Generate user-friendly HTML reports from differential expression and GO term enrichment analysis.
DEAGO generates a user-friendly HTML report from differential expression (DESeq2) and GO term enrichment (topGO) analysis of RNA-Seq data.
DEAGO has the following dependencies:
Details to install DEAGO are provided below. If you encounter an issue when installing DEAGO please contact your local system administrator. If you encounter a bug please log it here or email us at path-help@sanger.ac.uk.
Make sure you have installed all dependencies, then clone the repository:
git clone https://github.com/sanger-pathogens/Bio-Deago.git
Move into the directory and install all perl dependencies using DistZilla and cpanm:
cd Bio-Deago
dzil authordeps --missing | cpanm
dzil listdeps --missing | cpanm
Run the tests:
dzil test
If the tests pass, install Bio-Deago:
dzil install
By default, DEAGO will look for R in your $PATH and for the associated R libraries in $R_LIBS. Where there are multiple R versions or libraries installed, setting the environment variables below will enable you to overwrite this default behaviour.
| Dependency | Environment variable | Example |
|---|---|---|
| R bin | DEAGO_R | /path/to/R-3.4.0/bin |
| R library | DEAGO_R_LIBS | /path/to/personal/rlib |
Usage: deago [options]
RNA-Seq differential expression qc and analysis
Main options:
--output_directory (-o) output directory [.]
--convert_annotation convert annotation for use with deago (requires -a)
--annotation_delim annotation file delimiter [\t]
--build_config build configuration file from command line arguments (see configuration options)
--config_file configuration filename or output filename for configuration file if building [./deago.config]
--markdown_file output filename for markdown file [./deago_markdown.Rmd]
--html_file output filename for html file [./deago_markdown.html]
-v verbose output to STDOUT
-w print version and exit
-h print help message and exit
Configuration options (required):
-c STR directory containing count files (absolute path)
-t STR targets filename (absolute path)
Configuration options (optional):
-r STR results directory [current working directory]
-a STR annotation filename (absolute path)
-q NUM qvalue (DESeq2) [0.05]
--control name of control condition (must be present in targets file)
--keep_images keep images used in report
--qc QC only
--go GO term enrichment
--go_levels BP only, MF only or all [BP|MF|all]
--count_type type of count file [expression|featurecounts]
--count_column number of column containing count values
--skip_lines number of lines to skip in count file
--count_delim count file delimiter
--gene_ids name of column containing gene ids
DEAGO takes in a configuration file containing key/value pairs [default: ./deago.config]. You can
use your own configuration file with --config_file or specify parameters and let DEAGO build a
configuration file with --build_config (and --config_file if you don't want the default
configuration filename). For more information on configuration parameters run: build_deago_config -h.
DEAGO will then build a master R markdown file (--markdown_file if you don't want the default
markdown filename) from templates which utilize the companion DEAGO R package and the key/value
pairs set out in the configuration file. The R markdown will be processed and used to generate a
HTML report (--html_file if you don't want the default html filename).
To use custom gene names and for GO term enrichment (--go) and annotation file must be provided
(-a). Annotations downloaded from BioMart or those in a similar format can be converted for use
with DEAGO. For more information run: mart_to_deago -h.
To run DEAGO, the user must provide a path to the read count matrices for each sample and a sample/condition mapping file. For GO term enrichment analysis, an annotation file must also be provided.
| Input | Description |
|---|---|
| count data directory (required) | path to directory containing count matrix files (one per sample) |
| targets file (required) | sample to experimental condition mappings |
| annotation file (optional) | required for gene name annotation and GO term enrichment analysis |
Please read the DEAGO wiki for more information on the required file formats.
To run QC and differential expression analyses:
deago --build_config -c <path/to/count/data> -t <sample_mapping.txt>
To only generate QC plots:
deago --build_config -c <path/to/count/data> -t <sample_mapping.txt> --qc
To convert a delimited annotation file (e.g. BioMart):
deago --build_config -c <path/to/count/data> -t <sample_mapping.txt> --convert_annotation -a <annotation.txt>
GO term enrichment analysis requires an annotation file mapping the gene identifiers in the count matrices with their associated GO terms.
deago --build_config -c <path/to/count/data> -t <sample_mapping.txt> -a <annotation_file.txt> --go
DEAGO generates a user-friendly HTML report of the analysis (deago_markdown.html). The markdown file used to run the analysis and knit the report is also provided (deago_markdown.Rmd) along with a log file containing the STDOUT from the conversion. If --build-config was used instead of providing a configuration file, then a configuration file will be generated (deago.config).
| File(s) | Description |
|---|---|
| deago.config (optional) | Key/value parameters to define the analysis |
| deago_markdown.Rmd | R markdown file of analysis commands |
| deago_markdown.html | HTML report knitted from R markdown file |
| deago.rlog | Log file of STDOUT from R markdown conversion |
Differential expression and GO term enrichment analysis results are written to tab-delimited files within a timestamped results directory (results_). The corresponding results directory can be found in the Pipeline configuration section of the HTML report.
| File(s) | Description |
|---|---|
| <contrast>_<alpha>.txt | Differential expression analysis results and normalised counts |
| <contrast>_<go_level>.tsv | GO term enrichment analysis results |
DEAGO is free software, licensed under GPLv3.
Please report any issues to the issues page or email path-help@sanger.ac.uk.
For more information, please go to the DEAGO wiki.