Introduction | Setting up demonstration data | Function organization | Mutual nearest neighbors | Overview | The new, fast method | The old, classic method | The cluster-based method | Batch rescaling | Using data subsets | Selecting genes | Restricted correction | Other utilities | Multi-batch normalization | Multi-batch PCA | Session information | References
Package: batchelor 1.29.0
Aaron Lun
batchelor: Single-Cell Batch Correction Methods
Implements a variety of methods for batch correction of single-cell (RNA sequencing) data. This includes methods based on detecting mutually nearest neighbors, as well as several efficient variants of linear regression of the log-expression values. Functions are also provided to perform global rescaling to remove differences in depth between batches, and to perform a principal components analysis that is robust to differences in the numbers of cells across batches.
Authors:
batchelor_1.29.0.tar.gz
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batchelor_1.29.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
batchelor/json (API)
| # Install 'batchelor' in R: |
| install.packages('batchelor', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:batchelor-1.29.0(bioc 3.24)batchelor-1.28.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
sequencingrnaseqsoftwaregeneexpressiontranscriptomicssinglecellbatcheffectnormalizationcpp
Last updated from:165c212df5. Checks:10 WARNING, 2 ERROR, 2 OK. Indexed: yes.
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| linux-devel-arm64 | WARNING | 493 | ||
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| source / vignettes | OK | 682 | ||
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| linux-release-x86_64 | ERROR | 663 | ||
| macos-release-arm64 | WARNING | 336 | ||
| macos-release-x86_64 | WARNING | 730 | ||
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| windows-devel | WARNING | 1472 | ||
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| windows-oldrel | WARNING | 1482 | ||
| wasm-release | OK | 993 |
Exports:applyMultiSCEbatchCorrectcheckBatchConsistencycheckIfSCEcheckRestrictionsClassicMnnParamclusterAbundanceTestclusterAbundanceVarclusterMNNconvertPCsToSCEcorrectExperimentscosineNormdivideIntoBatchesfastMNNFastMnnParamfindMutualNNintersectRowsmnnCorrectmnnDeltaVariancemultiBatchNormmultiBatchPCAnoCorrectNoCorrectParamquickCorrectreducedMNNregressBatchesRegressParamrescaleBatchesRescaleParam
Dependencies:abindassortheadbeachmatBHBiobaseBiocGenericsBiocNeighborsBiocParallelBiocSingularclicodetoolscpp11DelayedArrayDelayedMatrixStatsformatRfutile.loggerfutile.optionsgenericsGenomicRangesglueigraphIRangesirlbalambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatspkgconfigRcppResidualMatrixrlangrsvdS4ArraysS4VectorsScaledMatrixscuttleSeqinfoSingleCellExperimentsnowSparseArraysparseMatrixStatsSummarizedExperimentvctrsXVector
Correcting batch effects in single-cell RNA-seq data
Last update: 2021-04-07
Started: 2019-02-11
Extending dispatch to more batch correction methods
Overview | Setting up | Deriving a BatchelorParam subclass | Defining a batchCorrect method | Input | Output | Demonstration | Session information
Last update: 2019-11-02
Started: 2019-02-11
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Apply function over multiple SingleCellExperiments | applyMultiSCE |
| Batch correction methods | batchCorrect batchCorrect,ClassicMnnParam-method batchCorrect,FastMnnParam-method batchCorrect,NoCorrectParam-method batchCorrect,RegressParam-method batchCorrect,RescaleParam-method |
| Using restriction | batchelor-restrict |
| BatchelorParam methods | BatchelorParam-class ClassicMnnParam ClassicMnnParam-class FastMnnParam FastMnnParam-class NoCorrectParam NoCorrectParam-class RegressParam RegressParam-class RescaleParam RescaleParam-class |
| Check batch inputs | checkBatchConsistency checkIfSCE checkRestrictions |
| Cluster-based MNN | clusterMNN |
| Convert corrected PCs to a SingleCellExperiment | convertPCsToSCE |
| Correct SingleCellExperiment objects | correctExperiments |
| Cosine normalization | cosineNorm |
| Cluster-based correction diagnostics | clusterAbundanceTest clusterAbundanceVar diagnostics-cluster |
| Divide into batches | divideIntoBatches |
| Fast mutual nearest neighbors correction | fastMNN |
| Take the intersection of rows across batches | intersectRows |
| Mutual nearest neighbors correction | mnnCorrect |
| Computes the variance of the paired MNN deltas | mnnDeltaVariance |
| Per-batch scaling normalization | multiBatchNorm |
| Multi-batch PCA | multiBatchPCA |
| No correction | noCorrect |
| Quickly perform batch correction | quickCorrect |
| MNN correction in reduced dimensions | reducedMNN |
| Regress out batch effects | regressBatches |
| Scale counts across batches | rescaleBatches |
