FilterFFPE

DOI:10.18129/B9.bioc.FilterFFPE

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, seeFilterFFPE.

FFPE Artificial Chimeric Read Filter for NGS data

Bioconductor version: 3.14

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

Installation

To install this package, start R (version "4.1") and enter:

if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("FilterFFPE")

For older versions of R, please refer to the appropriateBioconductor release.

Documentation

查看文档的版本包age installed in your system, start R and enter:

browseVignettes("FilterFFPE")

PDF	R Script	An introduction to FilterFFPE
PDF		Reference Manual
Text		NEWS

Details

biocViews	Alignment,Preprocessing,QualityControl,Sequencing,Software,StructuralVariation
Version	1.4.0
In Bioconductor since	BioC 3.12 (R-4.0) (1.5 years)
License	LGPL-3
Depends
Imports	foreach,doParallel,GenomicRanges,IRanges,Rsamtools, parallel,S4Vectors
LinkingTo
Suggests	BiocStyle
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow2021年欧洲杯比分预测 instructions to use this package in your R session.

Source Package	FilterFFPE_1.4.0.tar.gz
Windows Binary	FilterFFPE_1.4.0.zip(32- & 64-bit)
macOS 10.13 (High Sierra)	FilterFFPE_1.4.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/FilterFFPE
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/FilterFFPE
Package Short Url	//www.andersvercelli.com/packages/FilterFFPE/
Package Downloads Report	Download Stats