CollecTRI is a comprehensive resource of transcriptional regulation, published in 2023, consisting of 14 resources and original literature curation.
Usage
collectri(
resources = NULL,
organism = 9606L,
references_by_resource = TRUE,
exclude = NULL,
strict_evidences = TRUE,
...
)
Arguments
- resources
interactions not reported in these databases are removed. See
get_interaction_resources
for more information.- organism
Interactions are available for human, mouse and rat. Choose among: 9606 human (default), 10116 rat and 10090 Mouse
- references_by_resource
if FALSE, removes the resource name prefixes from the references (PubMed IDs); this way the information which reference comes from which resource will be lost and the PubMed IDs will be unique.
- exclude
Character: datasets or resources to exclude.
- strict_evidences
Logical: restrict the evidences to the queried datasets and resources. If set to FALSE, the directions and effect signs and references might be based on other datasets and resources. In case of CollecTRI this is not desirable for most of the applications. For most of the other interaction querying functions it is `FALSE` by default.
- ...
Optional additional arguments, passed to
import_transcriptional_interactions
.