ARNT.metadata           Metadata data frame
ARNT.peaks.bed          ChIP-Seq dataset
CM_list                 List of contingency matrix
DnaseHS_db              DHS databse
Entrez.gene.IDs         List of Entrez Gene IDs
GR2tfbs_db              Makes a TFBS-gene binding database
GSEA.result             Output of the function GSEA.run from the
                        TFEA.ChIP package
GSEA_ESpermutations     Calculate enrichment scores for a permutation
                        test.
GSEA_EnrichmentScore    Computes the weighted GSEA score of gene.set in
                        gene.list.
GSEA_run                Function to run a GSEA analysis
GeneID2entrez           Translates gene IDs from Gene Symbol or
                        Ensemble ID to Entrez ID.
Genes.Upreg             List of Entrez Gene IDs
Mat01                   TF-gene binding binary matrix
MetaData                TF-gene binding DB metadata
Select_genes            Extracts genes according to logFoldChange and
                        p-val limits
contingency_matrix      Computes 2x2 contingency matrices
getCMstats              Generate statistical parameters from a
                        contingency_matrix output
get_LFC_bar             Plots a color bar from log2(Fold Change)
                        values.
get_chip_index          Creates df containing accessions of ChIP-Seq
                        datasets and TF.
gr.list                 List of one ChIP-Seq dataset
highlight_TF            Highlight certain transcription factors in a
                        plotly graph.
hypoxia                 RNA-Seq experiment
hypoxia_DESeq           RNA-Seq experiment
log2.FC                 List of Entrez Gene IDs
makeTFBSmatrix          Function to search for a list of entrez gene
                        IDs.
plot_CM                 Makes an interactive html plot from an
                        enrichment table.
plot_ES                 Plots Enrichment Score from the output of
                        GSEA.run.
plot_RES                Plots all the RES stored in a GSEA_run output.
preprocessInputData     Extracts data from a DESeqResults object or a
                        data frame.
rankTFs                 Rank the TFs in the output from 'getCMstats'
set_user_data           Sets the data objects as default.
stat_mat                Data frame, output from the function getCMstats
                        from the TFEA.ChIP package
tfbs.database           TFBS database for 3 ChIP-Seq datasets.
txt2GR                  Function to filter a ChIP-Seq input.
