index.Rmd

---
title: "Leonardo Collado-Torres's CV"
author: Leonardo Collado-Torres
date: "`r Sys.Date()`"
output:
  pagedown::html_resume:
    css: ['nstrayer_cv/css/styles.css', 'resume']
    # set it to true for a self-contained HTML page but it'll take longer to render
    self_contained: true
---

```{r 'setup', include=FALSE}
knitr::opts_chunk$set(
  results='asis', 
  echo = FALSE
)

library(glue)
library(tidyverse)

# ======================================================================
# These variables determine how the the data is loaded and how the exports are
# done.

# Is data stored in google sheets? If no data will be gather from the csvs/
# folder in project
using_googlesheets <- TRUE

# Just the copied URL from the sheet
positions_sheet_loc <- "https://docs.google.com/spreadsheets/d/1fPY9wUeRcHWu5qijE4sZ8Xp6cGqasgdDNBJndmM3fBQ"

# Is this sheet available for anyone to read? If you're using a private sheet
# set this to false and go to gather_data.R and run the data loading manually
# once to cache authentication
sheet_is_publicly_readable <- TRUE

# Is the goal of this knit to build a document that is exported to PDF? If so
# set this to true to have links turned into footnotes at the end of the
# document
PDF_EXPORT <- FALSE


CV_PDF_LOC <- "http://lcolladotor.github.io/cv/en_CV_lcollado.pdf"
CV_HTML_LOC <- "http://lcolladotor.github.io/cv"


# A global (gasp) variable that holds all the links that were inserted for
# placement at the end
links <- c()

# ======================================================================
# Now we source two external scripts. One contains functions for building the
# text output and the other loads up our data from either googlesheets or csvs

# Functions for building sections from CSV data
source('nstrayer_cv/parsing_functions.R') 

# Load data for CV/Resume
source('nstrayer_cv/gather_data.R')
```



```{r 'fix_dots_pdf'}
# When in export mode the little dots are unaligned, so fix that. 
if(PDF_EXPORT){
  cat("
  <style>
  :root{
    --decorator-outer-offset-left: -6.5px;
  }
  </style>")
}
```


Aside
================================================================================


![avatar](https://lcolladotor.github.io/authors/admin/avatar_hu61670ae1305c5c407abf5eedc95c7971_127149_270x270_fill_q75_lanczos_center.JPG){width=100%}

```{r 'fix_dots_pdf_2'}
# When in export mode the little dots are unaligned, so fix that. 
if(PDF_EXPORT){
  glue("View this CV online with links at _{CV_HTML_LOC}_")
} else {
  glue("[<i class='fas fa-download'></i> Download a PDF of this CV]({CV_PDF_LOC})")
}
```

Contact {#contact}
--------------------------------------------------------------------------------

```{r 'contact_info'}
contact_info %>% 
  glue_data("- <i class='{iconpack} fa-{icon}'></i> {contact}")
```



Language Skills {#skills}
--------------------------------------------------------------------------------

```{r 'skill_bars'}
build_skill_bars(skills)
```


Disclaimer {#disclaimer}
--------------------------------------------------------------------------------

Made with the R package [**pagedown**](https://github.com/rstudio/pagedown). The source code is available at [lcolladotor/cv](https://github.com/lcolladotor/cv) and is powered by [nstrayer/cv](https://github.com/nstrayer/cv).

Last updated on `r Sys.Date()`.



Main
================================================================================

Leonardo Collado-Torres {#title}
--------------------------------------------------------------------------------

```{r 'intro'}
print_text_block(text_blocks, 'intro')
```


Table of Contents {#toc}
--------------------------------------------------------------------------------

1. [Education](#education)
1. [Research Experience](#research)
1. [Industry Experience](#industry)
1. [Funding Secured as (co-)PI](#grants)
1. [Honors and Awards](#honors)
1. [Publications](#publications)
1. [Software](#software)
1. [Leadership and Service](#leadership)
1. [Mentoring Experience](#mentoring)
1. [Teaching Experience](#teaching)
1. [Courses, Meetings, Talks, and Posters ](#courses)
1. [Languages](#languages)

Education {#education data-icon=graduation-cap data-concise=true} 
--------------------------------------------------------------------------------

```{r 'education'}
print_section(position_data, 'education')
```

::: aside
[Table of Contents](#toc)
:::

<br>
<br>
<br>

Research Experience {#research data-icon=laptop} 
--------------------------------------------------------------------------------

```{r 'work_research'}
print_section(position_data, 'research_positions')
```

::: aside
[Table of Contents](#toc)
:::

<br>
<br>
<br>

Industry Experience {#industry data-icon=suitcase}
--------------------------------------------------------------------------------

::: aside
```{r 'work_industry_intro'}
print_text_block(text_blocks, 'industy_experience_aside')
```
:::

```{r 'work_industry'}
print_section(position_data, 'industry_positions')
```

<br>
<br>
<br>

::: aside
[Table of Contents](#toc)
:::

Funding Secured as (co-)PI {#grants data-icon=money-bill-wave}
--------------------------------------------------------------------------------

```{r 'funding'}
print_section(position_data, 'grants')
```

::: aside
[Table of Contents](#toc)
:::

<br>
<br>
<br>

Honors and Awards {#honors data-icon=medal}
--------------------------------------------------------------------------------

```{r 'honors'}
print_section(position_data, 'honors')
```

::: aside
[Table of Contents](#toc)
:::

<br>
<br>
<br>


Publications {#publications data-icon=book}
--------------------------------------------------------------------------------

:::aside
$*$ indicates equal contribution, $\dagger$ indicates corresponding author
:::

```{r 'pubs'}
position_data$description_1 <-
  gsub(
    'Collado-Torres L',
    '__Collado-Torres L__',
    gsub(
      'L Collado-Torres',
      '__L Collado-Torres__',
      gsub(
        'Leonardo Collado-Torres',
        '__Leonardo Collado-Torres__',
        position_data$description_1
      )
    )
  )
print_section(position_data, 'pubs')
```

::: aside
[Table of Contents](#toc)
:::

<br>
<br>
<br>


Software {#software data-icon=laptop}
--------------------------------------------------------------------------------

:::aside
* __all_purpose__: R, Ranked 311/37,473 (top 0.83%) in the US and 1,132/356,811 (top 0.32%) worldwide by [Star Dev](https://stardev.io/developers/lcolladotor) as of May 9th, 2023. Does not take into account contributions at GitHub organizations.
* __statistics__: Stata
* __scripting__: bash
* __markup__: LaTeX, markdown
* __OS__: Linux
* __cluster queue__: Son of Grid Engine
:::

```{r 'getDownloads_fun', echo = FALSE}
getDownloads <- function(pkg, type = "software") {
    if(type == "experiment") {
        url <- paste0(
            'https://bioconductor.org/packages/stats/data-experiment/',
            pkg, '/', pkg, '_stats.tab'
        )
        
    } else if (type == "annotation") {
        url <- paste0(
            'https://bioconductor.org/packages/stats/data-annotation/',
            pkg, '/', pkg, '_stats.tab'
        )
        
    } else {
        url <- paste0(
            'https://bioconductor.org/packages/stats/bioc/',
            pkg, '/', pkg, '_stats.tab'
        )
        
    }
    info <- tryCatch(
        suppressWarnings(read.table(url, header = TRUE)),
        error = function(e) {
            return(data.frame(
                Nb_of_downloads = NA,
                'Month' = 'all'
            ))
        }
    )
    res <- sum(info$Nb_of_downloads[info$Month == 'all'])
    ## In case the download stats are currently unavailable
    if(is.na(res)) res <- paste0('(Not Available on ', Sys.Date(), ')')
    return(res)
}
```

### Bioconductor: author role

[recount3](http://bioconductor.org/packages/recount3): Explore and download data from the recount3 project -- `r getDownloads('recount3')` downloads. [biocthis](http://bioconductor.org/packages/biocthis): Automate package and project setup for Bioconductor packages -- `r getDownloads('biocthis')` downloads. [megadepth](http://bioconductor.org/packages/megadepth): BigWig and BAM related utilities -- `r getDownloads('megadepth')` downloads. [spatialLIBD](http://bioconductor.org/packages/LIBD): LIBD Visium spatial transcriptomics human pilot data inspector -- `r getDownloads('spatialLIBD', type = "experiment")` downloads. [GenomicState](http://bioconductor.org/packages/GenomicState): data for derfinder analyses -- `r getDownloads('GenomicState', type = "annotation")` downloads. [recount](http://bioconductor.org/packages/recount): Explore and download data from the recount2 project -- `r getDownloads('recount')` downloads. [derfinder](http://bioconductor.org/packages/derfinder): Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach -- `r getDownloads('derfinder')` downloads. [derfinderPlot](http://bioconductor.org/packages/derfinderPlot): plotting functions for derfinder results -- `r getDownloads('derfinderPlot')` downloads. [regionReport](http://bioconductor.org/packages/regionReport): Generate HTML or PDF reports for a set of genomic regions or DESeq2/edgeR results -- `r getDownloads('regionReport')` downloads. [derfinderHelper](http://bioconductor.org/packages/derfinderHelper): helper functions for derfinder package -- `r getDownloads('derfinderHelper')` downloads. [derfinderData](http://bioconductor.org/packages/derfinderData): data for derfinder examples -- `r getDownloads('derfinderData', type = "experiment")` downloads.


N/A

2014 - 2021

```{r 'software'}
print_section(position_data, 'software')
```

::: aside
[Table of Contents](#toc)
:::

<br>
<br>
<br>

Leadership and Service {#leadership data-icon=book}
--------------------------------------------------------------------------------

```{r 'service'}
print_section(position_data, 'service')
```

::: aside
[Table of Contents](#toc)
:::

<br>
<br>
<br>

Mentoring Experience {#mentoring data-icon=chalkboard-teacher}
--------------------------------------------------------------------------------


```{r 'mentoring'}
print_section(position_data, 'mentoring')
```

::: aside
[Table of Contents](#toc)
:::

<br>
<br>
<br>

Teaching Experience {#teaching data-icon=chalkboard-teacher}
--------------------------------------------------------------------------------

::: aside
```{r 'teaching_aside'}
print_text_block(text_blocks, 'teaching_experience_aside')
```
:::

```{r 'teaching'}
print_section(position_data, 'teaching')
```

::: aside
[Table of Contents](#toc)
:::

<br>
<br>
<br>

Courses, Meetings, Talks, and Posters {#courses data-icon=chalkboard-teacher}
--------------------------------------------------------------------------------

:::aside
Most recent slides are available via [speakerdeck](http://www.speakerdeck.com/lcolladotor) or [slideshare](http://www.slideshare.com/lcolladotor).
:::

```{r 'conf'}
print_section(position_data, 'conf')
```

::: aside
[Table of Contents](#toc)
:::

<br>
<br>
<br>

Languages {#languages data-icon=chalkboard-teacher}
--------------------------------------------------------------------------------

* Native: Spanish (Mexico)
* Bilingual: English
* Basic: French

::: aside
[Table of Contents](#toc)
:::


```{r 'more_pdf_stuff'}
if(PDF_EXPORT){
  cat("
  
Links {data-icon=link}
--------------------------------------------------------------------------------

<br>


")
  
  walk2(links, 1:length(links), function(link, index){
    print(glue('{index}. {link}'))
  })
}
```