Make plots for interpretation of differential abundance statistics
Input
name:type
description
pattern
meta{:bash}
:map
Groovy Map containing contrast information, to be passed as reference
and target levels, like ‘—reference_level $meta.reference
—treatment_level $meta.target’
e.g. [ variable:‘treatment’, reference:‘treated’, control:‘saline’, blocking:” ]
differential_result{:bash}
:file
statistic differential results
meta2{:bash}
:map
Groovy Map containing information on experiment represented by max,
features and samples, at a minimum an id.
e.g. [ id:‘test’ ]
sample{:bash}
:file
CSV or TSV-format sample sheet with sample metadata
feature_meta{:bash}
:file
CSV or TSV-format feature (e.g. gene) metadata
assay_file{:bash}
:file
CSV or TSV matrix file to use alongside differential statistics in
interpretation. Usually a normalised form.
Output
name:type
description
pattern
volcanos_png{:bash}
meta{:bash}
:map
Groovy Map containing contrast information
e.g. [ variable:‘treatment’, reference:‘treated’, control:‘saline’, blocking:” ]
*/png/volcano.png{:bash}
:file
Meta-keyed tuple containing a PNG output for a volcano plot built from
the differential result table.
volcanos_html{:bash}
meta{:bash}
:map
Groovy Map containing contrast information
e.g. [ variable:‘treatment’, reference:‘treated’, control:‘saline’, blocking:” ]
*/html/volcano.html{:bash}
:file
Meta-keyed tuple containing an HTML output for a volcano plot built
from the differential result table.
versions{:bash}
versions.yml{:bash}
:file
File containing software versions
versions.yml
Tools
shinyngs
AGPL v3
Provides Shiny applications for various array and NGS applications. Currently very RNA-seq centric, with plans for expansion.
