From be5fc316ee7491f6a399b37d24a58106b69cae98 Mon Sep 17 00:00:00 2001 From: almeidasilvaf Date: Thu, 2 Nov 2023 20:18:28 +0100 Subject: [PATCH] Updated README with short description of the package's features --- README.Rmd | 26 ++++++++++++++++++++++++-- README.md | 42 ++++++++++++++++++++++++++++++++++++++++-- 2 files changed, 64 insertions(+), 4 deletions(-) diff --git a/README.Rmd b/README.Rmd index b0d098f..61c9602 100644 --- a/README.Rmd +++ b/README.Rmd @@ -18,11 +18,33 @@ knitr::opts_chunk$set( [![GitHub issues](https://img.shields.io/github/issues/almeidasilvaf/HybridExpress)](https://github.com/almeidasilvaf/HybridExpress/issues) [![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental) -[![check-bioc](https://github.com/almeidasilvaf/HybridExpress/actions/workflows/check-bioc.yml/badge.svg)](https://github.com/almeidasilvaf/HybridExpress/actions/workflows/check-bioc.yml) +[![check-bioc](https://github.com/almeidasilvaf/HybridExpress/actions/workflows/rworkflows.devel.yml/badge.svg)](https://github.com/almeidasilvaf/HybridExpress/actions/workflows/rworkflows.devel.yml) [![Codecov test coverage](https://codecov.io/gh/almeidasilvaf/HybridExpress/branch/devel/graph/badge.svg)](https://app.codecov.io/gh/almeidasilvaf/HybridExpress?branch=devel) -The goal of `HybridExpress` is to ... +The goal of `HybridExpress` is to perform comparative transcriptomic analyses +of hybrids relative to their progenitor species (a.k.a. *experimental trios*). +The package features: + +1. **Calculation of midparent expression values**, which are *in silico* +samples obtained from the mean, sum, or weighted mean of random sample pairs +from each parent; +2. **Exploratory analyses of sample grouping** with PCA plots and heatmaps +of hierarchically-clustered pairwise sample correlations; +3. **Identification of differentially expressed genes** between hybrids and +their progenitor species, hybrids and midparent values, and the two parents. +If spike-in standards are available, `HybridExpress` uses them to normalize +the count data by transcriptome size; +4. **Classification of genes in expression-based categories and classes** +based on [Rapp et al. (2009)](https://doi.org/10.1186/1741-7007-7-18). The 12 +expression categories +proposed by [Rapp et al. (2009)](https://doi.org/10.1186/1741-7007-7-18) are +grouped into 5 major classes (transgressive up-regulation, transgressive +down-regulation, additivity, expression-level dominance toward parent 1, +and expression-level dominance toward parent 2); +5. **Functional analyses** through the identification of overrepresented +functional terms for gene sets of interest. + ## Installation instructions diff --git a/README.md b/README.md index d7a80d3..bd04643 100644 --- a/README.md +++ b/README.md @@ -9,12 +9,34 @@ issues](https://img.shields.io/github/issues/almeidasilvaf/HybridExpress)](https://github.com/almeidasilvaf/HybridExpress/issues) [![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental) -[![check-bioc](https://github.com/almeidasilvaf/HybridExpress/actions/workflows/check-bioc.yml/badge.svg)](https://github.com/almeidasilvaf/HybridExpress/actions/workflows/check-bioc.yml) +[![check-bioc](https://github.com/almeidasilvaf/HybridExpress/actions/workflows/rworkflows.devel.yml/badge.svg)](https://github.com/almeidasilvaf/HybridExpress/actions/workflows/rworkflows.devel.yml) [![Codecov test coverage](https://codecov.io/gh/almeidasilvaf/HybridExpress/branch/devel/graph/badge.svg)](https://app.codecov.io/gh/almeidasilvaf/HybridExpress?branch=devel) -The goal of `HybridExpress` is to … +The goal of `HybridExpress` is to perform comparative transcriptomic +analyses of hybrids relative to their progenitor species (a.k.a. +*experimental trios*). The package features: + +1. **Calculation of midparent expression values**, which are *in + silico* samples obtained from the mean, sum, or weighted mean of + random sample pairs from each parent; +2. **Exploratory analyses of sample grouping** with PCA plots and + heatmaps of hierarchically-clustered pairwise sample correlations; +3. **Identification of differentially expressed genes** between hybrids + and their progenitor species, hybrids and midparent values, and the + two parents. If spike-in standards are available, `HybridExpress` + uses them to normalize the count data by transcriptome size; +4. **Classification of genes in expression-based categories and + classes** based on [Rapp et + al. (2009)](https://doi.org/10.1186/1741-7007-7-18). The 12 + expression categories proposed by [Rapp et + al. (2009)](https://doi.org/10.1186/1741-7007-7-18) are grouped into + 5 major classes (transgressive up-regulation, transgressive + down-regulation, additivity, expression-level dominance toward + parent 1, and expression-level dominance toward parent 2); +5. **Functional analyses** through the identification of + overrepresented functional terms for gene sets of interest. ## Installation instructions @@ -45,6 +67,22 @@ R. Please run this yourself to check for any updates on how to cite ``` r print(citation('HybridExpress'), bibtex = TRUE) +#> To cite package 'HybridExpress' in publications use: +#> +#> Almeida-Silva F, Prost-Boxoen L, Van de Peer Y (2023). +#> _HybridExpress: Comparative analysis of RNA-seq data for hybrids and +#> their progenitors_. R package version 0.99.0, +#> . +#> +#> A BibTeX entry for LaTeX users is +#> +#> @Manual{, +#> title = {HybridExpress: Comparative analysis of RNA-seq data for hybrids and their progenitors}, +#> author = {Fabricio Almeida-Silva and Lucas Prost-Boxoen and Yves {Van de Peer}}, +#> year = {2023}, +#> note = {R package version 0.99.0}, +#> url = {https://github.com/almeidasilvaf/HybridExpress}, +#> } ``` Please note that the `HybridExpress` was only made possible thanks to