Package: AutoPipe 0.1.6
AutoPipe: Automated Transcriptome Classifier Pipeline: Comprehensive Transcriptome Analysis
An unsupervised fully-automated pipeline for transcriptome analysis or a supervised option to identify characteristic genes from predefined subclasses. We rely on the 'pamr' <http://www.bioconductor.org/packages//2.7/bioc/html/pamr.html> clustering algorithm to cluster the Data and then draw a heatmap of the clusters with the most significant genes and the least significant genes according to the 'pamr' algorithm. This way we get easy to grasp heatmaps that show us for each cluster which are the clusters most defining genes.
Authors:
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AutoPipe.pdf |AutoPipe.html✨
AutoPipe/json (API)
| # Install 'AutoPipe' in R: |
| install.packages('AutoPipe', repos = c('https://falafel19.r-universe.dev', 'https://cloud.r-project.org')) |
- rna - Rna egene expression of 48 meningiomas
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 6 years agofrom:3220705495. Checks:7 OK. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Mar 13 2025 |
| R-4.5-win | OK | Mar 13 2025 |
| R-4.5-mac | OK | Mar 13 2025 |
| R-4.5-linux | OK | Mar 13 2025 |
| R-4.4-mac | OK | Mar 13 2025 |
| R-4.4-linux | OK | Mar 13 2025 |
| R-4.4-win | OK | Feb 11 2025 |
Exports:AutoPipe_tSNEcons_clustGroups_Supread_expression_fileSupervised_Cluster_Heatmaptop_supervisedTopPAMUnSuperClassifier
Dependencies:ALLannotateAnnotationDbiapeaplotaskpassbabelgeneBHBiobaseBiocGenericsBiocParallelBiostringsbitbit64blobcachemcliclusterclusterProfilercodetoolscolorspaceConsensusClusterPluscowplotcpp11crayoncurldata.tableDBIdigestDOSEdplyrenrichplotfansifarverfastmapfastmatchfgseaformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataggforceggfunggnewscaleggplot2ggplotifyggrepelggtangleggtreeglueGO.dbGOSemSimgridGraphicsgsongtablehttrigraphIRangesisobandjsonliteKEGGRESTlabelinglambda.rlatticelazyevallifecyclemagrittrMASSMatrixmemoisemgcvmimemsigdbrmulttestmunsellnlmeopensslorg.Hs.eg.dbpamrpatchworkpillarpkgconfigplogrplyrpngpolyclippurrrqvalueR.methodsS3R.ooR.utilsR6RColorBrewerRcppRcppEigenreshape2rlangRSQLiteRtsneS4VectorsscalesscatterpiescrimesiggenessnowstringistringrsurvivalsyssystemfontstibbletidyrtidyselecttidytreetreeiotweenrUCSC.utilsutf8vctrsviridisLitewithrXMLxtableXVectoryulab.utils
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Implemented t-distributed stochastic neighbor embedding | AutoPipe_tSNE |
| A function to plot do a Consensus clustering to validate the results | cons_clust |
| cluster the samples | Groups_Sup |
| Input Expression File | read_expression_file |
| rna egene expression of 48 meningiomas | rna |
| Produce a Heatmap using a Supervised clustering Algorithm | Supervised_Cluster_Heatmap |
| A Function for Assisting Supervised Clustering | top_supervised |
| Compute Top genes | TopPAM |
| Unsupervised Clustering | UnSuperClassifier |
