GCAI.bias: Guided Correction Approach for Inherited bias (GCAI.bias)

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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

View on CRAN

Man pages

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

Files in this package

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