BitSeq-package
(Package: BitSeq) :
Bayesian Inference of Transcripts from Sequencing data
The BitSeq package is targeted for transcript expression analysis and differential expression analysis of RNA-seq data in two stage process.
● Data Source:
BioConductor
● Keywords: package
● Alias: BitSeq, BitSeq-package
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estimateDE
(Package: BitSeq) :
Estimate condition mean expression and calculate Probability of Positive Log Ratio(PPLR)
Estimate condition mean expression for both experimental conditions using the expression estimates obtained by estimateExpression
● Data Source:
BioConductor
● Keywords: differential expression
● Alias: estimateDE
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estimateExpression
(Package: BitSeq) :
Estimate expression of transcripts
Estimates the expression of transcripts using Markov chain Monte Carlo Algorithm
● Data Source:
BioConductor
● Keywords: transcript expression
● Alias: estimateExpression, estimateExpressionLegacy
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estimateHyperPar
(Package: BitSeq) :
Estimate hyperparameters for DE model using expression samples and joint mean expression
Estimate hyperparameters for the Differential Expression model using expression samples and produced smoothed values of the hyperparameters depending on joint mean expression.
● Data Source:
BioConductor
● Keywords: differential expression
● Alias: estimateHyperPar
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estimateVBExpression
(Package: BitSeq) :
Estimate expression of transcripts using VB
Estimates the expression of transcripts using Variational Bayes inference algorithm
● Data Source:
BioConductor
● Keywords: transcript expression
● Alias: estimateVBExpression
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getDE
(Package: BitSeq) :
Estimate Probability of Positive Log Ratio
Using expression samples, program estimates the probability of differential expression for each transcript.
● Data Source:
BioConductor
● Keywords: differential expression
● Alias: getDE
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getExpression
(Package: BitSeq) :
Estimate transcript expression
Estimate expression of transcripts. Starting from alignment and reference files function function handles the entire process of expression analysis resulting in transcript expression means and standard deviation together with file containing all the expression samples.
● Data Source:
BioConductor
● Keywords: transcript expression
● Alias: getExpression
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getGeneExpression
(Package: BitSeq) :
Calculate gene expression or relative within gene expression
Calculate either gene expression or relative within gene expression using transcript expression samples and transcript information file.
● Data Source:
BioConductor
● Keywords: gene expression
● Alias: getGeneExpression, getWithinGeneExpression
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getMeanVariance
(Package: BitSeq) :
Calculate mean and variance of expression samples
Calculate mean and variance of expression samples or log-expression samples
● Data Source:
BioConductor
● Keywords: expression mean
● Alias: getMeanVariance
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loadSamples
(Package: BitSeq) :
Loading and saving expression samples
Functions for loading expression samples into DataFrame and saving samples from DataFrame into a file.
● Data Source:
BioConductor
● Keywords: transcript expression
● Alias: loadSamples, writeSamples
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