Package: GRaNIE 1.9.1

Christian Arnold

GRaNIE: GRaNIE: Reconstruction cell type specific gene regulatory networks including enhancers using single-cell or bulk chromatin accessibility and RNA-seq data

Genetic variants associated with diseases often affect non-coding regions, thus likely having a regulatory role. To understand the effects of genetic variants in these regulatory regions, identifying genes that are modulated by specific regulatory elements (REs) is crucial. The effect of gene regulatory elements, such as enhancers, is often cell-type specific, likely because the combinations of transcription factors (TFs) that are regulating a given enhancer have cell-type specific activity. This TF activity can be quantified with existing tools such as diffTF and captures differences in binding of a TF in open chromatin regions. Collectively, this forms a gene regulatory network (GRN) with cell-type and data-specific TF-RE and RE-gene links. Here, we reconstruct such a GRN using single-cell or bulk RNAseq and open chromatin (e.g., using ATACseq or ChIPseq for open chromatin marks) and optionally (Capture) Hi-C data. Our network contains different types of links, connecting TFs to regulatory elements, the latter of which is connected to genes in the vicinity or within the same chromatin domain (TAD). We use a statistical framework to assign empirical FDRs and weights to all links using a permutation-based approach.

Authors:Christian Arnold [cre, aut], Judith Zaugg [aut], Rim Moussa [aut], Armando Reyes-Palomares [ctb], Giovanni Palla [ctb], Maksim Kholmatov [ctb]

GRaNIE_1.9.1.tar.gz
GRaNIE_1.9.1.zip(r-4.5)GRaNIE_1.9.1.zip(r-4.4)GRaNIE_1.9.1.zip(r-4.3)
GRaNIE_1.9.1.tgz(r-4.4-any)GRaNIE_1.9.1.tgz(r-4.3-any)
GRaNIE_1.9.1.tar.gz(r-4.5-noble)GRaNIE_1.9.1.tar.gz(r-4.4-noble)
GRaNIE_1.9.1.tgz(r-4.4-emscripten)GRaNIE_1.9.1.tgz(r-4.3-emscripten)
GRaNIE.pdf |GRaNIE.html✨
GRaNIE/json (API)
NEWS

# Install 'GRaNIE' in R:
install.packages('GRaNIE', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

On BioConductor:GRaNIE-1.9.1(bioc 3.20)GRaNIE-1.8.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

bioconductor-package

43 exports 1 stars 1.00 score 146 dependencies

Last updated 1 months agofrom:f05af0040c

Exports:add_featureVariationadd_TF_gene_correlationaddConnections_peak_geneaddConnections_TF_peakaddDataaddSNPDataaddTFBSAR_classification_wrapperbuild_eGRN_graphcalculateCommunitiesEnrichmentcalculateCommunitiesStatscalculateGeneralEnrichmentcalculateTFEnrichmentchangeOutputDirectorydeleteIntermediateDatafilterConnectionsForPlottingfilterDatafilterGRNAndConnectGenesgenerateStatsSummarygetCountsgetGRNConnectionsgetGRNSummarygetParametersgetTopNodesinitializeGRNloadExampleObjectnGenesnPeaksnTFsoverlapPeaksAndTFBSperformAllNetworkAnalysesplot_stats_connectionSummaryplotCommunitiesEnrichmentplotCommunitiesStatsplotCorrelationsplotDiagnosticPlots_peakGeneplotDiagnosticPlots_TFPeaksplotDiagnosticPlots_TFPeaks_GCplotGeneralEnrichmentplotGeneralGraphStatsplotPCA_allplotTFEnrichmentvisualizeGRN

Dependencies:abindAnnotationDbiAnnotationFilterAnnotationHubaskpassbackportsBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocManagerBiocParallelBiocVersionbiomaRtBiostringsbitbit64bitopsblobcachemcheckmatecirclizeclicliprclueclustercodetoolscolorspaceComplexHeatmapcpp11crayoncurldata.tableDBIdbplyrDelayedArrayDESeq2digestdoParalleldplyrensembldbfansifarverfastmapfilelockforcatsforeachformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesGetoptLongggplot2GlobalOptionsglueGO.dbgraphgridExtragtablehmshttrhttr2igraphIRangesisobanditeratorsjsonliteKEGGRESTlabelinglambda.rlatticelazyevallifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpatchworkpillarpkgconfigplogrplyrpngprettyunitsprogressProtGenericspurrrR6rappdirsRColorBrewerRcppRcppArmadilloRCurlreadrreshape2restfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsscalesshapesnowSparseArraySparseMstatmodstringistringrSummarizedExperimentsystibbletidyrtidyselecttopGOtzdbUCSC.utilsutf8vctrsviridisviridisLitevroomwithrXMLxml2XVectoryamlzlibbioc

Package Details

Christian Arnold

Rendered fromGRaNIE_packageDetails.Rmdusingknitr::rmarkdownon Jul 06 2024.

Last update: 2024-06-05
Started: 2022-09-14

GRaNIE single-cell eGRN inference

Christian Arnold

Rendered fromGRaNIE_singleCell_eGRNs.Rmdusingknitr::rmarkdownon Jul 06 2024.

Last update: 2024-06-05
Started: 2023-01-26

GRaNIE Workflow Example

Christian Arnold

Rendered fromGRaNIE_workflow.Rmdusingknitr::rmarkdownon Jul 06 2024.

Last update: 2023-10-26
Started: 2022-04-25

Readme and manuals

Help Manual

Help pageTopics
Quantify and interpret multiple sources of biological and technical variation for features (TFs, peaks, and genes) in a 'GRN' objectadd_featureVariation
Add TF-gene correlations to a 'GRN' object.add_TF_gene_correlation
Add peak-gene connections to a 'GRN' objectaddConnections_peak_gene
Add TF-peak connections to a 'GRN' objectaddConnections_TF_peak
Add data to a 'GRN' object.addData
Add TF activity data to GRN object using a simplified procedure for estimating it. EXPERIMENTAL.addData_TFActivity
Add SNP data to a 'GRN' object and associate SNPs to peaks.addSNPData
Add TFBS to a 'GRN' object.addTFBS
Run the activator-repressor classification for the TFs for a 'GRN' objectAR_classification_wrapper
Builds a graph out of a set of connectionsbuild_eGRN_graph
Run an enrichment analysis for the genes in each community in the filtered 'GRN' objectcalculateCommunitiesEnrichment
Generate graph communities and their summarizing statisticscalculateCommunitiesStats
Run an enrichment analysis for the genes in the whole network in the filtered 'GRN' objectcalculateGeneralEnrichment
Run an enrichment analysis for the set of genes connected to a particular TF or sets of TFs in the filtered 'GRN' objectcalculateTFEnrichment
Change the output directory of a GRN objectchangeOutputDirectory
Optional convenience function to delete intermediate data from the function 'AR_classification_wrapper' and summary statistics that may occupy a lot of spacedeleteIntermediateData
Filter connections for subsequent visualization with `visualizeGRN()` from the filtered eGRNfilterConnectionsForPlotting
Filter RNA-seq and/or peak data from a 'GRN' objectfilterData
Filter TF-peaks and peak-gene connections and combine them to TF-peak-gene connections to construct an eGRN.filterGRNAndConnectGenes
Generate a summary for the number of connections for different filtering criteria for a 'GRN' object.generateStatsSummary
Get counts for the various data defined in a 'GRN' objectgetCounts
Extract connections or links from a 'GRN' object as a data frame.getGRNConnections
Summarize a 'GRN' object to a named list for comparison with other 'GRN' objects.getGRNSummary
Retrieve parameters for previously used function calls and general parameters for a 'GRN' object.getParameters
Retrieve the top nodes (TFs or genes) with respect to either degree or Eigenvector centrality in the filtered 'GRN' object.getTopNodes
*GRaNIE* (*G*ene *R*egul*a*tory *N*etwork *I*nference including *E*nhancers): Reconstruction and evaluation of data-driven, cell type specific gene regulatory networks including enhancers using chromatin accessibility and RNAseq data (general package information)GRaNIE
Create, represent, investigate, quantify and visualize enhancer-mediated gene regulatory networks (*eGRNs*)GRN-class
Import externally derived TF Activity data. EXPERIMENTAL.importTFData
Create and initialize an empty 'GRN' object.initializeGRN
Load example GRN datasetloadExampleObject
Get the number of genes for a 'GRN' object.genes nGenes
Get the number of peaks for a 'GRN' object.nPeaks peaks
Get the number of TFs for a 'GRN' object.nTFs TFs
Overlap peaks and TFBS for a 'GRN' objectoverlapPeaksAndTFBS
Perform all network-related statistical and descriptive analyses, including community and enrichment analyses. See the functions it executes in the @seealso section below.performAllNetworkAnalyses
Plot various network connectivity summaries for a 'GRN' objectplot_stats_connectionSummary
Plot community-based enrichment results for a filtered 'GRN' objectplotCommunitiesEnrichment
Plot general structure & connectivity statistics for each community in a filtered 'GRN'plotCommunitiesStats
Plot scatter plots of the underlying count data for either TF-peak, peak-gene or TF-gene pairs for a 'GRN' objectplotCorrelations
Plot diagnostic plots for peak-gene connections for a 'GRN' objectplotDiagnosticPlots_peakGene
Plot diagnostic plots for TF-peak connections for a 'GRN' objectplotDiagnosticPlots_TFPeaks
Plot GC-specific diagnostic plots for TF-peak connections for a 'GRN' objectplotDiagnosticPlots_TFPeaks_GC
Plot the general enrichement resultsplotGeneralEnrichment
Plot general structure and connectivity statistics for a filtered 'GRN' objectplotGeneralGraphStats
Produce a PCA plot of the data from a 'GRN' objectplotPCA_all
Plot TF-based GO enrichment resultsplotTFEnrichment
Visualize a filtered eGRN in a flexible manner.visualizeGRN