FilterFFPE
This is the development version of FilterFFPE; for the stable release version, see FilterFFPE.
FFPE Artificial Chimeric Read Filter for NGS data
Bioconductor version: Development (3.24)
This package finds and filters artificial chimeric reads specifically generated in next-generation sequencing (NGS) process of formalin-fixed paraffin-embedded (FFPE) tissues. These artificial chimeric reads can lead to a large number of false positive structural variation (SV) calls. The required input is an indexed BAM file of a FFPE sample.
Author: Lanying Wei [aut, cre]
Maintainer: Lanying Wei <lanying.wei at uni-muenster.de>
citation("FilterFFPE")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("FilterFFPE")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("FilterFFPE")| An introduction to FilterFFPE | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Alignment, Preprocessing, QualityControl, Sequencing, Software, StructuralVariation |
| Version | 1.23.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (6 years) |
| License | LGPL-3 |
| Depends | |
| Imports | foreach, doParallel, GenomicRanges, IRanges, Rsamtools, parallel, S4Vectors |
| System Requirements | |
| URL |
See More
| Suggests | BiocStyle |
| 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 | FilterFFPE_1.23.0.tar.gz |
| Windows Binary (x86_64) | FilterFFPE_1.23.0.zip |
| macOS Binary (big-sur-x86_64) | FilterFFPE_1.23.0.tgz |
| macOS Binary (sonoma-arm64) | FilterFFPE_1.23.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/FilterFFPE |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/FilterFFPE |
| Bioc Package Browser | https://code.bioconductor.org/browse/FilterFFPE/ |
| Package Short Url | https://bioconductor.org/packages/FilterFFPE/ |
| Package Downloads Report | Download Stats |