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--- sepsis [2017/05/10 22:18]
tes17 [Neonatal Sepsis Analysis]
+++ sepsis [2018/09/05 13:46] (current)
alexskr
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 ===== Sepsis Multi-Cohort Analysis Papers =====
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-==== Sepsis vs. Non-Infectious Inflammation Manuscript (Sci Transl Med, 2015)====
-Full-text link to the manuscript (gets behind paywall):
+==== Sepsis vs. Non-Infectious Inflammation Manuscript (Sci Transl Med, 2015) ====
-**[[http://stm.sciencemag.org/cgi/content/full/7/287/287ra71?ijkey=zTwcB5uK7tk5w&keytype=ref&siteid=scitransmed|Sweeney TE, Shidham A, Wong HR, Khatri P. "A Comprehensive Time-Course-Based Multi-Cohort Analysis of Sepsis and Sterile Inflammation Reveals a Robust Diagnostic Gene Set". Science Translational Medicine, 7, 287ra71 (May 13, 2015).]]**
-\\ \\
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+Full-text link to the manuscript (gets behind paywall): **[[http://stm.sciencemag.org/cgi/content/full/7/287/287ra71?ijkey=zTwcB5uK7tk5w&keytype=ref&siteid=scitransmed|Sweeney TE, Shidham A, Wong HR, Khatri P. "A Comprehensive Time-Course-Based Multi-Cohort Analysis of Sepsis and Sterile Inflammation Reveals a Robust Diagnostic Gene Set". Science Translational Medicine, 7, 287ra71 (May 13, 2015).]]** \\
-<div data-badge-type='medium-donut' class='altmetric-embed' data-badge-details='right' data-doi='10.1126/scitranslmed.aaa5993'></div>
+<html> <div data-badge-type='medium-donut' class='altmetric-embed' data-badge-details='right' data-doi='10.1126/scitranslmed.aaa5993'></div> </html>
-</html>
 == A BBC interview discussing the impact of these results (sepsis discussion begins @ 13:53): ==
-[[http://www.bbc.co.uk/programmes/b0639w4c]]
-\\ \\
+[[http://www.bbc.co.uk/programmes/b0639w4c|http://www.bbc.co.uk/programmes/b0639w4c]]\\
 == The R scripts for running the multi-cohort analysis (data not included): ==
-{{:sepsis:sepsis_mc_analysis.zip|}}
-\\ \\
+{{:sepsis:sepsis_mc_analysis.zip|sepsis_mc_analysis.zip}}
+\\
 ----
+==== Bacterial - Viral Classification Manuscript (Sci Transl Med, 2016) ====
-==== Bacterial - Viral Classification Manuscript (Sci Transl Med, 2016)====
+\\
-\\
+Data and scripts for: **[[http://stm.sciencemag.org/content/8/346/346ra91|Sweeney TE, Wong HR, Khatri P. "Robust classification of bacterial and viral infections via integrated host gene expression diagnostics", Science Translational Medicine 06 Jul 2016: Vol. 8, Issue 346, pp. 346ra91]]**<html> <div data-badge-type='medium-donut' class='altmetric-embed' data-badge-details='right' data-doi='10.1126/scitranslmed.aaf7165'></div> </html> [[http://time.com/4393916/antibiotics-cold-flu-symptoms-drug-resistant|Link to Time Magazine story covering this work]]
-Data and scripts for: **[[http://stm.sciencemag.org/content/8/346/346ra91|Sweeney TE, Wong HR, Khatri P. "Robust classification of bacterial and viral infections via integrated host gene expression diagnostics", Science Translational Medicine  06 Jul 2016: Vol. 8, Issue 346, pp. 346ra91]]**
-<html>
-<div data-badge-type='medium-donut' class='altmetric-embed' data-badge-details='right' data-doi='10.1126/scitranslmed.aaf7165'></div>
-</html>
-[[http://time.com/4393916/antibiotics-cold-flu-symptoms-drug-resistant|Link to Time Magazine story covering this work]]
-\\ \\
+\\
 == The R scripts for running the multi-cohort analysis (same as above, data not included): ==
-{{:sepsis:sepsis_mc_analysis.zip|}}
-\\ \\
-COCONUT is available on CRAN for R:
+{{:sepsis:sepsis_mc_analysis.zip|sepsis_mc_analysis.zip}} \\
-[[https://cran.r-project.org/web/packages/COCONUT/index.html | COCONUT R package ]]
+COCONUT is available on CRAN for R: [[https://cran.r-project.org/web/packages/COCONUT/index.html|COCONUT R package ]]\\
-\\ \\
+[[:sepsis:bactviraldata|Link to COCONUT-conormalized data objects used in manuscript]]\\
-[[sepsis:bactviraldata | Link to COCONUT-conormalized data objects used in  manuscript]]
-\\ \\
 ----
 ==== Benchmarking sepsis gene expression diagnostics using public data ====
-Full-text link: [[http://journals.lww.com/ccmjournal/Fulltext/2017/01000/Benchmarking_Sepsis_Gene_Expression_Diagnostics.1.aspx|Sweeney TE & Khatri P, "Benchmarking sepsis gene expression diagnostics using public data". Critical Care Medicine, 2016]]
-\\ \\
-<html>
+Full-text link: [[http://journals.lww.com/ccmjournal/Fulltext/2017/01000/Benchmarking_Sepsis_Gene_Expression_Diagnostics.1.aspx|Sweeney TE & Khatri P, "Benchmarking sepsis gene expression diagnostics using public data". Critical Care Medicine, 2016]]\\
-<div data-badge-details="right" data-badge-type="medium-donut" data-doi="10.1097/CCM.0000000000002021" data-hide-no-mentions="true" data-hide-less-than="5" class="altmetric-embed"></div>
+<html> <div data-badge-details="right" data-badge-type="medium-donut" data-doi="10.1097/CCM.0000000000002021" data-hide-no-mentions="true" data-hide-less-than="5" class="altmetric-embed"></div> </html>\\
-</html>
+\\
-\\ \\
+{{:sepsis:benchmarking:sepsis_benchmarking_scripts.zip|Benchmarking scripts described in the manuscript}} \\
-{{:sepsis:benchmarking:sepsis_benchmarking_scripts.zip|Benchmarking scripts described in the manuscript}}
+\\
-\\ \\
+{{:sepsis:benchmarking:public_sepsis_datasets.rds|Link to data objects}}
-{{ :sepsis:benchmarking:public_sepsis_datasets.rds |Link to data objects}}
-\\ \\
+\\
 ----
 ==== Neonatal Sepsis Analysis ====
-Data for: [[http://academic.oup.com/jpids/article/doi/10.1093/jpids/pix021/3611547/Validation-of-the-Sepsis-MetaScore-for-Diagnosis?guestAccessKey=84e40f05-d79a-432e-bc67-73a476ed3a0d | Sweeney, TE et al., "Validation of the Sepsis MetaScore for Diagnosis of Neonatal Sepsis", J Ped Inf Dis Soc, 2017]]
-\\ \\
+Data for: [[http://academic.oup.com/jpids/article/doi/10.1093/jpids/pix021/3611547/Validation-of-the-Sepsis-MetaScore-for-Diagnosis?guestAccessKey=84e40f05-d79a-432e-bc67-73a476ed3a0d|Sweeney, TE et al., "Validation of the Sepsis MetaScore for Diagnosis of Neonatal Sepsis", J Ped Inf Dis Soc, 2017]]\\
+\\
 {{:sepsis:gse25504_coconut_unique.zip|COCONUT-normalized, unique patients from GSE25504 (Smith et al., 2015)}}
-\\ \\
+\\
 ----
 ==== Sepsis Mortality Analysis ====
-The preprint linked below will be updated with the final, peer-reviewed version once published.
-\\ \\
+The preprint linked below will be updated with the final, peer-reviewed version once published.\\
-[[http://biorxiv.org/content/early/2016/12/19/095489|Sweeney, TE et al., "Mortality prediction in sepsis via gene expression analysis: a community approach". BioArxiv, 2016]]
+\\
-\\ \\
+[[http://biorxiv.org/content/early/2016/12/19/095489|Sweeney, TE et al., "Mortality prediction in sepsis via gene expression analysis: a community approach". BioArxiv, 2016]]\\
 ----
 ==== COCONUT-normalized data from Herberg et al, JAMA 2016: GSE72829 ====
-The dataset [[http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE72829|GSE72829]] described in [[http://jama.jamanetwork.com/article.aspx?articleid=2545687|Herberg et al, JAMA 2016]] is composed of 4 smaller datasets spread across three microarray platforms. We used COCONUT to pool these data into a single dataset. Notably, since GSE80412 has no healthy controls, these were initially co-normalized using Limma with GSE72809, and then healthy controls between all three remaining datasets were used to make the final COCONUT-conormalized object. The pooled data are available as a .RDS (R object) {{:sepsis:gse72829coco.rds|here}}.
-\\ \\
+The dataset [[http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE72829|GSE72829]] described in [[http://jama.jamanetwork.com/article.aspx?articleid=2545687|Herberg et al, JAMA 2016]] is composed of 4 smaller datasets spread across three microarray platforms. We used COCONUT to pool these data into a single dataset. Notably, since GSE80412 has no healthy controls, these were initially co-normalized using Limma with GSE72809, and then healthy controls between all three remaining datasets were used to make the final COCONUT-conormalized object. The pooled data are available as a .RDS (R object) {{:sepsis:gse72829coco.rds|here}}.
+\\
 ----
 ==== Glue Grant Data Access ====
 Some of the data used in the manuscript (the Inflammation and Host Response to Injury Glue Grant data) require IRB access. This can be obtained by following the instructions here: [[https://www.gluegrant.org/|https://www.gluegrant.org/]]
-Briefly, you will need to first register as a Consortium Member:
+Briefly, you will need to first register as a Consortium Member: [[https://www.gluegrant.org/glueadmin/register_consortium.jsp|Glue Grant Consortium Registration]]
-[[https://www.gluegrant.org/glueadmin/register_consortium.jsp| Glue Grant Consortium Registration]]
-You will then be able to access the [[https://www.gluegrant.org/consortium/|consortium]] page, which explains exact instructions for obtaining data access at the bottom section, titled "Our Policies for Access to Data, Methodologies, and Protocols".
+You will then be able to access the [[https://www.gluegrant.org/consortium/|consortium]] page, which explains exact instructions for obtaining data access at the bottom section, titled "Our Policies for Access to Data, Methodologies, and Protocols".\\
-\\ \\
-When access to the Glue Grant database has been issued by the Glue Grant team, please email (1) IRB approval and (2) the letter of approval from the Glue Grant consortium to: __tes17 [at] stanford [dot] edu__ to request access to the data object.
-\\
 \\
+When access to the Glue Grant database has been issued by the Glue Grant team, please email (1) IRB approval and (2) the letter of approval from the Glue Grant consortium to: __tes17 [at] stanford [dot] edu__ to request access to the data object.\\
 == Link to glue grant data, if permission has been granted: ==
-[[sepsis:private|Data Object]]
+[[:sepsis:private|Data Object]]