FilterFFPE
This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see FilterFFPE.
FFPE Artificial Chimeric Read Filter for NGS data
Bioconductor version: 3.19
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")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
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 | 1.14.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (4 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_1.14.0.tar.gz |
| Windows Binary (x86_64) | FilterFFPE_1.14.0.zip |
| macOS Binary (x86_64) | FilterFFPE_1.14.0.tgz |
| macOS Binary (arm64) | FilterFFPE_1.14.0.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 |