarbenium intermediate mechanism"

description: This dataset comprises computational data associated with the research article titled "Plant fucosyltransferase FUT11 distorts the sugar acceptor to catalyze via a transient oxocarbenium intermediate mechanism".
DOI: 10.11588/duerer.online.696f52535dbe2
title: Bildnis des Albrecht Dürer, https://d-nb.info/gnd/119488783X
DOI: 10.15468/dl.kbp6u3
title: Occurrence Download

description: A dataset containing 832 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Paeonia coriacea"
 ]
}

 The dataset includes 832 records from 60 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002441-260119153935675/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.20387/bonares-m9xt-w736
title: Replicated data for: Reduced fertilization in agroforestry maintains ecosystem multifunctionality and economic returns

description: Agroforestry as a sustainable agricultural intensification strategy is expected to ensure optimal resource use, and uncompromised provision of ecosystem services and economic returns when compared to treeless open croplands. Here, we evaluated the effects of fertilization rates and land use management on ecosystem functions, based on 37 ecological indicators, measured over a 5-year period (2019–2023). Reduced fertilization did not significantly affect overall ecosystem multifunctionality or any ecosystem function in either agroforestry or open cropland, although some ecological indicators differed. This lack of reduced fertilization effect indicates a legacy effect of chronic over-fertilization in this agroecosystem. Compared to open cropland, agroforestry enhanced carbon sequestration but decreased water filtration due to spatially unadjusted fertilization rates in tree-crop competition zones. Economic performance among fertilization and land use managements was comparable. We conclude that adopting agroforestry and reducing current fertilization levels by 50% are feasible without compromising food production, ecological and economic benefits.
DOI: 10.15468/dl.ny548n
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{"type":"and","predicates":[{"type":"within","geometry":"POLYGON ((111.569 -1.58282, 111.49871 -1.588385, 111.43015 -1.604946, 111.365006 -1.632092, 111.304882 -1.669158, 111.251258 -1.715231, 111.205453 -1.769176, 111.168596 -1.829666, 111.141594 -1.895213, 111.125113 -1.964203, 111.119561 -2.034937, 111.125075 -2.105674, 111.14152 -2.174673, 111.168494 -2.240233, 111.205334 -2.300741, 111.251133 -2.354705, 111.304763 -2.400797, 111.364905 -2.43788, 111.430076 -2.46504, 111.498671 -2.481609, 111.569 -2.487178, 111.639329 -2.481609, 111.707924 -2.46504, 111.773095 -2.43788, 111.833237 -2.400797, 111.886867 -2.354705, 111.932666 -2.300741, 111.969506 -2.240233, 111.99648 -2.174673, 112.012925 -2.105674, 112.018439 -2.034937, 112.012887 -1.964203, 111.996406 -1.895213, 111.969404 -1.829666, 111.932547 -1.769176, 111.886742 -1.715231, 111.833118 -1.669158, 111.772994 -1.632092, 111.70785 -1.604946, 111.63929 -1.588385, 111.569 -1.58282))"},{"type":"equals","key":"CLASS_KEY","value":"212","matchCase":false},{"type":"greaterThanOrEquals","key":"YEAR","value":"2015","matchCase":false},{"type":"not","predicate":{"type":"in","key":"BASIS_OF_RECORD","values":["MATERIAL_CITATION","MATERIAL_SAMPLE","PRESERVED_SPECIMEN"],"matchCase":false}},{"type":"lessThanOrEquals","key":"COORDINATE_UNCERTAINTY_IN_METERS","value":"10000","matchCase":false},{"type":"equals","key":"LICENSE","value":"CC BY 4.0","matchCase":false}]}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002442-260119153935675/datasets/export for details.
DOI: 10.5281/zenodo.17527445
title: Cell-free DNA methylome and fragmentome analysis for relapse monitoring of Ewing Sarcoma - data processing and classifier building pipelines

description: This repository contains the input files and Nextflow workflows used to generate processed qseaSet objects from T7-MBD-seq data (an enrichment-based methylation capture method using a methyl-binding domain protein), and to construct the EwingSign classifier.

OverviewT7-MBD-seq was applied to 86 plasma cell-free DNA (cfDNA) samples derived from Ewing sarcoma (EwS) and CIC-rearranged patients, as well as 107 non-cancer controls (NCC) (83 of which were used for classifier training). After pre-processing fastq files using the in-house T7-MBD-seq Nextflow pipeline, the resulting qseaSet objects were used within a second Nextflow pipeline for the training and application of the EwingSign classifier. This classifier is an ensemble of 25 XGBoost models trained on EwS/CIC methylation array data from Koelsche et al., 2021 (Data Reference: GSE140686).

Contents of the repository:

1. Input FilesThese include all necessary input files for running both the T7-MBD-seq and EwingSign classifier Nextflow pipelines.

T7-MBD-seq pipeline inputs (T7MBDseqInputFiles.zip):- starterSheet.csv — contains file paths to the FASTQ files.- sampleTable.csv — contains metadata for each cfDNA sample.- config files 

EwingSign classifier pipeline inputs (ClassifierInputFiles.zip):- CSV files specifying paths to array methylation data (IDAT files)- NCC qseaSet object- CpG_beta_Count_lookupTable.csv — used to convert methylation data into qseaSet objects- Contrasts.csv — defines sample groups for differentially methylated region (DMR) selection- mix.csv — defines group proportions for generating in silico mixture samples

2. Nextflow Pipelines- T7MBDseqNextflowPipeline.zip — Nextflow main workflow, modules, and R scripts for T7-MBD-seq data preprocessing- ClassifierBuildingNextflowPipeline.zip — Nextflow main workflow, modules, and R scripts for training and applying the EwingSign classifier

3. Scripts.zip- Bash scripts to run the T7-MBD-seq Nextflow pipeline for specific cfDNA sample cohorts (EwS, NCC, and NCChigherDepth)- Bash script to run the EwingSign classifier- R script to generate NCC split qseaSet objects from the original NCC qseaSet object- R script to generate CSV files containing the paths to EWS/CIC and NCC split qseaSet objects.- R and bash scripts to generate in silico dilution mixture sets (using array data from Patrizi et al., 2024; Data Reference: GSE276012) and to obtain EwingSign classifier predictions (related to Figure 3B)

Code to reproduce all figures in the paper is available at https://doi.org/10.5281/zenodo.17527450 (unrestricted).
description: This work was funded by the CRUK National Biomarker Centre (CTRNBC-2022/100001), The Christie Charitable Trust and the Children's Cancer Research Fund (DIVE/2023). Support was received from the Manchester Experimental Cancer Medicines Centre and the National Institute for Health and Care Research (NIHR) Manchester Biomedical Research Centre (BRC) (NIHR203308).
DOI: 10.5281/zenodo.17527446
title: Cell-free DNA methylome and fragmentome analysis for relapse monitoring of Ewing Sarcoma - data processing and classifier building pipelines

description: This repository contains the input files and Nextflow workflows used to generate processed qseaSet objects from T7-MBD-seq data (an enrichment-based methylation capture method using a methyl-binding domain protein), and to construct the EwingSign classifier.

OverviewT7-MBD-seq was applied to 86 plasma cell-free DNA (cfDNA) samples derived from Ewing sarcoma (EwS) and CIC-rearranged patients, as well as 107 non-cancer controls (NCC) (83 of which were used for classifier training). After pre-processing fastq files using the in-house T7-MBD-seq Nextflow pipeline, the resulting qseaSet objects were used within a second Nextflow pipeline for the training and application of the EwingSign classifier. This classifier is an ensemble of 25 XGBoost models trained on EwS/CIC methylation array data from Koelsche et al., 2021 (Data Reference: GSE140686).

Contents of the repository:

1. Input FilesThese include all necessary input files for running both the T7-MBD-seq and EwingSign classifier Nextflow pipelines.

T7-MBD-seq pipeline inputs (T7MBDseqInputFiles.zip):- starterSheet.csv — contains file paths to the FASTQ files.- sampleTable.csv — contains metadata for each cfDNA sample.- config files 

EwingSign classifier pipeline inputs (ClassifierInputFiles.zip):- CSV files specifying paths to array methylation data (IDAT files)- NCC qseaSet object- CpG_beta_Count_lookupTable.csv — used to convert methylation data into qseaSet objects- Contrasts.csv — defines sample groups for differentially methylated region (DMR) selection- mix.csv — defines group proportions for generating in silico mixture samples

2. Nextflow Pipelines- T7MBDseqNextflowPipeline.zip — Nextflow main workflow, modules, and R scripts for T7-MBD-seq data preprocessing- ClassifierBuildingNextflowPipeline.zip — Nextflow main workflow, modules, and R scripts for training and applying the EwingSign classifier

3. Scripts.zip- Bash scripts to run the T7-MBD-seq Nextflow pipeline for specific cfDNA sample cohorts (EwS, NCC, and NCChigherDepth)- Bash script to run the EwingSign classifier- R script to generate NCC split qseaSet objects from the original NCC qseaSet object- R script to generate CSV files containing the paths to EWS/CIC and NCC split qseaSet objects.- R and bash scripts to generate in silico dilution mixture sets (using array data from Patrizi et al., 2024; Data Reference: GSE276012) and to obtain EwingSign classifier predictions (related to Figure 3B)

Code to reproduce all figures in the paper is available at https://doi.org/10.5281/zenodo.17527450 (unrestricted).
description: This work was funded by the CRUK National Biomarker Centre (CTRNBC-2022/100001), The Christie Charitable Trust and the Children's Cancer Research Fund (DIVE/2023). Support was received from the Manchester Experimental Cancer Medicines Centre and the National Institute for Health and Care Research (NIHR) Manchester Biomedical Research Centre (BRC) (NIHR203308).
DOI: 10.15468/dl.mfrn3c
title: Occurrence Download

description: A dataset containing 801 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Teucrium scorodonia, Teucrium scorodonia, Teucrium scorodonia)",
 "Geometry POLYGON ((8.643 46.99, 14.1 46.92, 14.43 50.75, 8.534 50.83, 8.643 46.99))",
 "Year is greater than or equal to 2010",
 "OccurrenceStatus is Present",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "CoordinateUncertaintyInMeters is less than or equal to 50",
 "BasisOfRecord is one of (Observation, Human Observation, Machine Observation, Material sample)"
 ]
}

 The dataset includes 801 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002443-260119153935675/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9atbjx
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{"type":"and","predicates":[{"type":"within","geometry":"POLYGON ((-79.42400000000001 -0.743817, -79.494269 -0.749383, -79.562808 -0.765945, -79.627931 -0.793095, -79.688034 -0.830165, -79.74163799999999 -0.876241, -79.78742200000001 -0.930191, -79.82426100000001 -0.990685, -79.851246 -1.056236, -79.86771299999999 -1.125228, -79.873255 -1.195963, -79.867735 -1.2667, -79.85128899999999 -1.335697, -79.82432 -1.401255, -79.787492 -1.46176, -79.741711 -1.515721, -79.688104 -1.561809, -79.62799099999999 -1.598889, -79.56285200000001 -1.626047, -79.494292 -1.642614, -79.42400000000001 -1.648182, -79.353708 -1.642614, -79.28514800000001 -1.626047, -79.220009 -1.598889, -79.159896 -1.561809, -79.106289 -1.515721, -79.060508 -1.46176, -79.02368 -1.401255, -78.996711 -1.335697, -78.980265 -1.2667, -78.974745 -1.195963, -78.980287 -1.125228, -78.996754 -1.056236, -79.02373900000001 -0.990685, -79.06057800000001 -0.930191, -79.106362 -0.876241, -79.159966 -0.830165, -79.220069 -0.793095, -79.285192 -0.765945, -79.353731 -0.749383, -79.42400000000001 -0.743817))"},{"type":"equals","key":"CLASS_KEY","value":"212","matchCase":false},{"type":"greaterThanOrEquals","key":"YEAR","value":"2015","matchCase":false},{"type":"not","predicate":{"type":"in","key":"BASIS_OF_RECORD","values":["MATERIAL_CITATION","MATERIAL_SAMPLE","PRESERVED_SPECIMEN"],"matchCase":false}},{"type":"lessThanOrEquals","key":"COORDINATE_UNCERTAINTY_IN_METERS","value":"10000","matchCase":false},{"type":"equals","key":"LICENSE","value":"CC BY 4.0","matchCase":false}]}

 The dataset includes 5 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002444-260119153935675/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.26190/unsworks/31941
title: Hydrodynamic Model of the Ganges–Brahmaputra–Meghna (GBM) Delta

description: This dataset contains the configuration files and simulation outputs of a high-resolution hydrodynamic model of the Ganges–Brahmaputra–Meghna (GBM) delta developed using Delft3D Flexible Mesh (FM). The dataset includes model setup files, grid-independence test results, calibration and validation outputs, and derived hydrodynamic analyses for six major estuarine channels. Data products comprise simulated water levels, tidal ranges, harmonic components (D1, D2, D4) obtained through complex demodulation, tidal phase information, and velocity-based asymmetry metrics including Peak Current Asymmetry (PCA) and Slack Water Asymmetry (SWA). The dataset supports analysis of tidal propagation, amplification and attenuation, and asymmetry dynamics across the GBM estuarine network. Observational data from the Bangladesh Water Development Board (BWDB) are not redistributed and must be obtained directly from BWDB.
description: The dataset was generated using a two-dimensional, depth-averaged hydrodynamic model of the Ganges–Brahmaputra–Meghna (GBM) delta implemented in Delft3D Flexible Mesh (FM). The model was configured with high-resolution unstructured grids and forced using tidal boundary conditions and river discharge. Model performance was evaluated through grid-independence testing and calibrated and validated against observed water levels at multiple coastal, estuarine, and riverine stations (observations not redistributed). Simulation outputs were post-processed to compute tidal ranges, extract diurnal (D1), semidiurnal (D2), and quarter-diurnal (D4) components using complex demodulation, and quantify tidal current asymmetry using Peak Current Asymmetry (PCA) and Slack Water Asymmetry (SWA). Along-channel analyses were conducted at fixed distances from estuary mouths to assess spatial variations in tidal propagation, harmonic distortion, and asymmetry.
DOI: 10.5281/zenodo.18311328
title: Sida dubia A.St.-Hil. & Naudin. In: Marchesi E., Mailhos A. & Bonifacino J.M. (Eds.). Flora Uruguaya: Flora Vascular del Uruguay. ISSN 3121-2050, V. 1.0.

description: Citable snapshot. Includes PDF and CSV of collections. Date: January 13th, 2026 at 16:54
DOI: 10.5281/zenodo.18311329
title: Sida dubia A.St.-Hil. & Naudin. In: Marchesi E., Mailhos A. & Bonifacino J.M. (Eds.). Flora Uruguaya: Flora Vascular del Uruguay. ISSN 3121-2050, V. 1.0.

description: Citable snapshot. Includes PDF and CSV of collections. Date: January 13th, 2026 at 16:54
DOI: 10.15468/dl.ws996g
title: Occurrence Download

description: A dataset containing 2914 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Specimen)",
 "Country is Ukraine",
 "TaxonKey is Asclepias syriaca"
 ]
}

 The dataset includes 2914 records from 37 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002445-260119153935675/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mhngsr
title: Occurrence Download

description: A dataset containing 112111 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (Spain, Portugal)",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Human Observation, Specimen)",
 "CoordinateUncertaintyInMeters is less than 1000",
 "TaxonKey is one of (Anyphaenidae, Araneidae, Cheiracanthiidae, Clubionidae, Dictynidae, Gnaphosidae, Linyphiidae, Mimetidae, Oecobiidae, Oonopidae, Oxyopidae, Philodromidae, Salticidae, Segestriidae, Tetragnathidae, Theridiidae, Thomisidae, Uloboridae)"
 ]
}

 The dataset includes 112111 records from 44 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002413-260119153935675/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15738099
title: Dataset for Rat111 and Rat183 (Control and Test)

description: raw video recordings and DeepLabCut extracted trajectory files from both habituation and test phases for  rat111 and rat183
DOI: 10.5281/zenodo.15738098
title: Dataset for Rat111 and Rat183 (Control and Test)

description: raw video recordings and DeepLabCut extracted trajectory files from both habituation and test phases for  rat111 and rat183
DOI: 10.15468/dl.u37qhn
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{"type":"and","predicates":[{"type":"within","geometry":"POLYGON ((116.401 -1.58082, 116.33071 -1.586385, 116.26215 -1.602946, 116.197006 -1.630092, 116.136882 -1.667158, 116.083258 -1.713231, 116.037453 -1.767176, 116.000596 -1.827667, 115.973594 -1.893213, 115.957114 -1.962203, 115.951561 -2.032937, 115.957075 -2.103674, 115.973521 -2.172673, 116.000495 -2.238233, 116.037334 -2.298741, 116.083133 -2.352705, 116.136764 -2.398797, 116.196905 -2.43588, 116.262076 -2.46304, 116.330672 -2.479609, 116.401 -2.485178, 116.471328 -2.479609, 116.539924 -2.46304, 116.605095 -2.43588, 116.665236 -2.398797, 116.718867 -2.352705, 116.764666 -2.298741, 116.801505 -2.238233, 116.828479 -2.172673, 116.844925 -2.103674, 116.850439 -2.032937, 116.844886 -1.962203, 116.828406 -1.893213, 116.801404 -1.827667, 116.764547 -1.767176, 116.718742 -1.713231, 116.665118 -1.667158, 116.604994 -1.630092, 116.53985 -1.602946, 116.47129 -1.586385, 116.401 -1.58082))"},{"type":"equals","key":"CLASS_KEY","value":"212","matchCase":false},{"type":"greaterThanOrEquals","key":"YEAR","value":"2015","matchCase":false},{"type":"not","predicate":{"type":"in","key":"BASIS_OF_RECORD","values":["MATERIAL_CITATION","MATERIAL_SAMPLE","PRESERVED_SPECIMEN"],"matchCase":false}},{"type":"lessThanOrEquals","key":"COORDINATE_UNCERTAINTY_IN_METERS","value":"10000","matchCase":false},{"type":"equals","key":"LICENSE","value":"CC BY 4.0","matchCase":false}]}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002447-260119153935675/datasets/export for details.