Commit 503e39c6 authored by Albert Hornos Vidal's avatar Albert Hornos Vidal
Browse files

feat: add ega datasets to host sequences section

parent 3d2f6168
......@@ -46,6 +46,7 @@ params:
isciiiRegistroCovid: /images/logos/isciii-registro-covid19-logo.png
isciii: /images/logos/isciii-logo-horizontal.svg
ena: /images/logos/ena-logo.png
ega: /images/logos/ega-logo.png
markup:
goldmark:
renderer:
......
......@@ -289,6 +289,9 @@ other="Study title"
["datasets_number"]
other="Number of datasets"
["datasets"]
other="Datasets"
[collection_date]
other = "Collection date"
......
<p>
These results are periodically retrieved from EGA.
</p>
<p class="text-right">
Powered by <a href="https://ega-archive.org/"><img src="{{ .Site.Params.images.logos.ega }}" alt="EGA" style="max-height: 3rem;"></a>
</p>
<div class="container-fluid">
<div class="row mb-2" id="host-actions">
</div>
</div>
<table class="table table-hover table-sm table-responsive" id="host-sequences-table" style="display: table;">
<a id="downloadButton" class="btn btn-primary d-inline-block" target="_blank" href="/files/c19dpes_genomics_host_sequences.csv">
{{ i18n "download_csv" }}
</a>
<table class="table table-hover table-sm table-responsive" id="host-sequences-table" style="display: table">
<thead class="thead-light">
<tr>
<th scope="col">{{ i18n "ega_study_accession_id" }}</th>
<th scope="col">{{ i18n "ega_study_title" }}</th>
<th scope="col">{{ i18n "datasets_number" }}</th>
<th scope="col" class="col-md-2">{{ i18n "ega_study_accession_id" }}</th>
<th scope="col" class="col-md-10">{{ i18n "ega_study_title" }}</th>
</tr>
</thead>
<tbody>
{{ range $index, $entry := $.Site.Data.c19dpes_genomics_host_sequences.ega_studies }}
<tr>
<td><a target="_blank" href='{{print "https://ega-archive.org/studies/" .study_accession}}'>{{ .study_accession }}</a></td>
<td>{{ .study_title }}</td>
<td>{{ len .datasets }}</td>
<td class="col-md-2"><a target="_blank" href='{{print "https://ega-archive.org/studies/" .study_accession}}'>{{ .study_accession }}</a></td>
<td class="col-md-10">
{{ .study_title }}
{{ if .datasets }}
<br/><a class="badge badge-primary dp-background-color--primary" data-toggle="collapse" href="#datasets{{ $index }}" role="button" aria-expanded="false" aria-controls="datasets{{ $index }}">
{{ i18n "datasets" }} <i class="bi bi-caret-down-fill"></i>
</a>
<div class="collapse" id="datasets{{ $index }}">
<div class="card card-body">
<table class="table table-hover table-sm">
<thead>
<th class="col-md-3">{{ i18n "accession_id" }}</th>
<th class="col-md-9">{{ i18n "title" }}</th>
</thead>
<tbody>
{{ range $ds := .datasets}}
<tr>
<td class="col-md-3">
<a href='{{print "https://ega-archive.org/datasets/" .dataset_accession}}'>{{ .dataset_accession }}</a>
</td>
<td class="col-md-9">
{{ .dataset_title }}
</td>
</tr>
{{ end }}
</tbody>
</table>
</div>
</div>
{{ end }}
</td>
</tr>
{{ end }}
</tbody>
......@@ -54,11 +90,14 @@
});
// When used with Bootstrap, datatables buttons must be appended to DOM to make them visible.
tableHostSequences.buttons().container().prependTo('#host-actions');
//tableHostSequences.buttons().container().prependTo('#host-actions');
// Move download button next to filter search box.
const downloadButtonHostSequences = document.querySelector('#host-actions .dt-buttons');
//const downloadButtonHostSequences = document.querySelector('#host-actions .dt-buttons');
const downloadButton = document.querySelector('#downloadButton');
downloadButton.classList.remove('btn-group', 'flex-wrap');
downloadButton.classList.add('d-flex');
const searchHostSequences = document.querySelector('#search-host-sequences');
searchHostSequences.insertAdjacentElement('afterend', downloadButtonHostSequences);
searchHostSequences.insertAdjacentElement('afterend', downloadButton);
});
</script>
Study_accession,Study title,Dataset accession,Dataset title
EGAS00001005465,Multi-omic single-cell profiling of peripheral blood immune cells from COVID-19 patients and controls.,EGAD00001007867,Cambridge COVID-19 Single-cell PBMC
EGAS00001005465,Multi-omic single-cell profiling of peripheral blood immune cells from COVID-19 patients and controls.,EGAD00001007866,Newcastle COVID-19 Single-cell PBMC
EGAS00001005465,Multi-omic single-cell profiling of peripheral blood immune cells from COVID-19 patients and controls.,EGAD00001007865,UCL COVID-19 Single-cell PBMC
EGAS00001005332,COVID-19 whole blood transcriptomic analysis,EGAD00001007776,Whole blood RNA-sequencing of covid-19 patients and healthy controls
EGAS00001005380,An analysis of humoral and cellular immune responses following COVID-19 vaccination.,EGAD00001007777,Covid vaccination BCR repertoire analysis
EGAS00001004571,ScRNA-seq of PBMC and whole blood samples reveals a dysregulated myeloid cell compartment in severe COVID-19,EGAD00001006550,ScRNA-seq of PBMC and whole blood samples reveales a dysregulated myeloid cell compartment in severe COVID-19
EGAS00001005060,SARS-CoV-2 escapes CD8 T cell surveillance via mutations in MHC-I restricted epitopes [10x],EGAD00001008109,analysis of T cell receptor repertoirs
EGAS00001005060,SARS-CoV-2 escapes CD8 T cell surveillance via mutations in MHC-I restricted epitopes [10x],EGAD00001006995,Single-cell gene expression data from CD8+ T cells from two Austrian COVID19 patients stimulated with wildtype and mutant SARS-Cov-2 peptides
EGAS00001004508,Three-dimensional human alveolar stem cell culture models reveal infection response to SARS-CoV-2,EGAD00001006242,"Single cell RNA sequencing data in ""Three-dimensional human alveolar stem cell culture models reveal infection response to SARS-CoV-2"""
EGAS00001004508,Three-dimensional human alveolar stem cell culture models reveal infection response to SARS-CoV-2,EGAD00001006241,"Bulk RNA sequencing data in ""Three-dimensional human alveolar stem cell culture models reveal infection response to SARS-CoV-2"""
EGAS00001004951,Upper respiratory microbiome of COVID-19 patients,EGAD00001006864,CONTAGIOUS trial - COVID-19 16S dataset
EGAS00001004951,Upper respiratory microbiome of COVID-19 patients,EGAD00001008006,CONTAGIOUS trial - COVID-19 16S metadata
EGAS00001004502,Swarm Learning to identify COVID-19 tuberculosis and leukemia patients based on blood transcriptomes,EGAD00001006231,Swarm Learning to identify COVID-19 tuberculosis and leukemia patients based on blood transcriptomes
EGAS00001005280,Impaired Humoral and Cellular Immunity after SARS-CoV2 BNT162b2 (Tozinameran) Prime-Boost Vaccination in Kidney Transplant Recipients,EGAD00001007689,RNA-Seq of response to Tozinameran vaccination in individuals with KTx/dialysis or healthy controls.
EGAS00001004689,COVID-19 Postmortem Lung snRNA-seq,EGAD00001006584,COVID-19 Postmortem Lung snRNA-seq
EGAS00001005039,SINGLE-CELL RNA SEQUENCING Single-cell RNA sequencing was performed on 13 ‘mild-moderate’ and 10 ‘critical’ COVID19 PBMC samples,EGAD00001006997,Single cell sequencing of mild and critical COVID19 PBMC
EGAS00001004717,Single-cell RNA sequencing of bronchoalveolar lavages from COVID-19 patients,EGAD00001006893,Single-cell RNA sequencing of bronchoalveolar lavages from COVID-19 patients
EGAS00001005304,COVID19 Host Genetic Initiative,EGAD00010002171,Hostage_2_genotype
EGAS00001005304,COVID19 Host Genetic Initiative,EGAD00010002172,BRACOVID_genotype
EGAS00001005304,COVID19 Host Genetic Initiative,EGAD00010002173,Hostage_3_genotype
EGAS00001005304,COVID19 Host Genetic Initiative,EGAD00010002174,INMUNGEN_CoV2_genotype
EGAS00001005304,COVID19 Host Genetic Initiative,EGAD00010002175,SweCovid_genotype
EGAS00001005304,COVID19 Host Genetic Initiative,EGAD00010002177,GEN_COVID_genotype
EGAS00001005304,COVID19 Host Genetic Initiative,EGAD00010002178,Hostage_4_genotype
EGAS00001005304,COVID19 Host Genetic Initiative,EGAD00010002179,BelCovid_2_genotype
EGAS00001005304,COVID19 Host Genetic Initiative,EGAD00010002180,Hostage_1_genotype
EGAS00001005304,COVID19 Host Genetic Initiative,EGAD00010002176,SPGRX_genotype
EGAS00001005304,COVID19 Host Genetic Initiative,EGAD00001007837,GEN_COVID_phenotype_lab
EGAS00001005304,COVID19 Host Genetic Initiative,EGAD00001007844,Hostage_4_phenotype_basic
EGAS00001005304,COVID19 Host Genetic Initiative,EGAD00001007832,BRACOVID_phenotype_basic
EGAS00001005304,COVID19 Host Genetic Initiative,EGAD00001007850,SweCovid_phenotype_lab
EGAS00001005304,COVID19 Host Genetic Initiative,EGAD00001007848,SPGRX_phenotype_basic
EGAS00001005304,COVID19 Host Genetic Initiative,EGAD00001007847,INMUNGEN_CoV2_phenotype_lab
EGAS00001005304,COVID19 Host Genetic Initiative,EGAD00001007846,INMUNGEN_CoV2_phenotype_basic
EGAS00001005304,COVID19 Host Genetic Initiative,EGAD00001007845,Hostage_4_phenotype_lab
EGAS00001005304,COVID19 Host Genetic Initiative,EGAD00001007843,Hostage_3_phenotype_lab
EGAS00001005304,COVID19 Host Genetic Initiative,EGAD00001007842,Hostage_3_phenotype_basic
EGAS00001005304,COVID19 Host Genetic Initiative,EGAD00001007841,Hostage_2_phenotype_lab
EGAS00001005304,COVID19 Host Genetic Initiative,EGAD00001007840,Hostage_2_phenotype_basic
EGAS00001005304,COVID19 Host Genetic Initiative,EGAD00001007839,Hostage_1_phenotype_lab
EGAS00001005304,COVID19 Host Genetic Initiative,EGAD00001007838,Hostage_1_phenotype_basic
EGAS00001005304,COVID19 Host Genetic Initiative,EGAD00001007836,GEN_COVID_phenotype_basic
EGAS00001005304,COVID19 Host Genetic Initiative,EGAD00001007835,BelCovid_2_phenotype_lab
EGAS00001005304,COVID19 Host Genetic Initiative,EGAD00001007834,BelCovid_2_phenotype_basic
EGAS00001005304,COVID19 Host Genetic Initiative,EGAD00001007833,BRACOVID_phenotype_lab
EGAS00001005304,COVID19 Host Genetic Initiative,EGAD00001007849,SweCovid_phenotype_basic
EGAS00001005461,Pre-activated anti-viral innate immunity in the upper airways controls early SARS-CoV-2 infection in children,EGAD00001007969,Pre-activated anti-viral innate immunity in the upper airways controls early SARS-CoV-2 infection in children
EGAS00001004716,Ancestry COVID-19 study,EGAD00010002011,Ancestry COVID-19 Study Phenotype
EGAS00001004716,Ancestry COVID-19 study,EGAD00010002012,Ancestry COVID-19 Study Genotype
EGAS00001005099,AncestryDNA COVID-19 GWAS with Eight Phenotypes,EGAD00010002104,AncestryDNA COVID-19 GWAS for Continuous_Severity_Score
EGAS00001005099,AncestryDNA COVID-19 GWAS with Eight Phenotypes,EGAD00010002109,AncestryDNA COVID-19 GWAS for ExposedPositive_ExposedNegative
EGAS00001005099,AncestryDNA COVID-19 GWAS with Eight Phenotypes,EGAD00010002111,AncestryDNA COVID-19 GWAS for Hospitalized_NotHosptialized
EGAS00001005099,AncestryDNA COVID-19 GWAS with Eight Phenotypes,EGAD00010002120,AncestryDNA COVID-19 GWAS for Positive_Negative
EGAS00001005099,AncestryDNA COVID-19 GWAS with Eight Phenotypes,EGAD00010002122,AncestryDNA COVID-19 GWAS for Symptomatic_Paucisymptomatic
EGAS00001005099,AncestryDNA COVID-19 GWAS with Eight Phenotypes,EGAD00010002129,AncestryDNA COVID-19 GWAS for Hospitalized_Unscreened
EGAS00001005099,AncestryDNA COVID-19 GWAS with Eight Phenotypes,EGAD00010002159,AncestryDNA COVID-19 GWAS for Positive_Unscreened
EGAS00001005099,AncestryDNA COVID-19 GWAS with Eight Phenotypes,EGAD00010002162,AncestryDNA COVID-19 GWAS for Unscreened_ExposedNegative
EGAS00001005206,High titers and low fucosylation of early phase anti-SARS-CoV-2 IgG promote hyper-inflammation by alveolar macrophages,EGAD00001007512,anti-SARS-CoV-2 IgG and Fostamatinib treated human primary IL10-M2 macrophages
EGAS00001004503,Peripheral immunoprofiling of stratifies COVID-19 patients based on disease-specific neutrophil signatures,EGAD00001006671,Peripheral immunoprofiling of stratifies COVID-19 patients based on disease-specific neutrophil signatures
EGAS00001004503,Peripheral immunoprofiling of stratifies COVID-19 patients based on disease-specific neutrophil signatures,EGAD00001006326,Peripheral immunoprofiling of stratifies COVID-19 patients based on disease-specific neutrophil signatures
EGAS00001004391,Paediatric_and_adult_nasal_RNAseq___COVID19,EGAD00001007718,The cellular immune and airway epithelial profile throughout childhood and in response to COVID-19 at multi-omic single cell level.
EGAS00001004772,Hypertension delays viral clearance and exacerbates airway hyperinflammation in patients with COVID-19,EGAD00001006828,Hypertension delays viral clearance and exacerbates airway hyperinflammation in patients with COVID-19
EGAS00001004481,Single-cell analysis of airway samples identifies immune cell activation correlating with COVID-19 disease severity,EGAD00001006339,COVID-19 severity correlates with airway epithelium–immune cell interactions identified by single-cell analysis
EGAS00001004419,SARS‐CoV‐2 receptor ACE2 and TMPRSS2 are primarily expressed in bronchial transient secretory cells,EGAD00001006185,ALI culture bronchial cells and alveolar lung surgical resection scRNA-Seq
EGAS00001004412,Potent neutralizing antibodies against SARS-CoV-2,EGAD00001006130,Potent neutralizing antibodies against SARS-CoV-2
\ No newline at end of file
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