RDocumentation
Moon
Learn R
Search all packages and functions
DEVis (version 1.0.1)
A Differential Expression Analysis Toolkit for Visual Analytics and Data Aggregation
Description
Differential expression analysis tools for data aggregation, visualization, exploratory analysis, and project organization.
Copy Link
Copy
Link to current version
Version
Version
1.0.1
1.0.0
Down Chevron
Install
install.packages('DEVis')
Monthly Downloads
16
Version
1.0.1
License
LGPL
Maintainer
Adam Price
Last Published
January 25th, 2019
Functions in DEVis (1.0.1)
Search functions
de_heat
Create heat maps of differentially expressed genes.
de_density_plot
Visualize density plots of fold-change or significance values for aggregated data sets.
de_diverge_plot
Visualize fold-change divergence for differentially expressed genes.
init_cutoffs
Initialize cutoff values for significance and fold-change filtering.
plot_poisson_dist
Visualize the poisson distances between samples.
create_master_res
Create a data set consisting of aggregated data for multiple contrasts.
create_relabel_field
Create a new metadata field by renaming existing levels of an existing field.
write_all_de_results
Write differentially expressed gene data for multiple result sets to file.
prep_counts
Read tab or comma delimited count data.
plot_mds
Visualize multi-dimensional scaled data for all samples, with group-wise metadata incorporated as colors and shapes.
init_data_paths
Initialize data paths for count and target files.
plot_mds_hulls
Visualize multi-dimensional scaled data for all samples, with group-wise metadata incorporated as colors, shapes, and convex hulls.
exclude_data_subset
Select a subset of count and target data based on metadata annotation.
get_de_data
Aggregate and retrieve data from multiple differentially expressed result sets.
DESeqResMeta-class
An S4 class extending the DESeqResults object containing additional fields for differential expression data.
de_boxplot
Visualize differentially expressed genes as a function of experimental design.
de_counts
Visualize differentially expressed gene counts as a stacked barplot.
keep_data_subset
Select a subset of count and target data based on metadata annotation.
create_dir_struct
Initialize the directory structure for automatically storing and structuring results.
de_profile_plot
Visualize gene-wise expression of differentially expressed genes.
make_composite_field
Create a composite metadata field by merging existing data.
prep_dds_from_data
Prepare a DESeq2 object based on count and target data.
prep_targets
Read tab or comma delimited target metadata file.
plot_dendro
Create dendrograms based on hierarchical clustering.
plot_euclid_dist
Visualize the Euclidian distances between samples.
de_series
Identify and visualize patterns of expression between differentially expressed genes across a series of result sets.
set_output_mode
Determine if visualizations are written to file, printed to screen, or both.
transpose_gene_ids
Rename gene IDs based on a 1-to-1 mapping file.
plot_gene
Visualize the expression of a specific gene with regard to metadata grouping.
plot_group_stats
Visualize overall data set as a function of a metadata grouping.
de_volcano
Visualize the expression & significance of differentially expressed genes.
enrich_res
Incorporate additional data about differentially expressed genes into a DESeq2 result set.
de_filter
Apply a custom fold-change filter to an aggregated data frame.