Pipeline

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1. targets
   • Turn scripts into manageable pipeline
   • Automatically save and load important objects, and keep them in track
   • Very suitable for median or large projects

Analysis

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Common

1. genekitr: 🧬 Welcome to genekitr! | Genekitr: Gene Analysis Toolkit based on R
   • More visualization for ORA and GSEA results
   • Better gene ID conversion function
     • Automatically identify input type
     • Distinguish from symbol and alias
2. tidyomics: tidyomics/tidyomics: Easily install and load packages from the tidyomcis ecosystem (github.com)
   • A collection of packages for omics data analysis that are consistent with tidyverse ecosystem

RNA-seq (bulk)

1. tidySummarizedExperiment: Brings SummarizedExperiment to the Tidyverse • tidySummarizedExperiment (stemangiola.github.io)
   • tidySummarizedExperiment provides a bridge between Bioconductor SummarizedExperiment and the tidyverse. It creates an invisible layer that enables viewing the Bioconductor SummarizedExperiment object as a tidyverse tibble, and provides SummarizedExperiment-compatible dplyr, tidyr, ggplot and plotly functions. This allows users to get the best of both Bioconductor and tidyverse worlds.
2. tidybulk
   • Seamlessly integrated with tidySummarizedExperiment
   • Provide many out-of-box functions for bulk RNA-seq pipeline

scRNA-seq

1. escape: ncborcherding/escape: Easy single cell analysis platform for enrichment (github.com)
   • The escape package allows users to easily incorporate multiple methods of GSEA and offers several visualization and analysis methods.

Visualization

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1. ggstatsplot: ggplot2 Based Plots with Statistical Details • ggstatsplot (indrajeetpatil.github.io)
   • Can automatically choose and perform statistical analysis, and depict it on plot
2. ggraph & tidyraph
   • Use tidyverse way to create network
3. tidyheatmaps
   • Use tidyverse way to create heatmaps
   • Support all features of pheatmap
4. ggsci: Scientific Journal and Sci-Fi Themed Color Palettes for ggplot2 • ggsci (nanx.me)
   • A collection of ggplot2 color palettes inspired by scientific journals and data visualization libraries
   • Only has up to 10 colors in each palette, and expanding the colors could be tricky
5. ggalign: A ggplot2 Extension for Consistent Axis Alignment • ggalign
   • Aligning and organizing multiple plots, particularly those that automatically reorder observations, such as dendrogram.
   • Alternative to ggheatmap and ComplexHeatmap