Files in kendomaniac/CASC
rCASC reproducible Classification Analysis of Single Cell Sequencing Data

.Rbuildignore
.Rproj.user/62455A5D/build_options
.Rproj.user/62455A5D/console06/INDEX001
.gitignore
CASC.Rproj
DESCRIPTION
LICENSE
NAMESPACE
R/SCannoByGtf.R R/anovaLike.R R/bootstrapsVideo.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/clustersFeatures.R R/counts2log.R R/crossLabel.R R/csvToSparse.R R/deDetection.R R/deTwoGroups.R R/deltaFilter.R R/demultiplexing.R R/dimensions.R R/downloadContainers.R R/fasterq.dump.R R/fastqc.R R/filterZeros.R R/genesUmi.R R/griphBootstrap.R R/h5tocsv.R R/hfc.R R/houseKeep.R R/impute.R R/indropCounts.R R/indropIndex.R R/lorenzFilter.R R/mergeMatrix.R R/mitoriboumi.R R/nClusterEvaluationSIMLR.R R/permAnalysis.R R/permAnalysisGriph.R R/permAnalysisSeurat.R R/permutationClustering.R R/permutationMovie.R R/recatPrediction.R R/runDocker.R R/scanpyBootstrap.R R/scanpyPermutation.R R/scnorm.R R/seuratBootstrap.R R/seuratPermutation.R R/seuratpcaeval.R R/seuratprior.R R/simlrBootstrap.R R/simlrGeneProritization.R R/simlrGenesSelection.R R/splitClusters.R R/subSetCell.R R/testDocker.R R/topX.R R/tsneBootstrap.R R/umiNormalization.R R/unstableFiltering.R README.md
casc_workflow.png
docs/LICENSE-text.html
docs/_pkgdown.yaml
docs/articles/index.html
docs/articles/rCASC_vignette.html
docs/authors.html
docs/docsearch.css
docs/docsearch.js
docs/index.html
docs/inst/img/Ziegenhain2017.jpeg
docs/inst/img/bootstrapsVideo_2.jpeg
docs/inst/img/buettner_raw_ccremover.jpeg
docs/inst/img/c2_connected.png
docs/inst/img/checkCountDepth0.jpg
docs/inst/img/counts_effect1.png
docs/inst/img/filterZero.jpeg
docs/inst/img/geneselection.jpeg
docs/inst/img/griph1.png
docs/inst/img/griph2.png
docs/inst/img/griph3.jpeg
docs/inst/img/griph4.jpeg
docs/inst/img/gui1.png
docs/inst/img/gui10.png
docs/inst/img/gui11.png
docs/inst/img/gui12.png
docs/inst/img/gui13.png
docs/inst/img/gui14.png
docs/inst/img/gui15.png
docs/inst/img/gui16.png
docs/inst/img/gui17.png
docs/inst/img/gui18.png
docs/inst/img/gui19.png
docs/inst/img/gui2.png
docs/inst/img/gui20.png
docs/inst/img/gui21.png
docs/inst/img/gui22.png
docs/inst/img/gui23.png
docs/inst/img/gui23a.png
docs/inst/img/gui24.png
docs/inst/img/gui25.png
docs/inst/img/gui26.png
docs/inst/img/gui27.png
docs/inst/img/gui28.png
docs/inst/img/gui3.png
docs/inst/img/gui4.png
docs/inst/img/gui5.png
docs/inst/img/gui6.png
docs/inst/img/gui7.png
docs/inst/img/gui8.png
docs/inst/img/gui9.png
docs/inst/img/hfc1.jpeg
docs/inst/img/indrop_v2.jpeg
docs/inst/img/indropv2.jpg
docs/inst/img/lorenz_filter.jpg
docs/inst/img/mitoRiboUmi.png
docs/inst/img/noMT-rib.png
docs/inst/img/pace_1.jpeg
docs/inst/img/pace_2.jpeg
docs/inst/img/rcasc_workflow.jpg
docs/inst/img/recat1.jpeg
docs/inst/img/scnorm.jpeg
docs/inst/img/seq_depth.jpeg
docs/inst/img/seurat01.png
docs/inst/img/seurat02.png
docs/inst/img/simlr_2.jpeg
docs/inst/img/simlr_3.jpeg
docs/inst/img/simlr_4.jpeg
docs/inst/img/simlr_5.jpeg
docs/link.svg
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/anovaLike.html
docs/reference/bootstrapsVideo.html
docs/reference/ccRemove.html
docs/reference/cellCycle2.html
docs/reference/cellrangerCount.html
docs/reference/checkCountDepth.html
docs/reference/clusterIdentification.html
docs/reference/clusterNgriph.html
docs/reference/clusterReorg.html
docs/reference/clustersFeatures.html
docs/reference/counts2log.html
docs/reference/crossLabel.html
docs/reference/deDetection.html
docs/reference/deltaFilter.html
docs/reference/demultiplexing.html
docs/reference/dockerTest.html
docs/reference/downloadContainers.html
docs/reference/fastqc.html
docs/reference/filterZeros.html
docs/reference/genesPrioritization.html
docs/reference/genesSelection.html
docs/reference/genesUmi.html
docs/reference/h5tocvs.html
docs/reference/hfc.html
docs/reference/houseKeep.html
docs/reference/impute.html
docs/reference/index.html
docs/reference/indropCounts.html
docs/reference/indropIndex.html
docs/reference/lorenzFilter.html
docs/reference/mitoRiboUmi.html
docs/reference/nClusterEvaluationSIMLR.html
docs/reference/permAnalysis.html
docs/reference/permAnalysisSeurat.html
docs/reference/permutationClustering.html
docs/reference/permutationMovie.html
docs/reference/recatPrediction.html
docs/reference/runDocker.html
docs/reference/scannobyGtf.html
docs/reference/scnorm.html
docs/reference/seuratBootstrap.html
docs/reference/seuratPCAEval.html
docs/reference/seuratPermutation.html
docs/reference/seuratPrior.html
docs/reference/simlrBootstrap.html
docs/reference/sraDownload.html
docs/reference/topx.html
docs/reference/tsneBootstrap.html
docs/reference/umiNorm.html
inst/containers/containers.txt
inst/containers/mini.txt
inst/examples/4t1_counts.txt
inst/examples/SampleSheet.csv
inst/examples/mb231_counts.txt
inst/examples/readme.txt
inst/extras/indrop.yaml
inst/extras/starchip-circles.params
inst/img/PCE_bowPlot.png
inst/img/Untitled.jpeg
inst/img/Ziegenhain2017.jpeg
inst/img/barron2016.jpeg
inst/img/bootstrapsVideo_2.jpeg
inst/img/bootstrapsvideo_1.jpeg
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
inst/img/c2_connected.png
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/checkCountDepth0.jpeg
inst/img/checkCountDepth0.jpg
inst/img/counts_effect1.jpeg
inst/img/counts_effect1.png
inst/img/filterZero.jpeg
inst/img/filtercounts.jpeg
inst/img/geneRank.jpeg
inst/img/genesUMI.jpeg
inst/img/genesUMI.jpg
inst/img/geneselection.jpeg
inst/img/griph1.jpeg
inst/img/griph1.png
inst/img/griph2.jpeg
inst/img/griph2.png
inst/img/griph3.jpeg
inst/img/griph4.jpeg
inst/img/gui1.png
inst/img/gui10.png
inst/img/gui11.png
inst/img/gui12.png
inst/img/gui13.png
inst/img/gui14.png
inst/img/gui15.png
inst/img/gui16.png
inst/img/gui17.png
inst/img/gui18.png
inst/img/gui19.png
inst/img/gui2.png
inst/img/gui20.png
inst/img/gui21.png
inst/img/gui22.png
inst/img/gui23.png
inst/img/gui23a.png
inst/img/gui24.png
inst/img/gui25.png
inst/img/gui26.png
inst/img/gui27.png
inst/img/gui28.png
inst/img/gui3.png
inst/img/gui4.png
inst/img/gui5.png
inst/img/gui6.png
inst/img/gui7.png
inst/img/gui8.png
inst/img/gui9.png
inst/img/hfc1.jpeg
inst/img/indrop_v2.jpeg
inst/img/indropv2.jpeg
inst/img/indropv2.jpg
inst/img/indropv3.jpeg
inst/img/indropv3.jpg
inst/img/jaccard.jpeg
inst/img/lorenz1.jpeg
inst/img/lorenz2.jpeg
inst/img/lorenz_filter.jpeg
inst/img/lorenz_filter.jpg
inst/img/mitoRiboUmi.png
inst/img/noMT-rib.jpg
inst/img/noMT-rib.png
inst/img/noMT.jpg
inst/img/ola_2i_bayes.png
inst/img/pace_1.jpeg
inst/img/pace_2.jpeg
inst/img/rCASC_logo.png
inst/img/rCASC_workflow.jpeg
inst/img/rcasc_workflow.jpg
inst/img/rcasc_workflow.png
inst/img/recat1.jpeg
inst/img/scnorm.jpeg
inst/img/searchStability.pdf
inst/img/seq_depth.jpeg
inst/img/seq_depth.png
inst/img/seurat01.png
inst/img/seurat02.png
inst/img/silhouette.jpeg
inst/img/silhouette.stability.jpg
inst/img/silhouette1.jpeg
inst/img/simlr.jpeg
inst/img/simlr1.jpeg
inst/img/simlr_1.jpeg
inst/img/simlr_2.jpeg
inst/img/simlr_3.jpeg
inst/img/simlr_4.jpeg
inst/img/simlr_5.jpeg
inst/img/workflows_comparison.png
man/SCannoByGtf.Rd man/anovaLike.Rd man/bootstrapsVideo.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/clustersFeatures.Rd man/counts2log.Rd man/crossLabel.Rd man/csvToSparse.Rd man/deDetection.Rd man/deTwoGroups.Rd man/deltaFilter.Rd man/demultiplexing.Rd man/dimensions.Rd man/dockerTest.Rd man/downloadContainers.Rd man/fastqc.Rd man/filterZeros.Rd man/genesPrioritization.Rd man/genesSelection.Rd man/genesUmi.Rd man/griphBootstrap.Rd man/h5tocsv.Rd man/hfc.Rd man/houseKeep.Rd man/impute.Rd man/indropCounts.Rd man/indropIndex.Rd man/lorenzFilter.Rd man/mergeMatrix.Rd man/mitoRiboUmi.Rd man/nClusterEvaluationSIMLR.Rd man/permAnalysis.Rd man/permAnalysisGriph.Rd man/permAnalysisSeurat.Rd man/permutationClustering.Rd man/permutationMovie.Rd man/recatPrediction.Rd man/runDocker.Rd man/scanpyBootstrap.Rd man/scanpyPermutation.Rd man/scnorm.Rd man/seuratBootstrap.Rd man/seuratPCAEval.Rd man/seuratPermutation.Rd man/seuratPrior.Rd man/simlrBootstrap.Rd man/splitClusters.Rd man/sraDownload.Rd man/subSetCell.Rd man/topx.Rd man/tsneBootstrap.Rd man/umiNorm.Rd man/unstableFiltering.Rd
rCASC.Rproj
vignettes/rCASC_vignette.Rmd
kendomaniac/CASC documentation built on July 18, 2019, 9:28 a.m.