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software.qmd
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---
title: "Software"
bibliography: references.bib
csl: publications/csl/elife.csl
---
::::::::::::::::::::::::::::::::: software-container
# Our Computational Tools {.page-title}
::: {.lead .text-center .mb-5}
We develop open-source software for genomic data analysis, with a focus on cancer research and single-cell methods.
:::
::::::::::::::::::::::: software-grid
::::::: {.software-card .fade-in}
::: software-icon
:::
::::: 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 .btn-sm} [GitHub](https://github.com/){.btn .btn-secondary .btn-sm}
:::
::: software-publications
#### Publications
- [@Hsu2023]
- [@Lê2021]
- [@hsu2020]
:::
:::::
:::::::
::::::: {.software-card .fade-in}
::: software-icon
:::
::::: 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 .btn-sm} [GitHub](https://github.com/){.btn .btn-secondary .btn-sm}
:::
::: software-publications
#### Publications
- [@Meng2016]
- [@Meng2019]
- [@Meng2014]
- [@Meng2016a]
- [@Lê2021]
:::
:::::
:::::::
::::::: {.software-card .fade-in}
::: software-icon
:::
::::: 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 .btn-sm} [GitHub](https://github.com/){.btn .btn-secondary .btn-sm}
:::
::: software-publications
#### Publications
- [@gusenleitner2012]
:::
:::::
:::::::
::::::: {.software-card .fade-in}
::: software-icon
:::
::::: 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 .btn-sm} [GitHub](https://github.com/){.btn .btn-secondary .btn-sm}
:::
::: software-publications
#### Publications
- [@Culhane2005]
:::
:::::
:::::::
:::::::::::::::::::::::
:::::::::: {.mt-5 .workshops-section .fade-in}
## 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}
:::
::::
:::::::::
::::::::::
:::::::::::::::::::::::::::::::::