Package index • mosdef

All functions

buttonifier(): Create sets of buttons for gene symbols

create_link_ENSEMBL(): Link to ENSEMBL 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_UniProt(): Link to UniProt database

create_link_dbPTM(): Link to dbPTM database

create_link_GeneCards(): Link to the GeneCards database

create_link_PubMed(): Link to Pubmed

de_table_painter(): DE table painter

de_volcano(): Generates a volcano plot using ggplot2

deresult_to_df(): Generate a table from the DESeq2 results

.info_enrichrun(): Printing some info before the enrichment runs

gene_plot(): Plot expression values for a gene

geneinfo_to_html(): Information on 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