gGnome

Default Boolean Operator: Terms in a search string will be connected by the AND operator, EXAMPLE: searching genomic melanoma will produce the same results as genomic AND melanoma .
AND, OR, NOT: Combine terms in a search with the boolean operators AND (to add specificity), OR (to broaden), or NOT (to eliminate a term). Operators must be capitalized (all other search terms are not case-sensitive).
Wild Card: Add wild card symbols * (open-ended) and ? (single character) to truncate terms. EXAMPLE: searching gen* shows results for 'gene', 'genetic', 'genomic, etc. Searching gene? returns results for 'gene' or 'genes' but not for 'genome'.
Phrase Searching: Enclose search in quotation marks "keyword or search term" to search for an exact phrase. EXAMPLE: "transcription factors" returns results for records where transcription is immediately followed by the word factors .
Diacritics: Words containing diacritics translate those characters to non-diacritic form. EXAMPLE: massague returns results for Massague&#769 .
Filter by: Located on the homepage (left panel), use filters to search for records or narrow the search. From search results page, filters can be removed by clicking on the term at the top of the page.

UID: 11273

Author(s): Imielinski, Marcin, Yao, Xiaotong, Choo, Zi-Ning, Shaiber, Alon, DeRose, Joseph, Mortensen, Rick, Chao, Max

Description: Description from GitHub:

"The gGnome package provides a flexible, queriable R interface to graphs and walks of reference genomic intervals. gGnome is written in the R6 object oriented standard and built around a powerful GenomicRanges, data.table, and igraph backend, and thus supports agile interaction with graphs consisting of hundreds of thousands of nodes and edges."

Subject(s)

Access via GitHub
Access Restrictions: Free to All
Access Instructions: Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the relevant conditions. Read more about access policy on GitHub.
Associated Publications: Setton J, Hadi K, Choo Z, Kuchin K, Tian H, Da Cruz Paula A, Rosiene J, Selenica P, Behr J, Yao X, Deshpande A, Sigouros M, Manohar J, Nauseef J, Mosquera J, Elemento O, Weigelt B, Riaz N, Reis-Filho J, Powell S, Imieliński M. Long-molecule scars of backup DNA repair in BRCA1- and BRCA2-deficient cancers. Nature. 2023; 621(7977):129-137.
Software Used: R
a free software environment for statistical computing and graphics.
Dataset Format(s): R, HTML, PNG, YML, JS, CSS, Rd

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