Many inherited biases and effects exists in RNA-seq due to both biological and technical effects. We observed the biological variance of testing target transcripts can influence the yield of sequencing reads, which might indicate a resource competition existing in RNA-seq. We developed this package to capture the bias depending on local sequence and perform the correction of this type of bias by borrowing information from spike-in measurement.

Author | Guoshuai Cai |

Date of publication | 2014-07-16 01:07:26 |

Maintainer | Guoshuai Cai <GCAI.bioinfo@gmail.com> |

License | GPL (>= 2) |

Version | 1.0 |

**coeplot:** Estimated Coefficients Visualization

**corplot:** Pairwise Correlation Calculation and Visualization

**correct.guided:** Guided Correction

**counts.preprocess:** Data Object Generation

**GCAI.bias-package:** Guided Correction Approach for Inherited bias (GCAI.bias)

**index.mat.generation:** Index Matrix Generation

**index.preprocess:** Binary Index Matrix Generation

**lm.estimate:** Linear Model Fitting

**obj.index:** Index S3 Class

**panel.cor:** Pearson Correlation Calculation

**panel.smooth.r:** Scatter Plot Generation

**posplot:** Correction Performance Visualization

**test.dat.counts:** Testing Counts Dataset

**test.dat.seq:** Testing Sequence Index Dataset

**train.dat.counts:** Training Counts Dataset

**train.dat.seq:** Training Sequence Index Dataset

GCAI.bias

GCAI.bias/NAMESPACE

GCAI.bias/data

GCAI.bias/data/train.dat.seq.rda

GCAI.bias/data/obj.index.rda

GCAI.bias/data/train.dat.counts.rda

GCAI.bias/data/test.dat.seq.rda

GCAI.bias/data/test.dat.counts.rda

GCAI.bias/R

GCAI.bias/R/posplot.R
GCAI.bias/R/lm.estimate.R
GCAI.bias/R/index.preprocess.R
GCAI.bias/R/correct.guided.R
GCAI.bias/R/corplot.R
GCAI.bias/R/panel.cor.R
GCAI.bias/R/counts.preprocess.R
GCAI.bias/R/index.mat.generation.R
GCAI.bias/R/panel.smooth.r.R
GCAI.bias/R/coeplot.R
GCAI.bias/MD5

GCAI.bias/DESCRIPTION

GCAI.bias/man

GCAI.bias/man/coeplot.Rd
GCAI.bias/man/GCAI.bias-package.Rd
GCAI.bias/man/counts.preprocess.Rd
GCAI.bias/man/posplot.Rd
GCAI.bias/man/panel.smooth.r.Rd
GCAI.bias/man/obj.index.Rd
GCAI.bias/man/index.preprocess.Rd
GCAI.bias/man/panel.cor.Rd
GCAI.bias/man/test.dat.seq.Rd
GCAI.bias/man/test.dat.counts.Rd
GCAI.bias/man/lm.estimate.Rd
GCAI.bias/man/corplot.Rd
GCAI.bias/man/train.dat.seq.Rd
GCAI.bias/man/train.dat.counts.Rd
GCAI.bias/man/correct.guided.Rd
GCAI.bias/man/index.mat.generation.Rd
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