Package: moanin 1.15.0
Nelle Varoquaux
moanin: An R Package for Time Course RNASeq Data Analysis
Simple and efficient workflow for time-course gene expression data, built on publictly available open-source projects hosted on CRAN and bioconductor. moanin provides helper functions for all the steps required for analysing time-course data using functional data analysis: (1) functional modeling of the timecourse data; (2) differential expression analysis; (3) clustering; (4) downstream analysis.
Authors:
moanin_1.15.0.tar.gz
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moanin.pdf |moanin.html✨
moanin/json (API)
| # Install 'moanin' in R: |
| install.packages('moanin', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- testData - Small data set for running examples
- testGenesGO - Small data set for running examples
- testMeta - Small data set for running examples
On BioConductor:moanin-1.13.0(bioc 3.20)moanin-1.12.0(bioc 3.19)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
timecoursegeneexpressionrnaseqmicroarraydifferentialexpressionclustering
Last updated 23 days agofrom:24c12c78c9. Checks:OK: 1 NOTE: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 30 2024 |
| R-4.5-win | NOTE | Oct 31 2024 |
| R-4.5-linux | NOTE | Oct 30 2024 |
| R-4.4-win | NOTE | Oct 31 2024 |
| R-4.4-mac | NOTE | Oct 31 2024 |
| R-4.3-win | NOTE | Oct 31 2024 |
| R-4.3-mac | NOTE | Oct 31 2024 |
Exports:basis_matrixconsensus_matrixcreate_go_term_mappingcreate_moanin_modelcreate_timepoints_contrastsDE_timecourseDE_timepointsdegrees_of_freedomdiscont_basisestimate_log_fold_changefind_enriched_go_termsget_auc_similarity_scoresget_log_datagroup_variablegroup_variable_namegroup_variable_name<-group_variable<-log_transformperWeek_barplotplot_cdf_consensusplot_model_explorerplot_splines_datapvalues_fisher_methodrescale_valuesshowspline_formulasplines_kmeanssplines_kmeans_predictsplines_kmeans_score_and_labeltime_by_group_variabletime_variabletime_variable_nametime_variable_name<-time_variable<-
Dependencies:abindAnnotationDbiaskpassBiobaseBiocGenericsBiostringsbitbit64blobcachemcliClusterRcolorspacecpp11crayoncurlDBIDelayedArrayedgeRfansifarverfastmapGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegmpGO.dbgraphgridExtragtablehttrIRangesisobandjsonliteKEGGRESTlabelinglatticelifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeNMIopensslpillarpkgconfigplogrplyrpngR6RColorBrewerRcppRcppArmadilloreshape2rlangRSQLiteS4ArraysS4VectorsscalesSparseArraySparseMstatmodstringistringrSummarizedExperimentsystibbletopGOUCSC.utilsutf8vctrsviridisviridisLitewithrXVectorzlibbioczoo
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Compute consensus matrix from labels | consensus_matrix |
| Run spline models and test for DE of contrasts. | DE_timecourse DE_timecourse,Moanin-method |
| Fit weekly differential expression analysis | create_timepoints_contrasts create_timepoints_contrasts,Moanin-method DE_timepoints DE_timepoints,Moanin-method |
| Provides set of basis functions on either side of a time point, allowing for a discontinuity in the fitted functions | discont_basis |
| Estimates log fold change | estimate_log_fold_change estimate_log_fold_change,Moanin-method |
| Small data set for running examples | exampleData testData testGenesGO testMeta |
| Find enriched GO terms | create_go_term_mapping find_enriched_go_terms |
| Class Moanin | create_moanin_model create_moanin_model,data.frame-method create_moanin_model,DataFrame-method create_moanin_model,matrix-method create_moanin_model,SummarizedExperiment-method Moanin Moanin-class |
| Helper methods for the Moanin class | basis_matrix basis_matrix,Moanin-method degrees_of_freedom degrees_of_freedom,Moanin-method get_log_data get_log_data,Moanin-method group_variable group_variable,Moanin-method group_variable<- group_variable<-,Moanin-method group_variable_name group_variable_name,Moanin-method group_variable_name<- group_variable_name<-,Moanin-method log_transform log_transform,Moanin-method Moanin-methods show show,Moanin-method spline_formula spline_formula,Moanin-method time_by_group_variable time_by_group_variable,Moanin-method time_variable time_variable,Moanin-method time_variable<- time_variable<-,Moanin-method time_variable_name time_variable_name,Moanin-method time_variable_name<- time_variable_name<-,Moanin-method [,Moanin,ANY,ANY,ANY-method [,Moanin,ANY,character,ANY-method [,Moanin,ANY,logical,ANY-method [,Moanin,ANY,numeric,ANY-method |
| Creates barplot of results of per-timepoint comparison | perWeek_barplot |
| Evaluate the consensus between sets of clusterings | get_auc_similarity_scores plot_cdf_consensus plot_model_explorer |
| Plotting splines | plot_splines_data plot_splines_data,Moanin,data.frame-method plot_splines_data,Moanin,DataFrame-method plot_splines_data,Moanin,matrix-method plot_splines_data,Moanin,missing-method plot_splines_data,Moanin,numeric-method |
| Fisher's method to combine pvalues | pvalues_fisher_method |
| Rescales rows of data to be between 0 and 1 | NULL-method rescale_values rescale_values, rescale_values,missing-method rescale_values,Moanin-method rescale_values,NULL-method |
| Performs splines clustering using K-means | splines_kmeans splines_kmeans,Moanin-method |
| Assign score and labels from raw data | splines_kmeans_predict splines_kmeans_predict,Moanin-method splines_kmeans_score_and_label splines_kmeans_score_and_label,Moanin-method |
