Package: DgeaHeatmap 0.99.0

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_0.99.0.tar.gz
DgeaHeatmap_0.99.0.zip(r-4.7)DgeaHeatmap_0.99.0.zip(r-4.6)DgeaHeatmap_0.99.0.zip(r-4.5)
DgeaHeatmap_0.99.0.tgz(r-4.6-any)DgeaHeatmap_0.99.0.tgz(r-4.5-any)
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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:

Conda:

bayesianclusteringdifferentialexpressiongeneexpressionnormalizationprincipalcomponentrnaseqregressionsequencingsoftwaretranscriptionalternativesplicingbatcheffectbiomedicalinformaticscellbiologycheminformaticsdataimportdifferentialsplicingepigeneticsexonarrayfunctionalgenomicsgenesetenrichmentgeneticsimmunooncologymetabolomicsmicrornaarraymicroarraymultiplecomparisononechannelpreprocessingproprietaryplatformsproteomicsqualitycontrolsystemsbiologytimecoursetwochannelmrnamicroarray

2.85 score 35 exports 147 dependencies

Last updated from:65a509be68. Checks:8 WARNING, 1 ERROR, 1 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING231
linux-devel-x86_64WARNING474
source / vignettesERROR278
linux-release-x86_64WARNING471
macos-release-arm64WARNING365
macos-oldrel-arm64WARNING545
windows-develWARNING486
windows-releaseWARNING468
windows-oldrelWARNING459
wasm-releaseOK220

Exports:add_demoElemadv_HeatmapaExprsDataQCbuild_matrixcolor_settingcolumn_clusteringcreate_contrast_matrix_edgeRDGEADESeq2DGEAedgeRDGEALimmadraw_adv_heatmapelbow_plotextract_genes_directionextractDEGenesfiltering_for_top_exprGenesfunction_complexHeatmap_vargenRawReadCountTableget_distget_heatmap_colorsindividual_matrixKmean_generationmost_variable_genespairwise_contrastsperforming_kMeansprepare_dge_listprint_heatmaprow_clusteringscale_countsset_annotationset_row_annotationset_sample_annotationshow_data_distributionsplit_data_by_columnsummarise_bio_replicatessummarize_edgeR_DEA

Dependencies:abindbase64encbeeswarmBHBiobaseBiocGenericsBiocParallelBiostringsbootbslibcachemcellrangercirclizecliclueclustercodetoolscolorspaceComplexHeatmapcpp11crayondata.tableDelayedArrayDESeq2digestdoParalleldotCall64dplyredgeREnvStatsevaluatefarverfastmapfontawesomefontBitstreamVerafontLiberationfontquiverforcatsforeachformatRfsfutile.loggerfutile.optionsfuturefuture.applygdtoolsgenericsGenomicRangesGeomxToolsGetoptLongGGallyggbeeswarmggiraphggplot2ggstatsggthemesGlobalOptionsglobalsgluegtablehighrhmshtmltoolshtmlwidgetsIRangesisobanditeratorsjquerylibjsonliteknitrlabelinglambda.rlatticelifecyclelimmalistenvlme4lmerTestlocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimeminqaNanoStringNCToolsnlmenloptrnortestnumDerivparallellypatchworkpheatmappillarpkgconfigplyrpngprettyunitsprogressprogressrpurrrR6rappdirsrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackreadxlreformulasrematchreshape2rjsonrlangrmarkdownS4ArraysS4VectorsS7sassscalesSeqinfoSeuratObjectshapesnowspspamSparseArraystatmodstringistringrSummarizedExperimentsystemfontstibbletidyrtidyselecttinytexutf8vctrsviporviridisLitewithrxfunXVectoryaml

Readme and manuals

Help Manual

Help pageTopics
Build a matrix from an input csv file, with one column as rownamesadd_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 rownamesbuild_matrix
Function to set color scheme for a heatmap.color_setting
Setting the column clusteringcolumn_clustering
create_contrast_matrix_edgeRcreate_contrast_matrix_edgeR
DGEADESeq2DGEADESeq2
DGEAedgeRDGEAedgeR
DGEALimmaDGEALimma
Draw the advanced heatmapdraw_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 regulationextract_genes_direction
extractDEGenesextractDEGenes
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 matrixget_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 contrastspairwise_contrasts
Function to perform k-Means clustering for a matrix and setting split to split a heatmap into clusters.performing_kMeans
DGEAedgeRprepare_dge_list
Function to build a heatmap using other functions.print_heatmap
Setting the row clusteringrow_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 annotationset_row_annotation
Setting the sample annotationset_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 edgeRsummarize_edgeR_DEA