cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.11004317
title: Raw data for the submitted manuscript: Response of the terrestrial crustacean Porcellio scaber and the mealworm Tenebrio molitor to agricultural microplastics exposure: comparison of nondegradable and biodegradable fossil-based mulching films

description: We uploaded two datasets on the response of terrestrial crustacean Porcellio scaber and the mealworm Tenebrio molitor to agricultural microplastics exposed in soil for 3 weeks and 4 weeks, respectively. 

a) Dataset "Response of the terrestrial crustacean Porcellio scaber to agricultural microplastics in soil" contains data on: electron transfer system activity, haemocyte viability, and share of hyalinocytes, semigranulocytes and granulocytes in haemolymph. 

b) Dataset "Response of the mealworm Tenebrio molitor to agricultural microplastics in soil" contains data on: larval moult and growth and animal survival 

These datasets are linked to publication entitled: Response of the terrestrial crustacean Porcellio scaber and the mealworm Tenebrio molitor to agricultural microplastics exposure: comparison of nondegradable and biodegradable fossil-based mulching films.  Methods are described in detail in publication. Manuscript under review.
DOI: 10.5281/zenodo.11004318
title: Raw data for the submitted manuscript: Response of the terrestrial crustacean Porcellio scaber and the mealworm Tenebrio molitor to agricultural microplastics exposure: comparison of nondegradable and biodegradable fossil-based mulching films

description: We uploaded two datasets on the response of terrestrial crustacean Porcellio scaber and the mealworm Tenebrio molitor to agricultural microplastics exposed in soil for 3 weeks and 4 weeks, respectively. 

a) Dataset "Response of the terrestrial crustacean Porcellio scaber to agricultural microplastics in soil" contains data on: electron transfer system activity, haemocyte viability, and share of hyalinocytes, semigranulocytes and granulocytes in haemolymph. 

b) Dataset "Response of the mealworm Tenebrio molitor to agricultural microplastics in soil" contains data on: larval moult and growth and animal survival 

These datasets are linked to publication entitled: Response of the terrestrial crustacean Porcellio scaber and the mealworm Tenebrio molitor to agricultural microplastics exposure: comparison of nondegradable and biodegradable fossil-based mulching films.  Methods are described in detail in publication. Manuscript under review.
DOI: 10.15468/dl.sw2ehy
title: Occurrence Download

description: A dataset containing 46 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Teredo mindanensis Bartsch, 1923"
 ]
}

 The dataset includes 46 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0109455-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vccnv3
title: Occurrence Download

description: A dataset containing 129 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Adesmia horrida Gillies ex Hook. & Arn."
 ]
}

 The dataset includes 129 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032966-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/pcra-c14-79453
title: Redemption tidings, vol. 58, nos. 1-52, 7 Jan. - 30 Dec. 1982

description: [description english/roman)] Issued weekly. "The pentecostal voice of Assemblies of God" -- subtitle. Includes Global action, 1 Apr. 1982 (in vol. 58, no. 13).
DOI: 10.15468/dl.5rfep2
title: Occurrence Download

description: A dataset containing 7 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Eriosyce odieri subsp. glabrescens (F.Ritter) Katt."
 ]
}

 The dataset includes 7 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032017-181108115102211/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.w999p7
title: Occurrence Download

description: A dataset containing 6722 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Bhutan Biodiversity Portal data"
 ]
}

 The dataset includes 6722 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0119294-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/pcra-c14-79449
title: Redemption tidings, vol. 58, nos. 1-52, 7 Jan. - 30 Dec. 1982

description: [description english/roman)] Issued weekly. "The pentecostal voice of Assemblies of God" -- subtitle. Includes Global action, 1 Apr. 1982 (in vol. 58, no. 13).
DOI: 10.15468/dl.hemkpc
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Ctenotus brachyonyx (Storr, 1971), Ctenotus brachyonyx Storr, 1971)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Machine Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 5 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032964-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wxuomc
title: Occurrence Download

description: A dataset containing 20 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-75.256 6.188,-75.134 6.188,-75.134 6.326,-75.256 6.326,-75.256 6.188))",
 "TaxonKey is Actinopterygii"
 ]
}

 The dataset includes 20 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003416-181003121212138/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fa6jbk
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Goniurosaurus huuliensis Orlov, Ryabov, Nguyen, Nguyen & Ho, 2008)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Machine Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032971-230224095556074/datasets/export for details.
DOI: 10.25549/pcra-c14-79429
title: Redemption tidings, vol. 58, nos. 1-52, 7 Jan. - 30 Dec. 1982

description: [description english/roman)] Issued weekly. "The pentecostal voice of Assemblies of God" -- subtitle. Includes Global action, 1 Apr. 1982 (in vol. 58, no. 13).
DOI: 10.15468/dl.ucfbwn
title: Occurrence Download

description: A dataset containing 2791 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Gymnotus carapo Linnaeus, 1758"
 ]
}

 The dataset includes 2791 records from 102 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0116551-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ztqwfe
title: Occurrence Download

description: A dataset containing 30 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Heritiera globosa Kosterm."
 ]
}

 The dataset includes 30 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0057663-200221144449610/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9ryhjx
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is incertae sedis",
 "Year is greater than 2013",
 "Geometry MULTIPOLYGON (((12.29322 44.354729,12.292916 44.355783,12.302003 44.355058,12.30251 44.355315,12.303097 44.354972,12.304491 44.35485,12.306615 44.355577,12.308252 44.35572,12.309929 44.355916,12.31043 44.356064,12.310795 44.356488,12.313433 44.359618,12.313562 44.359886,12.314201 44.360466,12.315056 44.360848,12.315401 44.36092,12.318399 44.361154,12.318407 44.361159,12.319165 44.361164,12.320832 44.360517,12.320917 44.360019,12.321475 44.359819,12.321794 44.360109,12.322639 44.359883,12.322438 44.359502,12.323576 44.359272,12.323557 44.359134,12.323345 44.358962,12.323362 44.358279,12.323882 44.356988,12.32507 44.355975,12.325271 44.355331,12.326351 44.35347,12.326792 44.351841,12.327903 44.349469,12.330098 44.345321,12.305974 44.335898,12.305243 44.335536,12.303491 44.340224,12.29322 44.354729)))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035452-230530130749713/datasets/export for details.
DOI: 10.25549/pcra-c14-79433
title: Redemption tidings, vol. 58, nos. 1-52, 7 Jan. - 30 Dec. 1982

description: [description english/roman)] Issued weekly. "The pentecostal voice of Assemblies of God" -- subtitle. Includes Global action, 1 Apr. 1982 (in vol. 58, no. 13).
DOI: 10.15468/dl.pkmg88
title: Occurrence Download

description: A dataset containing 29 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Benin",
 "Year 2004-2020",
 "TaxonKey is Ananas comosus (L.) Merr."
 ]
}

 The dataset includes 29 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0036208-200221144449610/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.y5qjdf
title: Occurrence Download

description: A dataset containing 80 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Onchocalanus magnus (Wolfenden, 1906)"
 ]
}

 The dataset includes 80 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0126941-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.10678014
title: CUPiD, A cfDNA methylation-based tissue-of-origin classifier for Cancers of Unknown Primary - classifier data and code

description: This repository holds code behind the article "A cfDNA methylation-based tissue-of-origin classifier for Cancers of Unknown Primary" by Conway, Pearce, Clipson et al, published in Nature Communications. This contains the code and data required to generate the CUPiD classifier itself.

Data and code to reproduce the figures in the paper are available from https://zenodo.org/uploads/10684337 (unrestricted).

Methyl-Binding Domain protein sequencing (MBD-Seq) was applied to circulating cell-free DNA (cfDNA) samples derived from patients with a range of known cancer types (143 patients), as well as 106 non-cancerous controls (79 used in training). 

The objects deposited here include R data files containing qseaSets from the R package qsea, which includes the read counts per sample per 300 base pair window across the genome, as well as information on copy number variation and metadata tables. These are provided in the inputFiles/nextflowOutput folder, and are some of the outputs of the nextflow pipeline.

The scripts folder contains numbered sub-folders, with numbered scripts within them, which should be ran in order. The scripts are setup to be run on a PBS-Torque system; files ending ".pbs" should be submitted via qsub, files ending ".sh" should be ran on a node and will submit individual jobs within a loop. R scripts without an associated .pbs or .sh file should just be ran directly. All files should be submitted from the base of the repository (e.g. qsub scripts/01-downloadData/01-getRawData.pbs) to set the paths appropriately via the environment variable PBS_O_WORKDIR. 



01-downloadData contains scripts to download and preprocess all the required data.

02-qseaSetNextFlowPipeline contains our custom in-house DSL2 Nextflow pipeline which takes fastq files to processed qseaSets, including QC checks. This requires the fastq files which will be deposited in EGA.

03-convertArrays converts downloaded (pre-processed) arrays into estimated qseaSets (containing solely the array sample), and then mixes each array with each NCC cfDNA at varying proportions.

04-DMRs calculates pairwise DMRs between each class.

05-prepForClassifier selects up to 10000 mixture sets per class, and generates a large table suitable for input into the ML model.

06-fitClassifier fits the ML model using xgboost within the tidymodels framework. This is repeated 100 times with different subsets of the mixture sets as input.

07-applyClassifier applies these classifiers to the "independent test cohort" - the set of 143 known tumour types, 27 additional NCCs and the 41 patients with CUP. These have been ran through the Nextflow pipeline separately to the 79 NCCs used to derive CUPiD, and have not been used to derive the classifier.

08-UMAPs generates some UMAPs on the array data.


A subset of these output files are provided in https://zenodo.org/uploads/10684337 , along with the code to reproduce the figures.
DOI: 10.5281/zenodo.10678015
title: CUPiD, A cfDNA methylation-based tissue-of-origin classifier for Cancers of Unknown Primary - classifier data and code

description: This repository holds code behind the article "A cfDNA methylation-based tissue-of-origin classifier for Cancers of Unknown Primary" by Conway, Pearce, Clipson et al, published in Nature Communications. This contains the code and data required to generate the CUPiD classifier itself.

Data and code to reproduce the figures in the paper are available from https://zenodo.org/uploads/10684337 (unrestricted).

Methyl-Binding Domain protein sequencing (MBD-Seq) was applied to circulating cell-free DNA (cfDNA) samples derived from patients with a range of known cancer types (143 patients), as well as 106 non-cancerous controls (79 used in training). 

The objects deposited here include R data files containing qseaSets from the R package qsea, which includes the read counts per sample per 300 base pair window across the genome, as well as information on copy number variation and metadata tables. These are provided in the inputFiles/nextflowOutput folder, and are some of the outputs of the nextflow pipeline.

The scripts folder contains numbered sub-folders, with numbered scripts within them, which should be ran in order. The scripts are setup to be run on a PBS-Torque system; files ending ".pbs" should be submitted via qsub, files ending ".sh" should be ran on a node and will submit individual jobs within a loop. R scripts without an associated .pbs or .sh file should just be ran directly. All files should be submitted from the base of the repository (e.g. qsub scripts/01-downloadData/01-getRawData.pbs) to set the paths appropriately via the environment variable PBS_O_WORKDIR. 



01-downloadData contains scripts to download and preprocess all the required data.

02-qseaSetNextFlowPipeline contains our custom in-house DSL2 Nextflow pipeline which takes fastq files to processed qseaSets, including QC checks. This requires the fastq files which will be deposited in EGA.

03-convertArrays converts downloaded (pre-processed) arrays into estimated qseaSets (containing solely the array sample), and then mixes each array with each NCC cfDNA at varying proportions.

04-DMRs calculates pairwise DMRs between each class.

05-prepForClassifier selects up to 10000 mixture sets per class, and generates a large table suitable for input into the ML model.

06-fitClassifier fits the ML model using xgboost within the tidymodels framework. This is repeated 100 times with different subsets of the mixture sets as input.

07-applyClassifier applies these classifiers to the "independent test cohort" - the set of 143 known tumour types, 27 additional NCCs and the 41 patients with CUP. These have been ran through the Nextflow pipeline separately to the 79 NCCs used to derive CUPiD, and have not been used to derive the classifier.

08-UMAPs generates some UMAPs on the array data.


A subset of these output files are provided in https://zenodo.org/uploads/10684337 , along with the code to reproduce the figures.
DOI: 10.25549/pcra-ouc11073701
title: Redemption tidings, vol. 59, nos. 1-52, 6 Jan. - 29 Dec. 1983

description: [description english/roman)] Issued weekly. "The pentecostal voice of Assemblies of God" -- subtitle.
DOI: 10.15468/dl.uhz2hy
title: Occurrence Download

description: A dataset containing 23 species occurrences available in GBIF matching the query:
{
 "and" : [
 "VerbatimScientificName is Zosterops ponapensis",
 "BasisOfRecord is one of (Machine Observation, Human Observation)",
 "Year 2011-2021",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen, Specimen, Material citation, Material sample)"
 ]
 }
 }
 ]
}

 The dataset includes 23 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0089663-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.t92pu2
title: Occurrence Download

description: A dataset containing 185047 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is EOD – eBird Observation Dataset",
 "TaxonKey is Charadrius melodus Ord, 1824",
 "Year 2000-2022"
 ]
}

 The dataset includes 185047 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0173619-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/pcra-c14-79553
title: Redemption tidings, vol. 59, nos. 1-52, 6 Jan. - 29 Dec. 1983

description: [description english/roman)] Issued weekly. "The pentecostal voice of Assemblies of God" -- subtitle.
DOI: 10.15468/dl.tx3k4z
title: Occurrence Download

description: A dataset containing 11256 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Machine Observation, Human Observation, Observation)",
 "Country is Rwanda",
 "Year 2018-2019"
 ]
}

 The dataset includes 11256 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0069891-200221144449610/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tu3re5
title: Occurrence Download

description: A dataset containing 9 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Epictia signata (Jan, 1861), Epicoma signata Walker, 1855)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Machine Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 9 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032945-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/pcra-c14-79579
title: Redemption tidings, vol. 59, nos. 1-52, 6 Jan. - 29 Dec. 1983

description: [description english/roman)] Issued weekly. "The pentecostal voice of Assemblies of God" -- subtitle.
DOI: 10.15468/dl.6bnfgb
title: Occurrence Download

description: A dataset containing 24 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON ((-84.2686491999999987 39.8024696000000020, -84.2686491999999987 39.8045774200000011, -84.2686491999999987 39.8060366799999983, -84.2686491999999987 39.8070095200000011, -84.2686491999999987 39.8084687799999983, -84.2686491999999987 39.8105765999999974, -84.2665422700000022 39.8105765999999974, -84.2650836600000019 39.8105765999999974, -84.2637871099999956 39.8105765999999974, -84.2617612500000064 39.8105765999999974, -84.2603026299999982 39.8105765999999974, -84.2588440199999980 39.8105765999999974, -84.2573043600000062 39.8105765999999974, -84.2548732999999999 39.8105765999999974, -84.2548732999999999 39.8095226900000014, -84.2548732999999999 39.8081444999999974, -84.2548732999999999 39.8072527300000019, -84.2548732999999999 39.8060366799999983, -84.2548732999999999 39.8051449100000028, -84.2548732999999999 39.8034424399999978, -84.2548732999999999 39.8024696000000020, -84.2570612600000004 39.8024696000000020, -84.2587629800000002 39.8024696000000020, -84.2598974600000048 39.8024696000000020, -84.2615181500000006 39.8024696000000020, -84.2630577999999986 39.8024696000000020, -84.2655698599999994 39.8024696000000020, -84.2669474399999956 39.8024696000000020, -84.2686491999999987 39.8024696000000020))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1932",
 "BasisOfRecord is one of (Human Observation, Living Specimen, Observation, Specimen, Machine Observation)"
 ]
}

 The dataset includes 24 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0102128-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.uzar7h
title: Occurrence Download

description: A dataset containing 60 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is United States of America",
 "DatasetKey is iNaturalist Research-grade Observations",
 "TaxonKey is Plethodon wehrlei Fowler & Dunn, 1917"
 ]
}

 The dataset includes 60 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0057671-200221144449610/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.k27a6z
title: Occurrence Download

description: A dataset containing 948 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Pholidoscelis auberi (Cocteau, 1838))",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Machine Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 948 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032965-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/pcra-c14-79581
title: Redemption tidings, vol. 59, nos. 1-52, 6 Jan. - 29 Dec. 1983

description: [description english/roman)] Issued weekly. "The pentecostal voice of Assemblies of God" -- subtitle.