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Rqc

Rqc is an optimized tool designed for quality control and assessment of high-throughput sequencing data. It performs parallel processing of entire files and produces a report which contains a set of high-resolution graphics.

Installation

Install via Bioconductor, stable version

source("http://bioconductor.org/biocLite.R")
biocLite("Rqc")

Install via GitHub, development vertion

install.packages("devtools")
library(devtools)
install_github("labbcb/Rqc")

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Version

Version

1.6.2

License

GPL (>= 2)

Issues

3

Pull Requests

0

Stars

0

Forks

1

Maintainer

Welliton Souza

Last Published

February 15th, 2017

Functions in Rqc (1.6.2)

detectFileFormat

Detect file format
matdist

Distance matrix of the similarity between the DNA sequences.
subsetByPair

Subset RqcResultSet object by pair files.
rqcReadFrequencyCalc

Read frequency plot
checkpoint

Save time storing longer analysis step on disk
rqcCycleQualityBoxCalc

Per cycle quality box plot
rqcReadQualityCalc

Per read quality plot
rqcReport

Quality Control HTML Report
rqcGroupCycleAverageQualityCalc

Per group average quality across cycles
rqcCycleBaseCallsCalc

Per cycle base calls plot
rqcShinyReport

Interactive Quality Control Report
rqcReadWidthCalc

Per read width plot
rqcCycleGCCalc

Per cycle percentual GC plot
rqc

Main Rqc function
rqcCycleQualityCalc

Per cycle quality plot
fromRRDNA

Revert codified DNA sequences to original DNA sequences.
rqcFileHeatmap

Heatmap of distance matrix of top over-represented reads
rqcReadQualityBoxCalc

Per read mean quality box plot
RqcResultSet-class

Class RqcResultSet
Rqc-package

Quality Control Tool for High-Throughput Sequencing Data
subsetByGroup

Subset RqcResultSet object by group name.
toRRDNA

Title: Convert DNA sequences to Reduced Representation format
rqcCycleAverageQualityPcaCalc

Biplot of PCA of per cycle read average quality
rqcCycleAverageQualityCalc

Per cycle average quality by files
rqcQA

Quality Assessment Rqc function
stats4trim

Minimun read mean quality and maximum percentage loss of reads estimations for trimming step.