MOSt frequently used and useful Differential Expression Functions

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Documentation for package ‘mosdef’ version 1.1.1

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.info_enrichrun Printing some info before the enrichment runs
buttonifier Create sets of buttons for gene symbols
create_link_dbPTM Link to dbPTM database
create_link_ENSEMBL Link to ENSEMBL database
create_link_GeneCards Link to the GeneCards database
create_link_GO Link to AMIGO database
create_link_GTEX Link to the GTEx Portal
create_link_HPA Link to the Human Protein Atlas
create_link_NCBI Link to NCBI database
create_link_PubMed Link to Pubmed
create_link_UniProt Link to UniProt database
deresult_to_df Generate a table from the 'DESeq2' results
de_table_painter DE table painter
de_volcano Generates a volcano plot using ggplot2
geneinfo_to_html Information on a gene
gene_plot Plot expression values for a gene
get_annotation_orgdb Get an annotation data frame from org db packages
get_expr_values Get expression values
go_to_html Information on a Gene Ontology identifier
go_volcano Generates a volcano plot using ggplot2 This function generates a base volcano plot highlighting genes associated with a certain GOterm that can then be expanded upon using further ggplot functions.
map_to_color Maps numeric values to color values
mosdef_de_container_check A function checking if your 'de_container' contains everything you need
mosdef_res_check A function checking if your res_de contains everything you need
pair_corr Pairwise scatter plot matrix and correlation plot of counts
plot_ma MA-plot from base means and log fold changes
res_enrich_macrophage_cluPro A sample enrichment object
res_enrich_macrophage_goseq A sample enrichment object
res_enrich_macrophage_topGO A sample enrichment object
res_macrophage_IFNg_vs_naive A sample 'DESeqResults' object
run_cluPro Extract functional terms enriched in the DE genes, based on clusterProfiler
run_goseq Extract functional terms enriched in the DE genes, based on goseq
run_topGO Extract functional terms enriched in the DE genes, based on topGO
styleColorBar_divergent Style DT color bars