From 80878482294fd1e1db60f244b6f679414220b83e Mon Sep 17 00:00:00 2001 From: Leonardo Collado Torres Date: Wed, 15 May 2019 15:14:52 -0400 Subject: [PATCH] Change email --- cross_studies_metadata/cross_studies_metadata.Rmd | 2 +- cross_studies_metadata/cross_studies_metadata.html | 2 +- cross_studies_metadata/recount_brain_ontologies.Rmd | 2 +- cross_studies_metadata/recount_brain_ontologies.html | 2 +- example_PMI/example_PMI.Rmd | 2 +- example_PMI/example_PMI.html | 2 +- example_SRP027383/example_SRP027383.Rmd | 2 +- example_SRP027383/example_SRP027383.html | 2 +- merged_metadata/merging_data.Rmd | 2 +- merged_metadata/merging_data.html | 2 +- metasra_comp/metasra_comp.Rmd | 2 +- metasra_comp/metasra_comp.html | 2 +- 12 files changed, 12 insertions(+), 12 deletions(-) diff --git a/cross_studies_metadata/cross_studies_metadata.Rmd b/cross_studies_metadata/cross_studies_metadata.Rmd index 65f852a..0d7b5b8 100644 --- a/cross_studies_metadata/cross_studies_metadata.Rmd +++ b/cross_studies_metadata/cross_studies_metadata.Rmd @@ -10,7 +10,7 @@ author: affiliation: - &libd Lieber Institute for Brain Development, Johns Hopkins Medical Campus - &ccb Center for Computational Biology, Johns Hopkins University - email: leo.collado@libd.org + email: lcolladotor@gmail.com - name: Michael D Wilson affiliation: - *ggb diff --git a/cross_studies_metadata/cross_studies_metadata.html b/cross_studies_metadata/cross_studies_metadata.html index 07bb8ca..31c7971 100644 --- a/cross_studies_metadata/cross_studies_metadata.html +++ b/cross_studies_metadata/cross_studies_metadata.html @@ -232,7 +232,7 @@

Merging recount_brain metadata with GTEx and TCGA metadata

Dustin Sokolowski1,2*, Leonardo Collado-Torres3,4** and Michael D Wilson1,2,5

1Program in Genetics and Genome Biology, Hospital for Sick Children, Toronto M5G 0A4, Canada
2Department of Molecular Genetics, University of Toronto, Toronto M5S 1A8, Canada
3Lieber Institute for Brain Development, Johns Hopkins Medical Campus
4Center for Computational Biology, Johns Hopkins University
5Heart and Stroke Richard Lewar Centre of Excellence in Cardiovascular Research, Toronto M5S 3H2, Canada

-

*djsokolowski95@gmail.com
**leo.collado@libd.org

+

*djsokolowski95@gmail.com
**lcolladotor@gmail.com

28 July 2018

diff --git a/cross_studies_metadata/recount_brain_ontologies.Rmd b/cross_studies_metadata/recount_brain_ontologies.Rmd index 69af0a6..b6600ef 100644 --- a/cross_studies_metadata/recount_brain_ontologies.Rmd +++ b/cross_studies_metadata/recount_brain_ontologies.Rmd @@ -9,7 +9,7 @@ author: affiliation: - &libd Lieber Institute for Brain Development, Johns Hopkins Medical Campus - &ccb Center for Computational Biology, Johns Hopkins University - email: leo.collado@libd.org + email: lcolladotor@gmail.com output: BiocStyle::html_document: self_contained: yes diff --git a/cross_studies_metadata/recount_brain_ontologies.html b/cross_studies_metadata/recount_brain_ontologies.html index 6481be8..8402ac6 100644 --- a/cross_studies_metadata/recount_brain_ontologies.html +++ b/cross_studies_metadata/recount_brain_ontologies.html @@ -301,7 +301,7 @@

Ontology-based metadata for recount-brain

Sean Davis1* and Leonardo Collado-Torres2,3**

1Genetics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
2Lieber Institute for Brain Development, Johns Hopkins Medical Campus
3Center for Computational Biology, Johns Hopkins University

-

*sdavis2@mail.nih.gov
**leo.collado@libd.org

+

*sdavis2@mail.nih.gov
**lcolladotor@gmail.com

15 April 2019

diff --git a/example_PMI/example_PMI.Rmd b/example_PMI/example_PMI.Rmd index 453f482..2f36031 100644 --- a/example_PMI/example_PMI.Rmd +++ b/example_PMI/example_PMI.Rmd @@ -5,7 +5,7 @@ author: affiliation: - Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA - Center for Computational Biology, Johns Hopkins University, Baltimore, MD, 21205, USA - email: leo.collado@libd.org + email: lcolladotor@gmail.com output: BiocStyle::html_document abstract: | diff --git a/example_PMI/example_PMI.html b/example_PMI/example_PMI.html index 16b0094..95ca94b 100644 --- a/example_PMI/example_PMI.html +++ b/example_PMI/example_PMI.html @@ -126,7 +126,7 @@

Using recount_brain to explore relationships with post-mortem interval

Leonardo Collado-Torres1,2*

1Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
2Center for Computational Biology, Johns Hopkins University, Baltimore, MD, 21205, USA

-

*leo.collado@libd.org

+

*lcolladotor@gmail.com

3 March 2018

Abstract

This is an example of how you can use recount_brain to check if some results from another study are replicated in brain samples from the SRA present in recount2. This example also shows how you can quantify the percent of mitochondrial transcription and options for comparing two sets of SRA studies.

diff --git a/example_SRP027383/example_SRP027383.Rmd b/example_SRP027383/example_SRP027383.Rmd index c398fe8..c9dc482 100644 --- a/example_SRP027383/example_SRP027383.Rmd +++ b/example_SRP027383/example_SRP027383.Rmd @@ -5,7 +5,7 @@ author: affiliation: - Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA - Center for Computational Biology, Johns Hopkins University, Baltimore, MD, 21205, USA - email: leo.collado@libd.org + email: lcolladotor@gmail.com output: BiocStyle::html_document abstract: | diff --git a/example_SRP027383/example_SRP027383.html b/example_SRP027383/example_SRP027383.html index 63bfcd0..8f1a843 100644 --- a/example_SRP027383/example_SRP027383.html +++ b/example_SRP027383/example_SRP027383.html @@ -126,7 +126,7 @@

recount_brain example with data from SRP027383

Leonardo Collado-Torres1,2*

1Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
2Center for Computational Biology, Johns Hopkins University, Baltimore, MD, 21205, USA

-

*leo.collado@libd.org

+

*lcolladotor@gmail.com

3 March 2018

Abstract

This is an example on how to use recount_brain applied to the SRP027383 study. We show how to download data from recount2, add the sample metadata from recount_brain, explore the sample metadata and the gene expression data, and perform a gene expression analysis.

diff --git a/merged_metadata/merging_data.Rmd b/merged_metadata/merging_data.Rmd index 36b2402..ad41bc5 100644 --- a/merged_metadata/merging_data.Rmd +++ b/merged_metadata/merging_data.Rmd @@ -5,7 +5,7 @@ author: affiliation: - &libd Lieber Institute for Brain Development, Johns Hopkins Medical Campus - &ccb Center for Computational Biology, Johns Hopkins University - email: leo.collado@libd.org + email: lcolladotor@gmail.com - name: Ashkaun Razmara affiliation: - *libd diff --git a/merged_metadata/merging_data.html b/merged_metadata/merging_data.html index 2b18a84..d83d2e2 100644 --- a/merged_metadata/merging_data.html +++ b/merged_metadata/merging_data.html @@ -232,7 +232,7 @@

Merging metadata and recount_brain

Leonardo Collado-Torres1,2* and Ashkaun Razmara1

1Lieber Institute for Brain Development, Johns Hopkins Medical Campus
2Center for Computational Biology, Johns Hopkins University

-

*leo.collado@libd.org

+

*lcolladotor@gmail.com

12 July 2018

diff --git a/metasra_comp/metasra_comp.Rmd b/metasra_comp/metasra_comp.Rmd index 49a108c..992d570 100644 --- a/metasra_comp/metasra_comp.Rmd +++ b/metasra_comp/metasra_comp.Rmd @@ -5,7 +5,7 @@ author: affiliation: - &libd Lieber Institute for Brain Development, Johns Hopkins Medical Campus - &ccb Center for Computational Biology, Johns Hopkins University - email: leo.collado@libd.org + email: lcolladotor@gmail.com output: BiocStyle::html_document: self_contained: yes diff --git a/metasra_comp/metasra_comp.html b/metasra_comp/metasra_comp.html index 5258578..a42e215 100644 --- a/metasra_comp/metasra_comp.html +++ b/metasra_comp/metasra_comp.html @@ -301,7 +301,7 @@

Comparing recount-brain and MetaSRA ‘UBERON:0000955’

Leonardo Collado-Torres1,2*

1Lieber Institute for Brain Development, Johns Hopkins Medical Campus
2Center for Computational Biology, Johns Hopkins University

-

*leo.collado@libd.org

+

*lcolladotor@gmail.com

16 April 2019