Package: rsemmed 1.17.0

Leslie Myint

rsemmed: An interface to the Semantic MEDLINE database

A programmatic interface to the Semantic MEDLINE database. It provides functions for searching the database for concepts and finding paths between concepts. Path searching can also be tailored to user specifications, such as placing restrictions on concept types and the type of link between concepts. It also provides functions for summarizing and visualizing those paths.

Authors:Leslie Myint [aut, cre]

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rsemmed.pdf |rsemmed.html✨
rsemmed/json (API)
NEWS

# Install 'rsemmed' in R:

install.packages('rsemmed', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/lmyint/rsemmed/issues

Datasets:

g_mini - Example data for the rsemmed package
g_small - Example data for the rsemmed package

On BioConductor:rsemmed-1.17.0(bioc 3.21)rsemmed-1.16.0(bioc 3.20)

software annotation pathways systemsbiology

4.00 score 8 scripts 128 downloads 10 exports 22 dependencies

Last updated 3 months agofrom:7e5464b3dd. Checks:7 OK. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Dec 26 2024
R-4.5-win	OK	Dec 26 2024
R-4.5-linux	OK	Dec 26 2024
R-4.4-win	OK	Dec 26 2024
R-4.4-mac	OK	Dec 26 2024
R-4.3-win	OK	Dec 26 2024
R-4.3-mac	OK	Dec 26 2024

Exports:find_nodes find_paths get_edge_features get_middle_nodes grow_nodes make_edge_weights plot_path summarize_predicates summarize_semtypes text_path

Dependencies:cli cpp11 dplyr fansi generics glue igraph lattice lifecycle magrittr Matrix pillar pkgconfig R6 rlang stringi stringr tibble tidyselect utf8 vctrs withr

The rsemmed User's Guide

Leslie Myint

Rendered fromrsemmed_user_guide.Rmdusingknitr::rmarkdownon Dec 26 2024.

Last update: 2020-09-12
Started: 2020-08-16

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Search for nodes by name or semantic type	find_nodes
Shortest paths between node sets	find_paths
Example data for the rsemmed package	g_mini
Example data for the rsemmed package	g_small
Get information about edges	get_edge_features
Obtain the middle nodes of a path	get_middle_nodes
Obtain immediate neighbors	grow_nodes
Create edge weights	make_edge_weights
Display path (plot form)	plot_path
Summarize predicates	summarize_predicates
Summarize semantic types	summarize_semtypes
Display path (text form)	text_path