# MOSt frequently used and useful Differential Expression Functions

## Documentation for package ‘mosdef’ version 1.6.0

- 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_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