Package: RNAsense 1.19.0

Marcus Rosenblatt

RNAsense: Analysis of Time-Resolved RNA-Seq Data

RNA-sense tool compares RNA-seq time curves in two experimental conditions, i.e. wild-type and mutant, and works in three steps. At Step 1, it builds expression profile for each transcript in one condition (i.e. wild-type) and tests if the transcript abundance grows or decays significantly. Dynamic transcripts are then sorted to non-overlapping groups (time profiles) by the time point of switch up or down. At Step 2, RNA-sense outputs the groups of differentially expressed transcripts, which are up- or downregulated in the mutant compared to the wild-type at each time point. At Step 3, Correlations (Fisher's exact test) between the outputs of Step 1 (switch up- and switch down- time profile groups) and the outputs of Step2 (differentially expressed transcript groups) are calculated. The results of the correlation analysis are printed as two-dimensional color plot, with time profiles and differential expression groups at y- and x-axis, respectively, and facilitates the biological interpretation of the data.

Authors:Marcus Rosenblatt [cre], Gao Meijang [aut], Helge Hass [aut], Daria Onichtchouk [aut]

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Bug tracker:https://github.com/marcusrosenblatt/rnasense/issues

On BioConductor:RNAsense-1.19.0(bioc 3.20)RNAsense-1.18.0(bioc 3.19)

bioconductor-package

5 exports 0.61 score 60 dependencies

Last updated 2 months agofrom:9b5181d141

Exports:combineResultsgetFCgetSwitchoutputGeneTablesplotSSGS

Dependencies:abindaskpassBiobaseBiocGenericsclicolorspacecrayoncurlDelayedArrayfansifarverGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegtablehttrIRangesisobandjsonlitelabelinglatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemunsellNBPSeqnlmeopensslpillarpkgconfigplyrqvalueR6RColorBrewerRcppreshape2rlangS4ArraysS4VectorsscalesSparseArraystringistringrSummarizedExperimentsystibbleUCSC.utilsutf8vctrsviridisLitewithrXVectorzlibbioc