Learn R Programming

TransProR

Installation

You can install the development version of TransProR like so:

install.packages("devtools")
devtools::install_github("SSSYDYSSS/TransProR", build_vignettes = TRUE)

install.packages("remotes")
remotes::install_github("SSSYDYSSS/TransProR", build_vignettes = TRUE)

More examples see

TransProR Manual：https://sssydysss.github.io/TransProRBook/

System Requirements

  • R (>= 4.3.0)

Example

This is a basic example which shows you how to solve a common problem:

library(TransProR)
## basic example code

Citation

Yu Dongyue (2023). TransProR: Analysis and visualization of transcriptomic data are currently in progress. Future directions include multi-modal fusion, sparse learning, and the investigation of spatio-temporal effects. https://github.com/SSSYDYSSS/TransProR, https://sssydysss.github.io/TransProRBook/.

Code of Conduct

Please note that the TransProR project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms. "# TransProR"

Copy Link

Version

Install

install.packages('TransProR')

Monthly Downloads

456

Version

1.0.2

License

MIT + file LICENSE

Issues

0

Pull Requests

0

Stars

5

Forks

0

Maintainer

Dongyue Yu

Last Published

February 14th, 2025

Functions in TransProR (1.0.2)

combat_tumor

Process and Correct Batch Effects in Tumor Data
enrichment_spiral_plots

Create Spiral Plots with Legends Using 'spiralize' and 'ComplexHeatmap'
extract_descriptions_counts

Extract and Count Descriptions with Specified Color
facet_density_foldchange

Create faceted high-density region plots with optional points and density contours
filter_diff_genes

Filter Differentially Expressed Genes
extract_ntop_pathways

Extract and Store Top Pathways for Each Sample
extract_positive_pathways

Extract Positive Pathways from SSGSEA Results and Select Random Samples
gather_graph_edge

Gather graph edge from data frame Please note that this function is from the 'ggraph' package and has not been altered in functionality, but it has been optimized and iterated. It is not original content of 'TransProR'. However, since 'ggraph' caused frequent GitHub Action errors during the creation of 'TransProR', the author directly referenced the involved functions in 'TransProR'. This is not the author's original creation. All users please be aware!
limma_analyze

Differential Gene Expression Analysis using limma and voom
four_degs_venn

Function to Create a Venn Diagram of DEGs
highlight_genes

Add Highlights for Genes on a Phylogenetic Tree
get_tcga_exp

TCGA Expression Data Processing
get_gtex_exp

Get GTEx Expression Data for Specific Organ
merge_method_color

Merge Data Frames with Specific Method and Color Columns
new_ggraph

Generate a graphical representation of pathway gene maps
log_transform

Log transformation decision and application on data
merge_density_foldchange

Create high-density region plot with optional points, density rugs, and contours
%>%

Pipe operator
gather_graph_node

Gather graph nodes from a data frame Please note that this function is from the 'ggraph' package and has not been altered in functionality, but it has been optimized and iterated. It is not original content of 'TransProR'. However, since 'ggraph' caused frequent GitHub Action errors during the creation of 'TransProR', the author directly referenced the involved functions in 'TransProR'. This is not the author's original creation. All users please be aware!
gene_color

Merge Genes with Color Information Based on Up/Down Regulation
gene_highlights

Add gene highlights to a ggtree object
gene_map_pathway

Create Pathway-Gene Mapping Data Frame
merge_gtex_tcga

Merge gene expression data from GTEx and TCGA datasets
gtree

Phylogenetic Tree Object
highlight_by_node

Highlight Nodes in a Phylogenetic Tree with Custom Fill Colors and Transparency
spiral_newrle

Render a Spiral Plot Using Run-Length Encoding
prep_limma

Prepare limma-voom DEG data for plotting
prep_edgeR

Prepare edgeR DEG data for plotting
pathway_count

Count Genes Present in Pathways Above a Threshold
prep_wilcoxon

Prepare Wilcoxon DEG data for plotting
prep_deseq2

Prepare DESeq2 data for plotting
pathway_description

Describe Genes Present in Selected Pathways
seek_gtex_organ

Load and Process GTEX Phenotype Data to Retrieve Primary Site Counts
merge_id_position

Merge Data Frames by Common Row Names with Additional Columns
selectPathways

Randomly Select Pathways with Limited Word Count
process_heatdata

Process Heatmap Data with Various Selection Options
adjust_color_tone

Adjust Color Tone by Modifying Saturation and Luminance
add_boxplot

Add a boxplot layer to a `ggtree` plot
adjust_export_pathway

Adjust and Export Pathway Analysis Results
Wilcoxon_analyze

Differential Gene Expression Analysis Using Wilcoxon Rank-Sum Test
adjust_alpha_scale

Adjust Alpha Scale for Data Visualization
add_new_tile_layer

Add a new tile layer with dynamic scales to a `ggtree` plot
Contrast_Venn

Function to Create a Venn Diagram of DEGs with Custom Colors
Combat_Normal

Process and Correct Batch Effects in TCGA's normal tissue and GTEX Data
DESeq2_analyze

Differential Gene Expression Analysis using 'DESeq2'
all_degs_venn

All DEGs Venn Diagram Data
edgeR_analyze

Differential Gene Expression Analysis using 'edgeR'
enrich_polar_bubble

Enrichment Polar Bubble Plot
enrichment_circlize

Draw Chord Diagram with Legends
deg_filter

Function to Filter Differentially Expressed Genes (DEGs)
compare_merge

Compare and merge specific columns from two DEG data frames
circos_fruits

Add multiple layers to a `ggtree` plot for visualizing gene expression and enrichment data
drawLegends

Draw Dual-Sided Legends on a Plot
enrich_circo_bar

Combine and Visualize Data with Circular Bar Chart
create_base_plot

Create a base plot with gene expression data on a phylogenetic tree