Description

Make plots for interpretation of differential abundance statistics

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing contrast information, to be passed as reference
and target levels, like ‘—reference_level meta.reference−−treatmentlevelmeta.reference --treatment_level meta.target’
e.g. [ variable:‘treatment’, reference:‘treated’, control:‘saline’, blocking:” ]

meta2 (map)

Groovy Map containing information on experiment represented by max,
features and samples, at a minimum an id.
e.g. [ id:‘test’ ]

differential_results (file)

CSV or TSV-format tabular file with differential analysis outputs

sample (file)

CSV or TSV-format sample sheet with sample metadata

feature_meta (file)

CSV or TSV-format feature (e.g. gene) metadata

assay_file (file)

CSV or TSV matrix file to use alongside differential statistics in
interpretation. Usually a normalised form.

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing contrast information
e.g. [ variable:‘treatment’, reference:‘treated’, control:‘saline’, blocking:” ]

volcanos_png (file)

Meta-keyed tuple containing a PNG output for a volcano plot built from
the differential result table.

volcanos_html (file)

Meta-keyed tuple containing an HTML output for a volcano plot built
from the differential result table.

versions (file)

File containing software versions

versions.yml
included in
differentialabundance
maintainer
Github user pinin4fjords
get in touch
Ask a question on Slack Open an issue on GitHub

Tools

shinyngs
AGPL v3

Provides Shiny applications for various array and NGS applications. Currently very RNA-seq centric, with plans for expansion.

github.com/pinin4fjords/shinyngs rawgit.com/pinin4fjords/shinyngs/master/vignettes/shinyngs https://github.com/pinin4fjords/shinyngs