API for nicohuttmann/pOmics
Framework for proteomics data analysis

Global functions
.add_data_attributes	Man page Source code
.data_columns	Man page Source code
.get_data_attributes	Man page Source code
.set_data_attributes	Man page Source code
.template_names	Man page Source code
.transpose_data_attributes	Man page Source code
.update_data_attributes	Man page Source code
TERM2GENE_2_list	Man page Source code
TERMS_in_proteins	Man page Source code
add_background_variable	Man page Source code
add_combined_dataset	Man page Source code
add_data	Man page Source code
add_database	Man page Source code
add_dataset	Man page Source code
add_group_columns	Man page Source code
add_import	Man page Source code
add_info_from_csv	Man page Source code
add_observations_data	Man page Source code
add_observations_set	Man page Source code
add_raw_dataset	Man page Source code
add_segment_pvalue	Man page Source code
add_variables_data	Man page Source code
adjacency	Man page Source code
annot_layer_discrete_x	Man page Source code
annotation_data2list	Man page Source code
ask_name	Man page Source code
assemble_heatmap_rowwise	Man page Source code
available_data_frames	Man page Source code
available_variables_data	Man page Source code
axis_limit_breaks	Man page Source code
bhc	Man page Source code
browse_msigdbr	Man page Source code
browse_proteins	Man page Source code
build_cor_list	Man page Source code
button_begin	Man page Source code
button_end	Man page Source code
cat_function	Man page Source code
cat_vector_string	Man page Source code
change_variables_manually	Man page Source code
check_buttons	Man page Source code
check_database	Man page Source code
choose_taxId	Man page Source code
choose_terms	Man page Source code
cleanup	Man page Source code
cluster_inner_borders	Man page Source code
colnames_class	Man page Source code
colnames_typeof	Man page Source code
common_prefix	Man page Source code
compare_enrichment_data	Man page Source code
connectivity	Man page Source code
copy2global	Man page Source code
copy_template	Man page Source code
correct_log2fc_anova	Man page Source code
count_variables_per_observation	Man page Source code
cutree_	Man page Source code
cv	Man page Source code
cv_m	Man page Source code
data.frame2tibble	Man page Source code
data2list	Man page Source code
data2tibble	Man page Source code
data_input	Man page Source code
dendrogram	Man page Source code
dendrogram2table	Man page Source code
distribute_quantiles	Man page Source code
distribute_quantiles_inner_limits	Man page Source code
do_2w_anova_i	Man page Source code
do_GSEA	Man page Source code
do_GSEA_KEGG	Man page Source code
do_GSEA_MSigDB	Man page Source code
do_GSEA_Reactome	Man page Source code
do_GSEA_topGO	Man page Source code
do_ORA	Man page Source code
do_ORA_GO	Man page Source code
do_ORA_KEGG	Man page Source code
do_ORA_MSigDB	Man page Source code
do_ORA_Reactome	Man page Source code
do_ORA_TERM2GENE	Man page Source code
do_ORA_groups	Man page Source code
do_ORA_topGO	Man page Source code
do_abundance_summary	Man page Source code
do_annotation_composition	Man page Source code
do_anova	Man page Source code
do_column_summary	Man page
do_cormat	Man page Source code
do_count_id_quant	Man page Source code
do_expr	Man page Source code
do_fun	Man page Source code
do_fun_enrich_dend	Man page Source code
do_hclust	Man page Source code
do_hclust_enrich_T2G	Man page Source code
do_hclust_transpose	Man page Source code
do_normalize	Man page Source code
do_nothing	Man page Source code
do_pca	Man page Source code
do_reverse_dend	Man page Source code
do_row_summary	Man page Source code
do_scale	Man page Source code
do_t.test	Man page Source code
do_transpose	Man page Source code
do_venn	Man page Source code
download_template	Man page Source code
enrichResult2data.frame	Man page Source code
enrich_dend_	Man page Source code
enrich_dend_fisher	Man page Source code
enrich_dend_ks	Man page Source code
eval_2w_anova_i	Man page Source code
eval_anova	Man page Source code
eval_dend_enrich	Man page Source code
export_DT_fun_enrich	Man page
export_DT_t.test	Man page Source code
export_GO_table	Man page
export_RMD_fun_enrich	Man page
export_RMD_t.test	Man page Source code
export_info_template	Man page Source code
export_pdf	Man page Source code
export_svg	Man page Source code
export_tiff	Man page Source code
extract_mqpar_info	Man page Source code
factorize_matrix	Man page Source code
findORchoose	Man page Source code
find_data_entry	Man page Source code
find_data_name	Source code
first_element	Man page Source code
fisher_test	Man page Source code
fun_enrich	Man page Source code
fun_enrich_t.test	Man page Source code
g2p	Man page Source code
geomean	Man page Source code
get_GO_proteins	Man page Source code
get_GOdata	Man page Source code
get_MaxQuant_defaults	Man page Source code
get_OrgDb	Man page Source code
get_all_attr	Man page Source code
get_all_variables	Man page Source code
get_child_terms	Man page Source code
get_cluster_cut	Man page Source code
get_cluster_proteins	Man page Source code
get_cor_data	Man page Source code
get_data	Man page Source code
get_data_name	Man page Source code
get_data_names	Man page Source code
get_data_template_names	Man page Source code
get_database	Man page Source code
get_dataset	Man page Source code
get_dataset_attr	Man page Source code
get_datasets	Man page Source code
get_default_data_name	Man page Source code
get_default_dataset	Man page Source code
get_defaults	Man page Source code
get_info_data	Man page Source code
get_input	Man page Source code
get_labels_column	Man page Source code
get_obs	Man page
get_obs_data	Man page
get_observations	Man page Source code
get_observations_data	Man page Source code
get_observations_data_names	Man page Source code
get_observations_set	Man page Source code
get_observations_sets	Man page Source code
get_observations_template	Man page Source code
get_protein	Man page Source code
get_protein_list	Man page Source code
get_proteins_TERM2GENE	Man page Source code
get_proteome	Man page Source code
get_raw_dataset	Man page Source code
get_taxId	Man page Source code
get_var	Man page
get_variables	Man page Source code
get_variables_data	Man page Source code
get_variables_data_names	Man page Source code
get_variables_template	Man page Source code
gg_extract_legend	Man page Source code
gg_legend.position	Man page Source code
gg_size	Man page Source code
identify_Id_type	Source code
identify_data_origin	Man page Source code
identify_id_columns	Source code
identify_observations	Man page Source code
identify_separator	Man page Source code
identify_taxId	Man page Source code
identify_variables	Man page Source code
import2grouped_data	Man page Source code
import2raw_dataset	Man page Source code
import_Top100_EV	Man page Source code
import_fasta	Man page Source code
import_files	Man page Source code
impute_missForest	Man page Source code
impute_norm	Man page Source code
in_	Man page Source code
include_groups	Man page Source code
include_observations_data	Man page Source code
include_variables_data	Man page Source code
initialize_data_structure	Man page Source code
intersect_m	Man page Source code
is_data_name	Man page Source code
is_data_origin	Man page Source code
is_dataset	Man page Source code
is_info_data	Man page Source code
is_observations_data	Man page Source code
is_observations_set	Man page Source code
is_raw_dataset	Man page Source code
is_variables_data	Man page Source code
ks_test	Man page Source code
last_	Man page Source code
latex_abbr_table	Man page Source code
list2TERM2GENE	Source code
list2group_vector	Man page Source code
list2tibble	Man page Source code
list_entries2vector	Man page Source code
list_files	Man page Source code
load_msigdb_data	Man page Source code
map_variables	Man page Source code
map_variables_data	Man page Source code
match_v2l	Man page Source code
matrix2tibble	Man page Source code
matrix_rows	Man page Source code
mean_or_0	Man page Source code
merge_TERM2GENE	Man page Source code
merge_enrichResults	Man page Source code
most_common_character	Man page Source code
new_analysis_list	Man page Source code
new_cache	Man page Source code
new_databases_list	Man page Source code
new_dataset	Man page Source code
new_datasets_list	Man page Source code
new_default_data	Man page Source code
new_imports_list	Man page Source code
new_info_list	Man page Source code
next_button	Man page Source code
nice_number	Man page Source code
normalize	Man page Source code
nulllist	Man page Source code
p2g	Man page Source code
p2n	Man page Source code
paste_terms_overlap_heatmap	Man page Source code
plot_ComplexHeatmap	Man page Source code
plot_bar_composition	Man page Source code
plot_cormat	Man page Source code
plot_count_id_quant	Man page Source code
plot_dend_enrich_lines	Man page Source code
plot_enrich	Man page Source code
plot_enrichment_barplot	Man page Source code
plot_euler	Man page Source code
plot_gg_bar	Man page Source code
plot_gg_bar_anova_eval	Man page Source code
plot_gg_box	Source code
plot_gg_count_id_quant	Man page Source code
plot_gg_heatmap_protein_overlap	Man page Source code
plot_gg_heatmap_terms	Man page Source code
plot_gg_xy_fc	Man page Source code
plot_heatmap	Man page Source code
plot_heatmap_	Source code
plot_heatmap_discrete	Man page Source code Source code
plot_lines	Man page Source code
plot_nothing	Man page Source code
plot_pca	Man page Source code
plot_upset	Man page Source code
plot_venn	Man page Source code
plot_volcano	Man page Source code
plot_xy	Man page Source code
pqn	Man page Source code
prep_data	Man page Source code
print_options	Man page Source code
protein2function	Man page Source code
protein2gene	Man page Source code
pull_data	Man page Source code
put_data	Man page Source code
quick_protein_count	Man page Source code
remove_dataset	Man page Source code
remove_observations_data	Man page Source code
remove_variables	Man page Source code
remove_variables_data	Man page Source code
reorder_data	Man page Source code
rm_functions	Man page Source code
same_prefix	Man page Source code
save2cache	Man page Source code
save_results	Man page Source code
save_wd	Man page Source code
search_dend_	Source code
select2output	Man page Source code
select_DisGeNet	Man page Source code
select_UniProt	Man page Source code
select_UniProt_2_TERM2GENE	Man page Source code
select_fasta	Man page Source code
select_org	Man page Source code
select_org_2_TERM2GENE	Man page Source code
sep_vector2list	Man page Source code
set_continuous_axes	Man page Source code
set_dataset_attr	Man page Source code
set_default_data_name	Man page Source code
set_default_dataset	Man page Source code
set_default_observations_set	Man page Source code
set_diagonal	Man page Source code
set_wd	Man page Source code
setup_CORUM_annotations	Man page Source code
setup_DisGeNET	Man page Source code
setup_EV_TOP_100	Man page Source code
setup_STRINGdb	Man page Source code
setup_UniProt	Man page Source code
setup_folders	Man page Source code
setup_fun_enrich	Man page Source code
setup_msigdb	Man page Source code
setup_org_database	Man page Source code
setup_taxonomy_information	Man page Source code
significant	Man page Source code
similarity	Man page Source code
simplify_GO_terms_semantic	Man page Source code
simplify_enrichment_results	Man page Source code
simplify_set_overlap	Man page Source code
str_locate_last	Man page Source code
str_rev	Man page Source code
strsplit_	Man page Source code
strsplit_keep	Man page Source code
strsplit_keep_first	Man page Source code
strsplit_keep_firstn	Man page Source code
subset_observations	Man page Source code
subset_variables	Man page Source code
summary_proteins	Man page Source code
summary_proteins_2	Man page Source code
t2g_get_genes	Man page Source code
t2g_get_matrix	Man page Source code
t2g_get_terms	Man page Source code
t2g_subset_genes	Man page Source code
t2g_subset_terms	Man page Source code
theme_epitope_peptides_plot	Man page Source code
theme_hjv_framed	Man page Source code
theme_hjv_framed_no_axes	Man page Source code
theme_hjv_half_open	Man page Source code
theme_hjv_heatmap	Man page Source code
theme_hjv_heatmap_only	Man page Source code
theme_hjv_heatmap_only_noframe	Man page Source code
theme_hjv_overlap_heatmap	Man page Source code
theme_iDC_annot_layer	Man page Source code
theme_iDC_dendrogram	Man page Source code
theme_iDC_heatmap_labels_x	Man page Source code
theme_iDC_heatmap_labels_y	Man page Source code
theme_iDC_heatmap_w_legend	Man page Source code
theme_phosprot_half_open	Man page Source code
theme_thesis_cor_matrix	Man page Source code
theme_thesis_framed_no_axis	Man page Source code
threshold	Man page Source code
tibble2data.frame	Man page Source code
tibble2matrix	Man page Source code
to_data_	Man page Source code
total_proteins_summary	Man page Source code
transfer_data_frames	Man page Source code
transfer_observations	Man page Source code
transfer_variables_data	Man page Source code
translate_Ids	Man page Source code
transpose_tibble	Man page Source code
useful_UniProt_entries	Man page Source code
v_db	Man page Source code
v_ds	Man page Source code
v_imp	Man page Source code
v_info	Man page Source code
variables2labels	Man page Source code
view_data	Man page Source code
view_default_attr	Man page Source code
view_observations	Man page Source code
view_variables	Man page Source code
which_names	Man page Source code