update blog to Rmd

Author: stemangiola

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blog/content/post/2025-01-15-introducing-tidyomics-ecosystem/index.qmd renamed to blog/content/post/2025-01-15-introducing-tidyomics-ecosystem/index.Rmd

@@ -1,53 +1,37 @@
 ---
-title: "Introducing the Tidyomics Ecosystem: A Comprehensive Guide to Tidy Transcriptomics"
+title: "The Tidyomics Ecosystem"
 author: "Stefano Mangiola"
-date: "`r Sys.Date()`"
-slug: []
+date: "2025-07-07"
+package: tidyomics
 tags:
   - tidyomics/tidyomicsBlog
   - ecosystem
   - transcriptomics
   - tidyverse
   - bioconductor
-lastmod: "`r Sys.Date()`"
-keywords: []
 description: "A comprehensive introduction to the tidyomics ecosystem, including core packages, publications, GitHub projects, and community resources for tidy transcriptomics analysis."
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 ---
 
-![Tidyomics Ecosystem Cover](images/tidyomics_book_cover.png){.cover-image width=100%}
+
+
+![](images/tidyomics_book_cover.png){.cover-image width=100%}
 
 # Introduction
 
 The tidyomics ecosystem was born from a common challenge faced by life-scientists: every omics technology and framework in R seemed to require learning a new data structure and synthax.  Switching from bulk RNA-seq to single-cell, or from expression data to genomic ranges, often felt climbing a different mountain. Tidyomics keeps the **underlying objects exactly the same** while giving them a single, tidyverse-flavoured grammar so that moving from bulk RNA-seq to single-cell or spatial data is no harder than shifting between two dplyr pipelines.  Its design principles take inspiration from the tidyverse philosophy of clear, human-readable code as articulated by Wickham *et al.* (2019) ([JOSS 10.21105/joss.01686](https://joss.theoj.org/papers/10.21105/joss.01686)).
 
-That question snowballed into an international collaboration—and ultimately into **tidyomics**.
+That question snowballed into an international collaboration—and ultimately into `tidyomics`.
 
 # What is Tidyomics?
 
-**Tidyomics** is an open project to develop and integrate software and documentation to enable a tidy data analysis framework for omics data objects ([Hutchison *et al.* 2024](https://doi.org/10.1038/s41592-024-02299-2)). The development of packages and tutorials is organized around [tidyomics open challenges](https://github.com/tidyomics/). Tidyomics enables the use of familiar tidyverse verbs (`select`, `filter`, `mutate`, etc.) to manipulate rich data objects in the Bioconductor ecosystem. Importantly, the data objects are not modified, but tidyomics provides a tidy *interface* to work on the native objects, leveraging existing Bioconductor classes and algorithms.
+![](images/logo.png){width="120px"}
+
+`tidyomics` is an open project to develop and integrate software and documentation to enable a tidy data analysis framework for omics data objects ([Hutchison *et al.* 2024](https://doi.org/10.1038/s41592-024-02299-2)). The development of packages and tutorials is organized around [tidyomics open challenges](https://github.com/tidyomics/). Tidyomics enables the use of familiar tidyverse verbs (`select`, `filter`, `mutate`, etc.) to manipulate rich data objects in the Bioconductor ecosystem. Importantly, the data objects are not modified, but tidyomics provides a tidy *interface* to work on the native objects, leveraging existing Bioconductor classes and algorithms.
 
-**Tidyomics** is a set of R packages by an international group of developers. The ecosystem allows for code such as:
+`tidyomics` is a set of R packages by an international group of developers. The ecosystem allows for code such as:
 
 ```r
 single_cell_data |>