fragCounter

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: 11271

Author(s): Imielinski, Marcin

Description: Description from GitHub:

"The goal of fragCounter is to correct Whole genome or targeted sequencing data for GC and mappability bias. The GC bias curve is determined by loess regression of read count by GC and mappability scores. Segmentation is done by circular binary segmentation (CBS) algorithm after getting tumor/normal ratios of corrected read counts."

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, TAR, BIGWIG, gzip, BAM, BAI, RDS, YML, MD

Do you have or know of a dataset that should be added to the catalog? Let us know!