MOSt frequently used and useful Differential Expression Functions

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Documentation for package ‘mosdef’ version 1.0.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

.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_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
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