DEP-package | DEP: A package for Differential Enrichment analysis of Proteomics data. |
add_rejections | Mark significant proteins |
analyze_dep | Differential expression analysis |
DEP | DEP: A package for Differential Enrichment analysis of Proteomics data. |
DiUbi | DiUbi - Ubiquitin interactors for different diubiquitin-linkages (UbIA-MS dataset) |
DiUbi_ExpDesign | Experimental design of the DiUbi dataset |
filter_missval | Filter on missing values |
get_df_long | Generate a long data.frame from a SummarizedExperiment |
get_df_wide | Generate a wide data.frame from a SummarizedExperiment |
get_prefix | Obtain the longest common prefix |
get_results | Generate a results table |
import_IsobarQuant | Import from IsobarQuant |
import_MaxQuant | Import from MaxQuant |
impute | Impute missing values |
LFQ | LFQ workflow |
make_se | Data.frame to SummarizedExperiment object conversion using an experimental design |
make_se_parse | Data.frame to SummarizedExperiment object conversion using parsing from column names |
make_unique | Make unique names |
manual_impute | Imputation by random draws from a manually defined distribution |
meanSdPlot | Plot row standard deviations versus row means |
normalize_vsn | Normalization using vsn |
plot_all | Visualize the results in different types of plots |
plot_cond | Plot frequency of significant conditions per protein and the overlap in proteins between conditions |
plot_cond_freq | Plot frequency of significant conditions per protein |
plot_cond_overlap | Plot conditions overlap |
plot_cor | Plot correlation matrix |
plot_coverage | Plot protein coverage |
plot_detect | Visualize intensities of proteins with missing values |
plot_frequency | Plot protein overlap between samples |
plot_gsea | Plot enriched Gene Sets |
plot_heatmap | Plot a heatmap |
plot_imputation | Visualize imputation |
plot_missval | Plot a heatmap of proteins with missing values |
plot_normalization | Visualize normalization |
plot_numbers | Plot protein numbers |
plot_pca | Plot PCA |
plot_p_hist | Plot a P value histogram |
plot_single | Plot values for a protein of interest |
plot_volcano | Volcano plot |
process | Proteomics data processing |
report | Generate a markdown report |
run_app | DEP shiny apps |
se2msn | SummarizedExperiment to MSnSet object conversion |
test_diff | Differential enrichment test |
test_gsea | Gene Set Enrichment Analysis |
theme_DEP1 | DEP ggplot theme 1 |
theme_DEP2 | DEP ggplot theme 2 |
TMT | TMT workflow |
UbiLength | UbiLength - Ubiquitin interactors of different linear ubiquitin lengths (UbIA-MS dataset) |
UbiLength_ExpDesign | Experimental design of the UbiLength dataset |