baySeq - Empirical Bayesian analysis of patterns of differential expression in count data
This package identifies differential expression in high-throughput 'count' data, such as that derived from next-generation sequencing machines, calculating estimated posterior likelihoods of differential expression (or more complex hypotheses) via empirical Bayesian methods.
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sequencingdifferentialexpressionmultiplecomparisonsagebayesiancoverage
7.42 score 3 dependents 91 scripts 956 downloadssegmentSeq - Methods for identifying small RNA loci from high-throughput sequencing data
High-throughput sequencing technologies allow the production of large volumes of short sequences, which can be aligned to the genome to create a set of matches to the genome. By looking for regions of the genome which to which there are high densities of matches, we can infer a segmentation of the genome into regions of biological significance. The methods in this package allow the simultaneous segmentation of data from multiple samples, taking into account replicate data, in order to create a consensus segmentation. This has obvious applications in a number of classes of sequencing experiments, particularly in the discovery of small RNA loci and novel mRNA transcriptome discovery.
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multiplecomparisonsequencingalignmentdifferentialexpressionqualitycontroldataimport
6.11 score 91 scripts 688 downloadsriboSeqR - Analysis of sequencing data from ribosome profiling experiments
Plotting functions, frameshift detection and parsing of sequencing data from ribosome profiling experiments.
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sequencinggeneticsvisualizationriboseq
5.13 score 1 stars 16 scripts 602 downloadsclusterSeq - Clustering of high-throughput sequencing data by identifying co-expression patterns
Identification of clusters of co-expressed genes based on their expression across multiple (replicated) biological samples.
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sequencingdifferentialexpressionmultiplecomparisonclusteringgeneexpression
4.08 score 2 scripts 509 downloads