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Merge pull request #389 from MoTrPAC/388_JZ_DAWG_PAC_Resources_Update
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Connects to #388. DAWG-PAC data analysis resources update.
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@jimmyzhen
jimmyzhen authored Feb 21, 2025
2 parents 912f873 + 5e935f1 commit a03f898
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277 changes: 140 additions & 137 deletions src/MultiOmicsWorkingGroups/dawgPAC.jsx
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Original file line number Diff line number Diff line change
Expand Up @@ -134,7 +134,8 @@ function DawgPAC({ profile }) {
</table>
</div>
<div className="bd-callout bd-callout-warning mb-4">
<b>2024DEC20 Soft Release →</b>{' '}
<b>2024DEC20 Soft Release →</b>
{' '}
<a href="https://docs.google.com/document/d/1-VphKxR9jQKFUFRjsF12YVY_pkO2oLOAHunjFc2Alxg/edit?tab=t.0#heading=h.ve0qe6m0m7t7" target="_blank" rel="noopener noreferrer">
Read Notes
</a>
Expand All @@ -147,191 +148,193 @@ function DawgPAC({ profile }) {
The primary aim was to collect a wide range of tissue samples
post-exercise for high-quality analysis at chemical analysis sites.
</p>
<h5>Resources</h5>
<ul>
<li>
<a
href="https://docs.google.com/document/d/1pE6SIaLxAd-gyJW34pqWyzbo6JINe2jlNTc-ONfOlqs/edit?usp=sharing"
target="_blank"
rel="noopener noreferrer"
>
Analysis Report
</a>
</li>
<li>
<a
href="https://drive.google.com/drive/folders/1oykRI3kffrSTfQk_G2MTt_9kjqBYxqvT"
target="_blank"
rel="noopener noreferrer"
>
Working Google Drive folder
Google Drive working folder
</a>
</li>
<li>
Source code is available in{' '}
Source code:
{' '}
<a
href="https://github.com/MoTrPAC/motrpac-rat-acute-6m"
target="_blank"
rel="noopener noreferrer"
>
this GitHub repository
https://github.com/MoTrPAC/motrpac-rat-acute-6m
</a>
</li>
<li>
Integrated R Notebooks for Omics Data Analysis (HTML format)
<strong>Integrated R Notebooks for Omics Data Analysis</strong>
{' '}
(HTML format)
<ul className="list-style mt-2">
<li className="mb-2">
<strong>Phenotypes:</strong>
{' '}
Comprehensive analysis of key variables from the rat phenotypic data,
including summary statistics, correlation analysis, statistical testing,
and regression models:
{' '}
{/* eslint-disable-next-line jsx-a11y/anchor-is-valid */}
<a
href="#"
data-toggle="modal"
data-target="#html-report-modal"
onClick={(e) => handleClickReport('phenotypes/pass1ac-6-pheno-analysis.html', 'pass1ac-6-pheno-analysis.html')}
>
pass1ac-6-pheno-analysis.html
</a>
</li>
<li>
Phenotypes
<strong>Transcriptomics</strong>
<ul className="list-style mb-2">
<li>
Comprehensive analysis of key variables from the rat phenotypic data,
including summary statistics, correlation analysis, statistical
testing, and regression models:
QC + DEA:
{' '}
{/* eslint-disable-next-line jsx-a11y/anchor-is-valid */}
<a
href="#"
data-toggle="modal"
data-target="#html-report-modal"
onClick={(e) =>
handleClickReport(
'phenotypes/pass1ac-pheno-analysis.html',
'pass1ac-pheno-analysis.html',
)
}
>
pass1ac-pheno-analysis.html
</a>
pass1ac-6-rna-seq-analysis-report.html
</li>
</ul>
</li>
<li>
Transcriptomics
<strong>Metabolomics</strong>
<ul className="list-style mb-2">
<li>
QC + DEA:{' '}
{/* eslint-disable-next-line jsx-a11y/anchor-is-valid */}
<a
href="#"
data-toggle="modal"
data-target="#html-report-modal"
onClick={(e) =>
handleClickReport(
'transcriptomics/pass1ac-rna-seq-analysis-report.html',
'pass1ac-rna-seq-analysis-report.html',
)
}
>
pass1ac-rna-seq-analysis-report.html
</a>
QC + DA:
{' '}
pass1ac-6-metabolomics-analysis-report.html
</li>
</ul>
</li>
<li>
Metabolomics
<strong>Proteomics</strong>
<ul className="list-style mb-2">
<li>
QC: {/* eslint-disable-next-line jsx-a11y/anchor-is-valid */}
<a
href="#"
data-toggle="modal"
data-target="#html-report-modal"
onClick={(e) =>
handleClickReport(
'metabolomics/metabolomics-qc.html',
'metabolomics-qc.html',
)
}
>
metabolomics-qc.html
</a>
Coming soon
</li>
</ul>
</li>
<li>
<strong>ATAC-seq</strong>
<ul className="list-style mb-2">
<li>
DA: {/* eslint-disable-next-line jsx-a11y/anchor-is-valid */}
<a
href="#"
data-toggle="modal"
data-target="#html-report-modal"
onClick={(e) =>
handleClickReport(
'metabolomics/metabolomics-da.html',
'metabolomics-da.html',
)
}
>
metabolomics-da.html
</a>
Coming soon
</li>
</ul>
</li>
</ul>
</li>
<li>
<strong>Preliminary Analysis Report:</strong>
<ul className="list-style mt-2">
<li>
Proteomics
<a
href="https://docs.google.com/document/d/1pE6SIaLxAd-gyJW34pqWyzbo6JINe2jlNTc-ONfOlqs/edit?usp=sharing"
target="_blank"
rel="noopener noreferrer"
>
Link to the report
</a>
{' '}
(Google Doc)
</li>
<li>
R Notebooks for Omics Data Analysis (HTML format)
<ul className="list-style mt-2">
<li>
1A1C-independent-analyses
<ul className="list-style mb-2">
{proteomics1A1CIndependentAnalyses.map((report) => (
<li key={report}>
{/* eslint-disable-next-line jsx-a11y/anchor-is-valid */}
<a
href="#"
data-toggle="modal"
data-target="#html-report-modal"
onClick={(e) =>
handleClickReport(
`proteomics/1a1c-independent-analyses/${report}`,
report,
)
}
>
{report}
</a>
</li>
))}
</ul>
</li>
<li>
DA
Metabolomics
<ul className="list-style mb-2">
{proteomicsReportsDA.map((report) => (
<li key={report}>
{/* eslint-disable-next-line jsx-a11y/anchor-is-valid */}
<a
href="#"
data-toggle="modal"
data-target="#html-report-modal"
onClick={(e) =>
handleClickReport(`proteomics/da/${report}`, report)
}
>
{report}
</a>
</li>
))}
<li>
QC:
{' '}
{/* eslint-disable-next-line jsx-a11y/anchor-is-valid */}
<a
href="#"
data-toggle="modal"
data-target="#html-report-modal"
onClick={(e) => handleClickReport('metabolomics/metabolomics-qc.html', 'metabolomics-qc.html')}
>
metabolomics-qc.html
</a>
</li>
<li>
DA:
{' '}
{/* eslint-disable-next-line jsx-a11y/anchor-is-valid */}
<a
href="#"
data-toggle="modal"
data-target="#html-report-modal"
onClick={(e) => handleClickReport('metabolomics/metabolomics-da.html', 'metabolomics-da.html')}
>
metabolomics-da.html
</a>
</li>
</ul>
</li>
<li>
QC-norm
<ul className="list-style mb-2">
{proteomicsReportsQCNorm.map((report) => (
<li key={report}>
{/* eslint-disable-next-line jsx-a11y/anchor-is-valid */}
<a
href="#"
data-toggle="modal"
data-target="#html-report-modal"
onClick={(e) =>
handleClickReport(
`proteomics/qc-norm/${report}`,
report,
)
}
>
{report}
</a>
</li>
))}
Proteomics
<ul className="list-style mt-2">
<li>
1A1C-independent-analyses
<ul className="list-style mb-2">
{proteomics1A1CIndependentAnalyses.map((report) => (
<li key={report}>
{/* eslint-disable-next-line jsx-a11y/anchor-is-valid */}
<a
href="#"
data-toggle="modal"
data-target="#html-report-modal"
onClick={(e) => handleClickReport(`proteomics/1a1c-independent-analyses/${report}`, report)}
>
{report}
</a>
</li>
))}
</ul>
</li>
<li>
DA
<ul className="list-style mb-2">
{proteomicsReportsDA.map((report) => (
<li key={report}>
{/* eslint-disable-next-line jsx-a11y/anchor-is-valid */}
<a
href="#"
data-toggle="modal"
data-target="#html-report-modal"
onClick={(e) => handleClickReport(`proteomics/da/${report}`, report)}
>
{report}
</a>
</li>
))}
</ul>
</li>
<li>
QC-norm
<ul className="list-style mb-2">
{proteomicsReportsQCNorm.map((report) => (
<li key={report}>
{/* eslint-disable-next-line jsx-a11y/anchor-is-valid */}
<a
href="#"
data-toggle="modal"
data-target="#html-report-modal"
onClick={(e) => handleClickReport(`proteomics/qc-norm/${report}`, report)}
>
{report}
</a>
</li>
))}
</ul>
</li>
</ul>
</li>
</ul>
Expand Down
10 changes: 5 additions & 5 deletions src/lib/teamInfo.js
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Original file line number Diff line number Diff line change
Expand Up @@ -85,11 +85,6 @@ const teamInfo = {
title: 'Bioinformatics/Software Engineer',
image: MihirImg,
},
{
name: 'Samiya Shimly, Ph.D.',
title: 'Postdoctoral Scholar',
image: SamiyaImg,
},
{
name: 'Laurens van de Wiel, Ph.D.',
title: 'Postdoctoral Scholar',
Expand Down Expand Up @@ -174,6 +169,11 @@ const teamInfo = {
title: 'Alumni',
image: ChelseaImg,
},
{
name: 'Samiya Shimly, Ph.D.',
title: 'Alumni',
image: SamiyaImg,
},
{
name: 'Aditya Singh, Ph.D.',
title: 'Alumni',
Expand Down

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