nanotatoR
This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.
This package is for version 3.20 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see nanotatoR.
Next generation structural variant annotation and classification
Bioconductor version: Release (3.20)
Whole genome sequencing (WGS) has successfully been used to identify single-nucleotide variants (SNV), small insertions and deletions (INDELs) and, more recently, small copy number variants (CNVs). However, due to utilization of short reads, it is not well suited for identification of structural variants (SV). Optical mapping (OM) from Bionano Genomics, utilizes long fluorescently labeled megabase size DNA molecules for de novo genome assembly and identification of SVs with a much higher sensitivity than WGS. Nevertheless, currently available SV annotation tools have limited number of functions. NanotatoR is an R package written to provide a set of annotations for SVs identified by OM. It uses Database of Genomic Variants (DGV), Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources (DECIPHER) as well as a subset (154 samples) of 1000 Genome Project to calculate the population frequencies of the SVs (an optional internal cohort SV frequency calculation is also available). NanotatoR creates a primary gene list (PG) from NCBI databases based on proband’s phenotype specific keywords and compares the list to the set of genes overlapping/near SVs. The output is given in an Excel file format, which is subdivided into multiple sheets based on SV type (e.g., INDELs, Inversions, Translocations). Users then have a choice to filter SVs using the provided annotations for de novo (if parental samples are available) or inherited rare variants.
Author:
Maintainer: Surajit Bhattacharya <sbhattach2 at childrensnational.org>
citation("nanotatoR")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("nanotatoR")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
| Reference Manual |
Details
| biocViews | GenomeAssembly, Software, VariantAnnotation, WorkflowStep |
| Version | 1.22.0 |
| In Bioconductor since | BioC 3.9 (R-3.6) (5.5 years) |
| License | file LICENSE |
| Depends | R (>= 4.1) |
| Imports | hash (>= 2.2.6), openxlsx (>= 4.0.17), rentrez (>= 1.1.0), stats, rlang, stringr, knitr, testthat, utils, AnnotationDbi, httr, GenomicRanges, tidyverse, VarfromPDB, org.Hs.eg.db, curl, dplyr, XML, XML2R |
| System Requirements | |
| URL | https://github.com/VilainLab/nanotatoR |
| Bug Reports | https://github.com/VilainLab/nanotatoR/issues |
See More
| Suggests | rmarkdown, yaml |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/nanotatoR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/nanotatoR |
| Package Short Url | https://bioconductor.org/packages/nanotatoR/ |
| Package Downloads Report | Download Stats |