Package: DgeaHeatmap 0.99.3

Leonie Johanna Lancelle

DgeaHeatmap: Implementation of Functions to Analyze Nanostring and Other Data for DGE and to Generate Heatmaps

Package for data extraction from Nanostring GeoMx DSP data, also works for other data. Simple functions for Differential Expression Analysis. User-friendly and highly customizable functions for heatmap generation.

Authors:Leonie Johanna Lancelle [aut, cre]

DgeaHeatmap_0.99.3.tar.gz
DgeaHeatmap_0.99.3.zip(r-4.7-any)DgeaHeatmap_0.99.3.zip(r-4.6-any)DgeaHeatmap_0.99.3.zip(r-4.5-any)
DgeaHeatmap_0.99.3.tgz(r-4.6-any)DgeaHeatmap_0.99.3.tgz(r-4.5-any)
DgeaHeatmap_0.99.3.tar.gz(r-4.7-any)DgeaHeatmap_0.99.3.tar.gz(r-4.6-any)
DgeaHeatmap_0.99.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
DgeaHeatmap/json (API)

# Install 'DgeaHeatmap' in R:

install.packages('DgeaHeatmap', repos = c('https://biocstaging.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/biocstaging/dgeaheatmap/issues

On CRAN:

clustering differentialexpression software

3.85 score 1 stars 35 exports 147 dependencies

Last updated from:6b0d3c54a4. Checks:1 NOTE, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	193
linux-devel	OK	499
source / vignettes	OK	330
linux-release	OK	464
macos-release	OK	406
macos-oldrel	OK	507
windows-devel	OK	391
windows-release	OK	400
windows-oldrel	OK	249
wasm-release	OK	195

Exports:add_demoElem adv_Heatmap aExprsDataQC build_matrix color_setting column_clustering create_contrast_matrix_edgeR DGEADESeq2 DGEAedgeR DGEALimma draw_adv_heatmap elbow_plot extract_genes_direction extractDEGenes filtering_for_top_exprGenes function_complexHeatmap_var genRawReadCountTable get_dist get_heatmap_colors individual_matrix Kmean_generation most_variable_genes pairwise_contrasts performing_kMeans prepare_dge_list print_heatmap row_clustering scale_counts set_annotation set_row_annotation set_sample_annotation show_data_distribution split_data_by_column summarise_bio_replicates summarize_edgeR_DEA

Dependencies:abind base64enc beeswarm BH Biobase BiocGenerics BiocParallel Biostrings boot bslib cachem cellranger circlize cli clue cluster codetools colorspace ComplexHeatmap cpp11 crayon data.table DelayedArray DESeq2 digest doParallel dotCall64 dplyr edgeR EnvStats evaluate farver fastmap fontawesome fontBitstreamVera fontLiberation fontquiver forcats foreach formatR fs futile.logger futile.options future future.apply gdtools generics GenomicRanges GeomxTools GetoptLong GGally ggbeeswarm ggiraph ggplot2 ggstats ggthemes GlobalOptions globals glue gtable highr hms htmltools htmlwidgets IRanges isoband iterators jquerylib jsonlite knitr labeling lambda.r lattice lifecycle limma listenv lme4 lmerTest locfit magrittr MASS Matrix MatrixGenerics matrixStats memoise mime minqa NanoStringNCTools nlme nloptr nortest numDeriv parallelly patchwork pheatmap pillar pkgconfig plyr png prettyunits progress progressr purrr R6 rappdirs rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen Rdpack readxl reformulas rematch reshape2 rjson rlang rmarkdown S4Arrays S4Vectors S7 sass scales Seqinfo SeuratObject shape snow sp spam SparseArray statmod stringi stringr SummarizedExperiment systemfonts tibble tidyr tidyselect tinytex utf8 vctrs vipor viridisLite withr xfun XVector yaml

DgeaHeatmap Vignette

DgeaHeatmap | Installation | Usage | Differential Gene Expression Analysis Using Nanostring Data

Rendered fromDgeaHeatmap_Vignette.Rmdusingknitr::rmarkdown

Last update: 2026-08-21
Started: 2024-10-11

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Build a matrix from an input csv file, with one column as rownames	add_demoElem
Creating a color scheme based on the available color palettes of RColorBrewer for the heatmap.	adv_Heatmap
Function for automatized quality control.	aExprsDataQC
Builds a matrix from an input csv file, with one column as rownames	build_matrix
Function to set color scheme for a heatmap.	color_setting
Setting the column clustering	column_clustering
create_contrast_matrix_edgeR	create_contrast_matrix_edgeR
DGEADESeq2	DGEADESeq2
DGEAedgeR	DGEAedgeR
DGEALimma	DGEALimma
Draw the advanced heatmap	draw_adv_heatmap
Function to create an elbow plot to choose k for clustering by k-Means.	elbow_plot
Get list of genes and their direction of regulation	extract_genes_direction
extractDEGenes	extractDEGenes
Function to filter a matrix to extract a chosen number of most variable rows through calculation of the variance.	filtering_for_top_exprGenes
Creating a heatmap with annotation of x most variable rows(genes).	function_complexHeatmap_var
Function to generating a raw read count table.	genRawReadCountTable
Calculates the distance matrix	get_dist
Creating a color scheme based on the available color palettes of RColorBrewer for the heatmap.	get_heatmap_colors
Creates a matrix only containing chosen columns of an original matrix with more data.	individual_matrix
Generates K-means for the columns and rows of a matrix.	Kmean_generation
Function to determine the most variable genes of each cluster to enable annotation..	most_variable_genes
Create pairwise contrasts	pairwise_contrasts
Function to perform k-Means clustering for a matrix and setting split to split a heatmap into clusters.	performing_kMeans
DGEAedgeR	prepare_dge_list
Function to build a heatmap using other functions.	print_heatmap
Setting the row clustering	row_clustering
Function to Z-count scale the values of a matrix.	scale_counts
Function to set row annotation for a heatmap.	set_annotation
Setting the row annotation	set_row_annotation
Setting the sample annotation	set_sample_annotation
Function to visualize the data distribution within the data of a matrix.	show_data_distribution
Splitting data by group column with feature, pheno or protocol data to then get the mean.	split_data_by_column
Summarizes columns biological replicates of a matrix into one.	summarise_bio_replicates
Summarize the results of the DEA with edgeR	summarize_edgeR_DEA