software.qmd

---
title: "Software"
bibliography: references.bib
csl: publications/csl/elife.csl
page-layout: full
---

<style>
/* Modern Software Page Styling */
:root {
  --primary-color: #0a2463;
  --secondary-color: #3e92cc;
  --accent-color: #d81159;
  --light-bg: #f8f9fa;
  --card-bg: #ffffff;
  --text-primary: #1a1a2e;
  --text-secondary: #4a4e69;
  --text-light: #6c757d;
  --shadow: 0 10px 30px rgba(0, 0, 0, 0.08);
  --border-color: #e9ecef;
  --radius: 8px;
  --transition: all 0.3s ease;
}

body {
  font-family: system-ui, -apple-system, BlinkMacSystemFont, 'Segoe UI', Roboto, 'Helvetica Neue', Arial, sans-serif;
  line-height: 1.6;
  background-color: var(--light-bg);
  color: var(--text-primary);
  margin: 0;
  padding: 0;
}

/* Page title styling */
.page-title {
  font-size: 2.5rem;
  font-weight: 700;
  color: var(--primary-color);
  text-align: center;
  margin: 2rem 0 1rem;
}

.lead {
  text-align: center;
  max-width: 800px;
  margin: 0 auto 3rem;
  font-size: 1.1rem;
  color: var(--text-secondary);
  padding: 0 1rem;
}

/* Software card styling */
.software-grid {
  display: grid;
  grid-template-columns: repeat(auto-fit, minmax(300px, 1fr));
  gap: 2rem;
  margin: 0 auto;
  padding: 0 1rem;
  max-width: 1200px;
}

.software-card {
  background-color: var(--card-bg);
  border-radius: var(--radius);
  box-shadow: var(--shadow);
  overflow: hidden;
  transition: var(--transition);
  border: 1px solid var(--border-color);
}

.software-card:hover {
  transform: translateY(-5px);
  box-shadow: 0 15px 35px rgba(0, 0, 0, 0.1);
}

.software-icon {
  padding: 1.5rem;
  background-color: var(--light-bg);
  display: flex;
  align-items: center;
  justify-content: center;
}

.software-icon img {
  max-width: 120px;
  height: auto;
}

.software-info {
  padding: 1.5rem;
  text-align: center;
}

.software-info h2 {
  font-size: 1.8rem;
  font-weight: 700;
  color: var(--primary-color);
  margin: 0 0 1rem 0;
}

.software-info p {
  font-size: 1rem;
  color: var(--text-secondary);
  margin-bottom: 1.5rem;
}

.software-links {
  display: flex;
  justify-content: center;
  gap: 1rem;
  margin-bottom: 1.5rem;
}

.btn {
  display: inline-block;
  padding: 0.5rem 1rem;
  border-radius: 50px;
  font-size: 0.9rem;
  font-weight: 500;
  text-decoration: none;
  transition: var(--transition);
}

.btn-primary {
  background-color: var(--secondary-color);
  color: white;
}

.btn-primary:hover {
  background-color: var(--primary-color);
  color: white;
  transform: translateY(-2px);
}

.btn-secondary {
  background-color: transparent;
  color: var(--secondary-color);
  border: 1px solid var(--secondary-color);
}

.btn-secondary:hover {
  background-color: rgba(62, 146, 204, 0.1);
  color: var(--secondary-color);
  transform: translateY(-2px);
}

.software-publications {
  padding-top: 1.25rem;
  border-top: 1px solid var(--border-color);
  text-align: left;
}

.software-publications h4 {
  font-size: 1rem;
  font-weight: 600;
  color: var(--primary-color);
  margin-top: 0;
  margin-bottom: 0.75rem;
}

.software-publications ul {
  margin: 0;
  padding-left: 1.25rem;
  list-style-type: disc;
}

.software-publications li {
  font-size: 0.9rem;
  color: var(--text-secondary);
  margin-bottom: 0.25rem;
}

/* Workshops section */
.workshops-section {
  margin-top: 5rem;
  padding: 0 1rem;
  max-width: 1200px;
  margin: 0 auto;
}

.workshops-section h2 {
  font-size: 2.2rem;
  font-weight: 700;
  color: var(--primary-color);
  text-align: center;
  margin-bottom: 2.5rem;
  position: relative;
  padding-bottom: 1rem;
}

.workshops-section h2::after {
  content: '';
  position: absolute;
  bottom: 0;
  left: 50%;
  transform: translateX(-50%);
  width: 80px;
  height: 4px;
  background: linear-gradient(90deg, var(--secondary-color), var(--accent-color));
  border-radius: 2px;
}

.card-deck {
  display: grid;
  grid-template-columns: repeat(auto-fit, minmax(300px, 1fr));
  gap: 1.5rem;
}

.card {
  background-color: var(--card-bg);
  border-radius: var(--radius);
  box-shadow: var(--shadow);
  transition: var(--transition);
  position: relative;
  overflow: hidden;
  border: 1px solid var(--border-color);
}

.card::before {
  content: '';
  position: absolute;
  top: 0;
  left: 0;
  right: 0;
  height: 4px;
  background: linear-gradient(90deg, var(--secondary-color), var(--accent-color));
}

.card:hover {
  transform: translateY(-5px);
  box-shadow: 0 15px 35px rgba(0, 0, 0, 0.1);
}

.card-body {
  padding: 1.5rem;
  text-align: center;
}

.card-body h3 {
  font-size: 1.3rem;
  font-weight: 600;
  color: var(--primary-color);
  margin: 0 0 1rem 0;
}

.card-body p {
  font-size: 0.95rem;
  color: var(--text-secondary);
  margin-bottom: 1.5rem;
}

/* Responsive adjustments */
@media (max-width: 768px) {
  .page-title {
    font-size: 2rem;
  }

  .software-grid {
    grid-template-columns: 1fr;
  }

  .card-deck {
    grid-template-columns: 1fr;
  }
}
</style>

# Our Computational Tools {.page-title}

::: {.lead}
We develop open-source software for genomic data analysis, with a focus on cancer research and single-cell methods.
:::

::: {.software-grid}
::: {.software-card}
::: {.software-icon}
![](contents/hexstickers/corral_sticker.png)
:::
::: {.software-info}
## Corral

Single-cell RNA-seq dimension reduction, batch integration, and visualization with correspondence analysis.

::: {.software-links}
[Bioconductor](https://bioconductor.org/){.btn .btn-primary} [GitHub](https://github.com/){.btn .btn-secondary}
:::

::: {.software-publications}
#### Publications
- [@Hsu2023]
- [@Lê2021]
- [@hsu2020]
:::
:::
:::

::: {.software-card}
::: {.software-icon}
![](contents/hexstickers/mogsa_sticker.png)
:::
::: {.software-info}
## MOGSA

Multi-Omics Gene Set Analysis: Integrative analysis of multiple experimental and molecular data types.

::: {.software-links}
[Bioconductor](https://bioconductor.org/){.btn .btn-primary} [GitHub](https://github.com/){.btn .btn-secondary}
:::

::: {.software-publications}
#### Publications
- [@Meng2016]
- [@Meng2019]
- [@Meng2014]
- [@Meng2016a]
- [@Lê2021]
:::
:::
:::

::: {.software-card}
::: {.software-icon}
![](https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/iBBiG/iBBiG.png)
:::
::: {.software-info}
## iBBiG

Iterative Binary Bi-clustering of Gene Sets for biclustering and pattern discovery in gene expression data.

::: {.software-links}
[Bioconductor](https://bioconductor.org/){.btn .btn-primary} [GitHub](https://github.com/){.btn .btn-secondary}
:::

::: {.software-publications}
#### Publications
- [@gusenleitner2012]
:::
:::
:::

::: {.software-card}
::: {.software-icon}
![](https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/made4/made4.png)
:::
::: {.software-info}
## made4

Multivariate Analysis of Microarray Data using ADE4 for visualization and analysis of microarray data.

::: {.software-links}
[Bioconductor](https://bioconductor.org/){.btn .btn-primary} [GitHub](https://github.com/){.btn .btn-secondary}
:::

::: {.software-publications}
#### Publications
- [@Culhane2005]
:::
:::
:::
:::

::: {.workshops-section}
## Workshops & Training Materials

::: {.card-deck}
::: {.card}
::: {.card-body}
### Hitchhiker's Guide to PCA

A comprehensive tutorial on Principal Component Analysis for genomic data.

[View Workshop](#){.btn .btn-primary}
:::
:::

::: {.card}
::: {.card-body}
### Quick Guide to scRNAseq

Introduction to single-cell RNA sequencing analysis methods.

[View Workshop](#){.btn .btn-primary}
:::
:::

::: {.card}
::: {.card-body}
### BIRSBiointegration Hackathon

Datasets and code from our multi-omics integration hackathon.

[Explore Hackathon](#){.btn .btn-primary}
:::
:::
:::
:::