Files in kendomaniac/CASC

rCASC reproducible Classification Analysis of Single Cell Sequencing Data

.DS_Store

.Rbuildignore

.Rproj.user/62455A5D/build_options

.Rproj.user/62455A5D/console06/INDEX001

.gitignore

CASC.Rproj

DESCRIPTION

LICENSE

NAMESPACE

R/BCsc_function.R R/BCsc_wrapper.R R/SCannoByGtf.R R/SHARPBootstrap.R R/anovaLike.R R/autoAnalysis.R R/autoClusters.R R/autoFeature.R R/autoanalysis4Clustering.R R/autocluster4clustering.R R/autoencoder.R R/autoencoder4Pseudobulk.R R/autoencoder4clustering.R R/autoencoderDB.R R/autoencoderforclusteringgpu.R R/bootstrapsVideo.R R/bulkClusters.R R/ccRemove.R R/cellCycle_2.R R/cellrangerIndexing.R R/cellranger_count.R R/checkCountDepth.R R/clusterIdentification.R R/clusterNgriph.R R/clusterReorg.R R/clusterStability.R R/clusteringWA_Wrapper.R R/clustering_WADB_wrapper.R R/clustersFeatures.R R/cometSC2.R R/cometsc.R R/counts2log.R R/crossLabel.R R/csvToSparse.R R/deDetection.R R/dePblkae.R R/deTwoGroups.R R/deepClustering.R R/deltaFilter.R R/demultiplexing.R R/dimensions.R R/downloadContainers.R R/fasterq.dump.R R/fastqc.R R/filterZeros.R R/geneVisualization.R R/geneVisualization2.R R/geneVisualizationSpatial.R R/genesUmi.R R/gibbscluster.R R/griphBootstrap.R R/gsea.R R/h5tocsv.R R/harmony.R R/hfc.R R/houseKeep.R R/impute.R R/indropCounts.R R/indropIndex.R R/integrationCircos.R R/integrationPblk.R R/integrationPblkae.R R/logTransform.R R/lorenzFilter.R R/mergeMatrix.R R/mitoriboumi.R R/mixcr.R R/mixmodels.R R/nClusterEvaluationSIMLR.R R/permAnalysis.R R/permAnalysisGriph.R R/permAnalysisSeurat.R R/permutationClustering.R R/permutationClusteringSHARP.R R/permutationMovie.R R/recatPrediction.R R/runDocker.R R/saver.R R/scAtomic.R R/scanpyBootstrap.R R/scanpyPermutation.R R/schcl.R R/scnorm.R R/seuratBootstrap.R R/seuratIntegration.R R/seuratIntegrationMulti.R R/seuratIntegrationPermutation.R R/seuratPermutation.R R/seurat_cCycle.R R/seuratpcaeval.R R/seuratprior.R R/simlrBootstrap.R R/simlrGeneProritization.R R/simlrGenesSelection.R R/slogos.R R/spatialAnalysis.R R/spatialAnalysisPlus.R R/spatialPipe.R R/splitClusters.R R/subSetCell.R R/testDocker.R R/topX.R R/toprnk.R R/tsneBootstrap.R R/umap.R R/umiNormalization.R R/unstableFiltering.R R/vioHTMLbyGenes.R R/wrapperAutoencoder.R R/wrapperClustersIntegration.R R/wrapperMixModelsUmap.R README.md

docs/.DS_Store

docs/404.html

docs/LICENSE-text.html

docs/_pkgdown.yaml

docs/articles/fig1.png

docs/articles/index.html

docs/articles/rCASC_vignette.html

docs/articles/rCASC_vignette_files/accessible-code-block-0.0.1/empty-anchor.js

docs/articles/rCASC_vignette_files/header-attrs-2.11/header-attrs.js

docs/authors.html

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docs/inst/img/5clusters.png

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docs/inst/img/cellrangeIndex.png

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docs/reference/cometsc.html

docs/reference/cometsc2.html

docs/reference/counts2log.html

docs/reference/crossLabel.html

docs/reference/csvToSparse.html

docs/reference/deDetection.html

docs/reference/dePblkae.html

docs/reference/deTwoGroups.html

docs/reference/deepClustering.html

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docs/reference/dimensions.html

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docs/reference/downloadContainers.html

docs/reference/fastqc.html

docs/reference/filterZeros.html

docs/reference/geneVisualization.html

docs/reference/geneVisualization2.html

docs/reference/geneVisualizationSpatial.html

docs/reference/genesPrioritization.html

docs/reference/genesSelection.html

docs/reference/genesUmi.html

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docs/reference/hfc.html

docs/reference/houseKeep.html

docs/reference/impute.html

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docs/reference/indropCounts.html

docs/reference/indropIndex.html

docs/reference/integrationCircos.html

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docs/reference/integrationPsblk.html

docs/reference/logTransform.html

docs/reference/lorenzFilter.html

docs/reference/mergeMatrix.html

docs/reference/mitoRiboUmi.html

docs/reference/mixcr.html

docs/reference/mixmodels.html

docs/reference/nClusterEvaluationSIMLR.html

docs/reference/permAnalysis.html

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docs/reference/permAnalysisSeurat.html

docs/reference/permutationClustering.html

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docs/reference/seuratPrior.html

docs/reference/seurat_ccycle.html

docs/reference/sharpBootstrap.html

docs/reference/simlrBootstrap.html

docs/reference/slogosR.html

docs/reference/spatialAnalysis.html

docs/reference/spatialAnalysis2.html

docs/reference/splitClusters.html

docs/reference/sraDownload.html

docs/reference/stpipeline.html

docs/reference/subSetCell.html

docs/reference/toprnk.html

docs/reference/topx.html

docs/reference/tsneBootstrap.html

docs/reference/umap.html

docs/reference/umiNorm.html

docs/reference/unstableFiltering.html

docs/reference/vioHTMLByGenes.html

docs/reference/wrapperAutoencoder.html

docs/reference/wrapperClustersIntegration.html

docs/reference/wrapperMixModelsUmap.html

docs/sitemap.xml

fig1.png

inst/.DS_Store

inst/containers/containers.txt

inst/containers/mini.txt

inst/containers/nano.txt

inst/containers/sca_only.txt

inst/examples/4t1_counts.txt

inst/examples/Esempio.tar.xz

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inst/examples/SampleSheet.csv

inst/examples/example_harmony.tar.gz

inst/examples/mb231_counts.txt

inst/examples/readme.txt

inst/examples/setA.csv.zip

inst/extras/indrop.yaml

inst/extras/starchip-circles.params

inst/img/5clusters.png

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inst/img/Ziegenhain2017.jpeg

inst/img/barron2016.jpeg

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inst/img/buettner_fig19c.jpeg

inst/img/buettner_fig19e.jpeg

inst/img/buettner_raw_ccremover.jpeg

inst/img/c1_c2_specific1.jpeg

inst/img/c1_c2_specific2.jpeg

inst/img/c1_specific1.jpeg

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inst/img/c2_disease_biofuctions.jpg

inst/img/c2_ipa_enrichment.jpg

inst/img/casc_description2.jpeg

inst/img/casc_description3.jpeg

inst/img/casc_workflow.jpeg

inst/img/cellrangeIndex.png

inst/img/checkCountDepth0.jpeg

inst/img/checkCountDepth0.jpg

inst/img/comet01.png

inst/img/counts_effect1.jpeg

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inst/img/noMT.jpg

inst/img/ola_2i_bayes.png

inst/img/pace_1.jpeg

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inst/img/recat1.jpeg

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inst/img/searchStability.pdf

inst/img/seq_depth.jpeg

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man/.DS_Store

man/BCscTool.Rd man/BCscWrapper.Rd man/anovaLike.Rd man/autoFeature.Rd man/autocluster4clustering.Rd man/autoencoder.Rd man/autoencoder4clustering.Rd man/autoencoder4clusteringGPU.Rd man/autoencoder4pseudoBulk.Rd man/autoencoderAnalysis.Rd man/autoencoderAnalysis4Clustering.Rd man/autoencoderClustering.Rd man/autoencoderDB.Rd man/bootstrapsVideo.Rd man/bulkClusters.Rd man/ccRemove.Rd man/cellCycle2.Rd man/cellrangerCount.Rd man/cellrangerIndexing.Rd man/checkCountDepth.Rd man/clusterIdentification.Rd man/clusterNgriph.Rd man/clusterReorg.Rd man/clusterStability.Rd man/clusteringWADB_Wrapper.Rd man/clusteringWA_Wrapper.Rd man/clustersFeatures.Rd man/cometsc.Rd man/cometsc2.Rd man/counts2log.Rd man/crossLabel.Rd man/csvToSparse.Rd man/deDetection.Rd man/dePblkae.Rd man/deTwoGroups.Rd man/deepClustering.Rd man/deltaFilter.Rd man/demultiplexing.Rd man/dimensions.Rd man/dockerTest.Rd man/downloadContainers.Rd man/fastqc.Rd man/filterZeros.Rd man/geneVisualization.Rd man/geneVisualization2.Rd man/geneVisualizationSpatial.Rd man/genesPrioritization.Rd man/genesSelection.Rd man/genesUmi.Rd man/gibbsR.Rd man/griphBootstrap.Rd man/gseaXLmHG.Rd man/h5tocsv.Rd man/harmony.Rd man/hfc.Rd man/houseKeep.Rd man/impute.Rd man/indropCounts.Rd man/indropIndex.Rd man/integrationCircos.Rd man/integrationPblkae.Rd man/integrationPsblk.Rd man/logTransform.Rd man/lorenzFilter.Rd man/mergeMatrix.Rd man/mitoRiboUmi.Rd man/mixcr.Rd man/mixmodels.Rd man/nClusterEvaluationSIMLR.Rd man/permAnalysis.Rd man/permAnalysisGriph.Rd man/permAnalysisSeurat.Rd man/permutationClustering.Rd man/permutationClusteringSHARP.Rd man/permutationMovie.Rd man/recatPrediction.Rd man/runDocker.Rd man/saver.Rd man/scAtomic.Rd man/scannobyGtf.Rd man/scanpyBootstrap.Rd man/scanpyPermutation.Rd man/schcl.Rd man/scnorm.Rd man/seuratBootstrap.Rd man/seuratIntegration.Rd man/seuratIntegrationMulti.Rd man/seuratIntegrationPermutation.Rd man/seuratPCAEval.Rd man/seuratPermutation.Rd man/seuratPrior.Rd man/seurat_ccycle.Rd man/sharpBootstrap.Rd man/simlrBootstrap.Rd man/slogosR.Rd man/spatialAnalysis.Rd man/spatialAnalysis2.Rd man/splitClusters.Rd man/sraDownload.Rd man/stpipeline.Rd man/subSetCell.Rd man/toprnk.Rd man/topx.Rd man/tsneBootstrap.Rd man/umap.Rd man/umiNorm.Rd man/unstableFiltering.Rd man/vioHTMLByGenes.Rd man/wrapperAutoencoder.Rd man/wrapperClustersIntegration.Rd man/wrapperMixModelsUmap.Rd

rCASC.Rproj

vignettes/fig1.png

vignettes/rCASC_vignette.Rmd

kendomaniac/CASC documentation built on June 30, 2024, 3:27 a.m.