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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.

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Version

Install

install.packages('DEVis')

Monthly Downloads

6

Version

1.0.1

License

LGPL

Maintainer

Adam Price

Last Published

January 25th, 2019

Functions in DEVis (1.0.1)

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.