Introduction | Changes for HELP in current BioC release | Data import and Design information | Quality Control and Data Exploration | Single-sample quantile normalization | Data summarization | Data Visualization | Previous Release Notes
Package: HELP 1.71.0
Reid F. Thompson
HELP: Tools for HELP data analysis
The package contains a modular pipeline for analysis of HELP microarray data, and includes graphical and mathematical tools with more general applications.
Authors:
HELP_1.71.0.tar.gz
HELP_1.71.0.zip(r-4.7)HELP_1.71.0.zip(r-4.6)HELP_1.71.0.zip(r-4.5)
HELP_1.71.0.tgz(r-4.6-any)HELP_1.71.0.tgz(r-4.5-any)
HELP_1.71.0.tar.gz(r-4.7-any)HELP_1.71.0.tar.gz(r-4.6-any)
HELP_1.71.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
HELP/json (API)
| # Install 'HELP' in R: |
| install.packages('HELP', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- base.stacking.thermodynamics - Base-stacking thermodynamic parameters
On BioConductor:HELP-1.71.0(bioc 3.24)HELP-1.70.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
cpgislanddnamethylationmicroarraytwochanneldataimportqualitycontrolpreprocessingvisualization
Last updated from:74ec2b221c. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 151 | ||
| linux-devel-x86_64 | NOTE | 145 | ||
| source / vignettes | OK | 145 | ||
| linux-release-x86_64 | NOTE | 185 | ||
| macos-release-arm64 | NOTE | 78 | ||
| macos-oldrel-arm64 | NOTE | 70 | ||
| windows-devel | NOTE | 75 | ||
| windows-release | NOTE | 85 | ||
| windows-oldrel | NOTE | 71 | ||
| wasm-release | OK | 92 |
Exports:calcGCcalcPrototypecalcTmcombineDatacreateWiggleexprs2exprs2<-fuzzyMatchesgetFeaturesgetSamplesplotBinsplotChipplotFeatureplotPairsquantileNormalizereadDesignreadPairsreadSampleKey
Dependencies:BiobaseBiocGenericsgenerics
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Base-stacking thermodynamic parameters | base.stacking.thermodynamics |
| Calculate GC percent | calcGC |
| Calculate GC percent (methods) | calcGC,character-method calcGC,ExpressionSet-method calcGC,missing-method calcGC,NULL-method calcGC-methods |
| Calculate prototype | calcPrototype |
| Calculate prototype (methods) | calcPrototype,ExpressionSet-method calcPrototype,matrix-method calcPrototype,missing-method calcPrototype,vector-method calcPrototype-methods |
| Calculate Tm | calcTm |
| Calculate Tm (methods) | calcTm,character-method calcTm,ExpressionSet-method calcTm,missing-method calcTm,NULL-method calcTm-methods |
| Combine data | combineData |
| Combine data (methods) | combineData,ExpressionSet,missing,missing-method combineData,ExpressionSet,vector,missing-method combineData,matrix,vector,matrix-method combineData,matrix,vector,missing-method combineData,missing,missing,missing-method combineData,vector,missing,missing-method combineData,vector,missing,vector-method combineData,vector,vector,missing-method combineData,vector,vector,vector-method combineData-methods |
| Create wiggle track | createWiggle |
| Create wiggle track (methods) | createWiggle,ExpressionSet,matrix-method createWiggle,ExpressionSet,missing-method createWiggle,matrix,matrix-method createWiggle,missing,missing-method createWiggle,vector,matrix-method createWiggle-methods |
| Retrieve microarray data (for signal channel 2) from ExpressionSets | exprs2 exprs2<- |
| Retrieve microarray data (for signal channel 2) from ExpressionSets (methods) | exprs2,ExpressionSet-method exprs2,missing-method exprs2-methods exprs2<-,ExpressionSet,matrix-method exprs2<-,ExpressionSet,missing-method |
| Fuzzy matching | fuzzyMatches |
| Fuzzy matching (methods) | fuzzyMatches,missing,missing-method fuzzyMatches,NULL,vector-method fuzzyMatches,vector,missing-method fuzzyMatches,vector,NULL-method fuzzyMatches,vector,vector-method fuzzyMatches-methods |
| Get features (methods) | getFeatures |
| Get features (methods) | getFeatures,AnnotatedDataFrame,missing-method getFeatures,AnnotatedDataFrame,NULL-method getFeatures,AnnotatedDataFrame,vector-method getFeatures,ExpressionSet,missing-method getFeatures,ExpressionSet,NULL-method getFeatures,ExpressionSet,vector-method getFeatures,matrix,vector-method getFeatures,missing,missing-method getFeatures,vector,missing-method getFeatures,vector,NULL-method getFeatures,vector,vector-method getFeatures-methods |
| Get samples | getSamples |
| Get samples (methods) | getSamples,ExpressionSet,missing-method getSamples,ExpressionSet,NULL-method getSamples,ExpressionSet,vector-method getSamples,matrix,missing-method getSamples,matrix,NULL-method getSamples,matrix,vector-method getSamples,missing,missing-method getSamples,vector,missing-method getSamples,vector,NULL-method getSamples,vector,vector-method getSamples-methods |
| Plot bins | plotBins |
| Plot bins (methods) | plotBins,ExpressionSet,ExpressionSet-method plotBins,ExpressionSet,missing-method plotBins,ExpressionSet,vector-method plotBins,matrix,missing-method plotBins,missing,missing-method plotBins,vector,ExpressionSet-method plotBins,vector,missing-method plotBins,vector,vector-method plotBins-methods |
| Plot chip image | plotChip |
| Plot chip image (methods) | plotChip,ExpressionSet,ExpressionSet,missing-method plotChip,ExpressionSet,missing,missing-method plotChip,ExpressionSet,vector,missing-method plotChip,matrix,missing,missing-method plotChip,missing,missing,missing-method plotChip,vector,vector,ExpressionSet-method plotChip,vector,vector,vector-method plotChip-methods |
| Plot feature versus two-color intensity | plotFeature |
| Plot feature versus two-color intensity (methods) | plotFeature,ExpressionSet,missing-method plotFeature,ExpressionSet,vector-method plotFeature,matrix,vector-method plotFeature,missing,missing-method plotFeature-methods |
| Plot tree-pairs | plotPairs |
| Plot tree-pairs (methods) | plotPairs,ExpressionSet-method plotPairs,matrix-method plotPairs,missing-method plotPairs-methods |
| Quantile normalization | quantileNormalize |
| Quantile normalization (methods) | quantileNormalize,ExpressionSet,ExpressionSet-method quantileNormalize,ExpressionSet,missing-method quantileNormalize,ExpressionSet,vector-method quantileNormalize,matrix,missing-method quantileNormalize,missing,missing-method quantileNormalize,vector,ExpressionSet-method quantileNormalize,vector,missing-method quantileNormalize,vector,vector-method quantileNormalize-methods |
| Read NimbleGen design files | readDesign |
| Read NimbleGen design files (methods) | readDesign,character,character,character-method readDesign,character,character,ExpressionSet-method readDesign,missing,missing,missing-method readDesign,vector,missing,missing-method readDesign,vector,vector,missing-method readDesign-methods |
| Read Nimblegen .pair files | readPairs |
| Read Nimblegen .pair files (methods) | readPairs,character,character,character-method readPairs,character,character,ExpressionSet-method readPairs,missing,missing,missing-method readPairs,vector,missing,missing-method readPairs,vector,vector,missing-method readPairs-methods |
| Read sample key | readSampleKey |
