cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.7003604
title: oncoEnrichR use cases

description: <strong>Use case analyses - oncoEnrichR</strong> This Zenodo repository hosts two use case output reports from oncoEnrichR, a dedicated tool for geneset interpretation in cancer. Directory structure: <strong><em>reports </em></strong>- holds pre-computed HTML reports and Excel woorkbooks for two use cases FGFR1 network (protein proximity screen) <em>fgfr1_network_oncoEnrichR.v1.4.1.html</em> <em>fgfr1_network_oncoEnrichR.v1.4.1.xlsx</em> EGFRi drug resistance drivers (CRISPR screen) <em>egfr_drug_resistance_oncoEnrichR.v1.4.1.html</em> <em>egfr_drug_resistance_oncoEnrichR.v1.4.1.xlsx</em> <em><strong>input </strong></em>- holds input data for the two use cases<br> 1. fgfr1_network_input.tsv<br> 2. egfr_drug_resistance_input.tsv <em><strong>docker</strong></em> - holds input and code for re-running use case analyses through<br> a Docker container Instructions Install Docker on your local computer/client (OS X/Linux) Download the <em>input</em> and <em>output</em> directory of the <em>docker</em> directory to your local computer/client Pull the Docker image with the following Docker command on the command-line: <em>docker pull sigven/oeusecase:latest</em> Run the use case analyses with the following Docker command: <em>docker run --rm -ti -v &lt;LOCAL_DIRECTORY&gt;/input:/input -v /LOCAL_DIRECTORY/output:/output sigven/oeusecase:latest</em> <strong>NOTE</strong>: replace <em>LOCAL_DIRECTORY</em> with the full path on your local computer where you have downloaded the <em>input</em> and <em>output</em> folders The above command will generate HTML reports and Excel workbooks for the two use cases in the <em>output</em> directory
DOI: 10.5281/zenodo.7115732
title: oncoEnrichR use cases

description: Two use cases demonstrating the functionality of oncoEnrichR for gene list interpretation and hit prioritization.
DOI: 10.5281/zenodo.7179920
title: oncoEnrichR use cases

description: Two use cases demonstrating the functionality of oncoEnrichR for gene list interpretation and hit prioritization. ### Use case analyses - oncoEnrichR This Zenodo repository hosts two use case output reports from<br> [oncoEnrichR](https://github.com/sigven/oncoEnrichR), a dedicated tool for gene<br> set interpretation in cancer. Directory structure: * __`reports`__ - holds pre-computed HTML reports and Excel workbooks for<br> two use cases: 1. FGFR1 network (protein proximity screen)<br> - `fgfr1_network_oncoEnrichR.v1.3.2.html`<br> - `fgfr1_network_oncoEnrichR.v1.3.2.xlsx`<br> 2. EGFR drug resistance drivers (CRISPR screen)<br> - `egfr_drug_resistance_oncoEnrichR.v1.3.2.html`<br> - `egfr_drug_resistance_oncoEnrichR.v1.3.2.xlsx` * __`input`__ - holds input data for the two use cases<br> 1. fgfr1_network_input.tsv<br> 2. egfr_drug_resistance_input.tsv * __`docker`__ - holds input and code for re-running use case analyses through<br> a Docker container __Docker instructions__ - [Install Docker](https://docs.docker.com/get-docker/) on your local computer/client (OS X/Linux)<br> - Download the `input` and `output` directory of the `docker` directory to your local computer/client<br> - Pull the Docker image with the following Docker command on the command-line:<br> * `docker pull sigven/oeusecase:latest`<br> - Run the use case analyses with the following Docker command:<br> * `docker run --rm -ti -v &lt;LOCAL_DIRECTORY&gt;/input:/input -v /LOCAL_DIRECTORY/output:/output sigven/oeusecase:latest`<br> - _NOTE_: replace `LOCAL_DIRECTORY` with the full path on your local computer where you have downloaded the `input` and `output` folders<br> * The above command will generate HTML reports and Excel workbooks for the two use cases in the `output` directory
DOI: 10.5281/zenodo.7180091
title: oncoEnrichR use cases

description: <strong>Use case analyses - oncoEnrichR</strong> This Zenodo repository hosts two use case output reports from oncoEnrichR, a dedicated tool for geneset interpretation in cancer. Directory structure: <strong><em>reports </em></strong>- holds pre-computed HTML reports and Excel woorkbooks for two use cases FGFR1 network (protein proximity screen) <em>fgfr1_network_oncoEnrichR.v1.3.2.html</em> <em>fgfr1_network_oncoEnrichR.v1.3.2.xlsx</em> EGFRi drug resistance drivers (CRISPR screen) egfr_drug_resistance_oncoEnrichR.v1.3.2.html egfr_drug_resistance_oncoEnrichR.v1.3.2.xlsx <em><strong>input </strong></em>- holds input data for the two use cases<br> 1. fgfr1_network_input.tsv<br> 2. egfr_drug_resistance_input.tsv <em><strong>docker</strong></em> - holds input and code for re-running use case analyses through<br> a Docker container Instructions Install Docker on your local computer/client (OS X/Linux) Download the <em>input</em> and <em>output</em> directory of the <em>docker</em> directory to your local computer/client Pull the Docker image with the following Docker command on the command-line: <em>docker pull sigven/oeusecase:latest</em> Run the use case analyses with the following Docker command: <em>docker run --rm -ti -v &lt;LOCAL_DIRECTORY&gt;/input:/input -v /LOCAL_DIRECTORY/output:/output sigven/oeusecase:latest</em> <strong>NOTE</strong>: replace <em>LOCAL_DIRECTORY</em> with the full path on your local computer where you have downloaded the <em>input</em> and <em>output</em> folders The above command will generate HTML reports and Excel workbooks for the two use cases in the <em>output</em> directory
DOI: 10.5281/zenodo.7662441
title: oncoEnrichR use cases

description: <strong>Use case analyses - oncoEnrichR</strong> This Zenodo repository hosts two use case output reports from oncoEnrichR, a dedicated tool for geneset interpretation in cancer. Directory structure: <strong><em>reports </em></strong>- holds pre-computed HTML reports and Excel woorkbooks for two use cases FGFR1 network (protein proximity screen) <em>fgfr1_network_oncoEnrichR.v1.4.0.html</em> <em>fgfr1_network_oncoEnrichR.v1.4.0.xlsx</em> EGFRi drug resistance drivers (CRISPR screen) egfr_drug_resistance_oncoEnrichR.v1.4.0html egfr_drug_resistance_oncoEnrichR.v1.4.0.xlsx <em><strong>input </strong></em>- holds input data for the two use cases<br> 1. fgfr1_network_input.tsv<br> 2. egfr_drug_resistance_input.tsv <em><strong>docker</strong></em> - holds input and code for re-running use case analyses through<br> a Docker container Instructions Install Docker on your local computer/client (OS X/Linux) Download the <em>input</em> and <em>output</em> directory of the <em>docker</em> directory to your local computer/client Pull the Docker image with the following Docker command on the command-line: <em>docker pull sigven/oeusecase:latest</em> Run the use case analyses with the following Docker command: <em>docker run --rm -ti -v &lt;LOCAL_DIRECTORY&gt;/input:/input -v /LOCAL_DIRECTORY/output:/output sigven/oeusecase:latest</em> <strong>NOTE</strong>: replace <em>LOCAL_DIRECTORY</em> with the full path on your local computer where you have downloaded the <em>input</em> and <em>output</em> folders The above command will generate HTML reports and Excel workbooks for the two use cases in the <em>output</em> directory
DOI: 10.5281/zenodo.8051181
title: oncoEnrichR use cases

description: <strong>Use case analyses - oncoEnrichR</strong> This Zenodo repository hosts two use case output reports from oncoEnrichR, a dedicated tool for geneset interpretation in cancer. Directory structure: <strong><em>reports </em></strong>- holds pre-computed HTML reports and Excel woorkbooks for two use cases FGFR1 network (protein proximity screen) <em>fgfr1_network_oncoEnrichR.v1.4.1.html</em> <em>fgfr1_network_oncoEnrichR.v1.4.1.xlsx</em> EGFRi drug resistance drivers (CRISPR screen) <em>egfr_drug_resistance_oncoEnrichR.v1.4.1.html</em> <em>egfr_drug_resistance_oncoEnrichR.v1.4.1.xlsx</em> <em><strong>input </strong></em>- holds input data for the two use cases<br> 1. fgfr1_network_input.tsv<br> 2. egfr_drug_resistance_input.tsv <em><strong>docker</strong></em> - holds input and code for re-running use case analyses through<br> a Docker container Instructions Install Docker on your local computer/client (OS X/Linux) Download the <em>input</em> and <em>output</em> directory of the <em>docker</em> directory to your local computer/client Pull the Docker image with the following Docker command on the command-line: <em>docker pull sigven/oeusecase:latest</em> Run the use case analyses with the following Docker command: <em>docker run --rm -ti -v &lt;LOCAL_DIRECTORY&gt;/input:/input -v /LOCAL_DIRECTORY/output:/output sigven/oeusecase:latest</em> <strong>NOTE</strong>: replace <em>LOCAL_DIRECTORY</em> with the full path on your local computer where you have downloaded the <em>input</em> and <em>output</em> folders The above command will generate HTML reports and Excel workbooks for the two use cases in the <em>output</em> directory
DOI: 10.5281/zenodo.8051193
title: bonnemaisonia_californica_spades_01.fasta.gz

description: .
DOI: 10.5281/zenodo.8051192
title: bonnemaisonia_californica_spades_01.fasta.gz

description: .
DOI: 10.15468/dl.8wzzct
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Narcissus bulbocodium var. ectandrus Barra & G.López",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016652-200127171203522/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fre4rx
title: Occurrence Download

description: A dataset containing 178 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Digitonthophagus gazella (Fabricius, 1787)",
 "Geometry POLYGON((-125.859375 44.087585,-125.859375 -30.751277,-33.75 -30.751277,-33.75 44.087585,-125.859375 44.087585))"
 ]
}

 The dataset includes 178 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002724-150831095807960/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.11151262
title: Gene and protein sequence features augment HLA class I ligand predictions

description: Dataset and analyses supporting the manuscript "Gene and protein sequence features augment HLA class I ligand predictions".

The "peptides" files contain the mass-spec detected peptides obtained from HLA ligandomics performed on the indicated tumor lines. 

The "protein data" files contain the RNAseq data (TPM) and Ribosome profiling data (ribosome occupancy) per protein, for each tumor line. 

The "source data" zip archive contains the source data underlying the figures of the manuscript.

The "HLA ligandome analyses" zip archive contains the R scripts used for all data analysis in the manuscript, including all data and output files. These analyses can also be found at https://github.com/kasbress/HLA_Ligandome_Analyses/
DOI: 10.5281/zenodo.11151263
title: Gene and protein sequence features augment HLA class I ligand predictions

description: Dataset and analyses supporting the manuscript "Gene and protein sequence features augment HLA class I ligand predictions".

The "peptides" files contain the mass-spec detected peptides obtained from HLA ligandomics performed on the indicated tumor lines. 

The "protein data" files contain the RNAseq data (TPM) and Ribosome profiling data (ribosome occupancy) per protein, for each tumor line. 

The "source data" zip archive contains the source data underlying the figures of the manuscript.

The "HLA ligandome analyses" zip archive contains the R scripts used for all data analysis in the manuscript, including all data and output files. These analyses can also be found at https://github.com/kasbress/HLA_Ligandome_Analyses/
DOI: 10.15468/dl.w4ckvf
title: Occurrence Download

description: A dataset containing 25540 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Deroceras reticulatum (O.F.Müller, 1774)",
 "Year 1670-2020"
 ]
}

 The dataset includes 25540 records from 198 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0083903-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mz2aun
title: Occurrence Download

description: A dataset containing 237059 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-77.36572 8.45064,-77.93701 7.27529,-77.23389 3.95194,-76.57471 3.68886,-76.00342 8.05923,-76.92627 7.88515,-77.36572 8.45064))",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 {
 "or" : [
 "TaxonKey is Chordata",
 "TaxonKey is Mammalia"
 ]
 }
 ]
}

 The dataset includes 237059 records from 224 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0278644-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ap7gm8
title: Occurrence Download

description: A dataset containing 86 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Amphioctopus kagoshimensis (Ortmann, 1888)"
 ]
}

 The dataset includes 86 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0052764-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ha53f7
title: Occurrence Download

description: A dataset containing 10 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Cuphea splendida var. viridiflava S.A.Graham & T.B.Cavalc.)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 10 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0052766-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wiuav4
title: Occurrence Download

description: A dataset containing 113 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Leucauge blanda (L.Koch, 1878)"
 ]
}

 The dataset includes 113 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007249-181108115102211/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5lqzw9
title: Occurrence Download

description: A dataset containing 7331 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Canada",
 "TaxonKey is Danaus plexippus (Linnaeus, 1758)"
 ]
}

 The dataset includes 7331 records from 52 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016656-190621201848488/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gp3wsg
title: Occurrence Download

description: A dataset containing 36734 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "Year is greater than or equal to 2000",
 "Year is less than or equal to 2024",
 "Geometry POLYGON ((-130.7383528944533 -59.46314024951374, -130.7383528944533 32.71876227804215, -26.26729810228821 32.71876227804215, -26.26729810228821 -59.46314024951374, -130.7383528944533 -59.46314024951374))",
 "OccurrenceStatus is Present",
 "TaxonKey is Pseudoleistes virescens (Vieillot, 1819)"
 ]
}

 The dataset includes 36734 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0052761-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.frpcjm
title: Occurrence Download

description: A dataset containing 11109 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "Country is Spain",
 "Country is Portugal"
 ]
 },
 "TaxonKey is Mus musculus Linnaeus, 1758"
 ]
}

 The dataset includes 11109 records from 40 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006901-180131172636756/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hgqs5u
title: Occurrence Download

description: A dataset containing 1086784 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Catharus ustulatus (Nuttall, 1840))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Human Observation, Observation, Specimen)",
 "Year is greater than 1945"
 ]
}

 The dataset includes 1086784 records from 215 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0278642-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sfcpbr
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Dioscorea cavenensis Lam.",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016656-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mmgves
title: Occurrence Download

description: A dataset containing 76 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Etropus microstomus (Gill, 1864)",
 "Country is United States of America",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is less than or equal to 1980",
 "Year is greater than or equal to 1900"
 ]
}

 The dataset includes 76 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006901-180412121330197/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xkzted
title: Occurrence Download

description: A dataset containing 44 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "TaxonKey is Ajania quercifolia (W.W.Sm.) Y.Ling & C.Shih"
 ]
}

 The dataset includes 44 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0288088-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.lgz3ma
title: Occurrence Download

description: A dataset containing 697 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 {
 "or" : [
 "TaxonKey is Platystele Schltr.",
 "TaxonKey is Masdevallia Ruiz & Pav.",
 "TaxonKey is Lepanthopsis (Cogn.) Ames"
 ]
 }
 ]
}

 The dataset includes 697 records from 39 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002725-180824113759888/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3f3nwt
title: Occurrence Download

description: A dataset containing 12 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Gastrotheca chrysosticta Laurent, 1976"
 ]
}

 The dataset includes 12 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016663-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.edrvle
title: Occurrence Download

description: A dataset containing 135 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Peromyscus slevini Mailliard, 1924",
 "HasCoordinate is TRUE"
 ]
}

 The dataset includes 135 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006901-180508205500799/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kapbmu
title: Occurrence Download

description: A dataset containing 8260 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is South America",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Bromelia L."
 ]
}

 The dataset includes 8260 records from 217 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0052762-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mufxid
title: Occurrence Download

description: A dataset containing 3701 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Quercus petraea (Matt.) Liebl.",
 "Country is Spain"
 ]
}

 The dataset includes 3701 records from 36 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002726-150528172251762/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wkpqib
title: Occurrence Download

description: A dataset containing 150 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "BasisOfRecord is Specimen",
 "BasisOfRecord is Human Observation",
 "BasisOfRecord is Observation",
 "BasisOfRecord is Living Specimen"
 ]
 },
 "Geometry POLYGON((75 21,125 21,125 42,75 42,75 21))",
 "HasCoordinate is true",
 "TaxonKey is Phleum L.",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 150 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016667-190621201848488/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.1rvqtl
title: Occurrence Download

description: A dataset containing 32080 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "BasisOfRecord is Observation",
 "BasisOfRecord is Human Observation",
 "BasisOfRecord is Unknown evidence"
 ]
 },
 "TaxonKey is Pseudotsuga menziesii (Mirb.) Franco"
 ]
}

 The dataset includes 32080 records from 204 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006901-180824113759888/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.radxtg
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 2000",
 "Month is greater than or equal to January",
 "Country is Mexico",
 "TaxonKey is Sphenisciformes"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002726-150721130643939/datasets/export for details.
DOI: 10.15468/dl.cymhwp
title: Occurrence Download

description: A dataset listing the 5550 species recorded in GBIF matching the query:
{
 "DatasetKey" : [
 "is The Himalayan Uplands Plant database (HUP Version 1)"
 ]
}

 The dataset's 5550 records were derived from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0251604-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.