Files in jlaffy/scalop

Single Cell Analysis Operations

.Rbuildignore

.Rprofile

.gitignore

.travis.yml

DESCRIPTION

LICENSE.md

NAMESPACE

R/AllGenerics.R R/GGsave.R R/GeneInfo.R R/Markers_Normal.R R/NormalBrainSignatures2.R R/NormalBrainSignatures3.R R/NormalSignatures.R R/Overlap.R R/Signatures_Gavish2023.R R/Unlist.R R/add_to_dataframe.R R/aggr_dup_genes.R R/all-stats.R R/annomap.R R/as_bulk.R R/as_four_state_gbm.R R/assign_bulk_states.R R/bin.R R/cluster.methods.R R/col_subset.R R/combine_group2_dea.R R/comply.R R/cor.methods.R R/cpm.R R/data.R R/dea.R R/deaOrder.R R/discrete_colours-data.R R/dist.methods.R R/doubletCells.R R/enricher.R R/ensembl2symbol.R R/filter_signatures.R R/fitBimodal.R R/flip.R R/foldchange.R R/futurama-data.R R/geneLength.R R/genericModel.R R/getGRCh.R R/get_signatures.R R/get_snn_graph_clusters.R R/ggdensity.R R/ggmap.R R/ggoutliers.R R/ggpubr-data.R R/ggraster.R R/ggvolcano.R R/gmap.R R/graster.R R/grombine.R R/grouped_reorder.R R/grouped_rowcenter.R R/hca.R R/hierarchy.R R/hms_span.R R/id2many.R R/jacFilt.R R/jaccard.R R/jacmap.R R/ldcast.R R/logRowMeans.R R/logcpm.R R/logtpm.R R/map_genes.R R/mat01.R R/matrix-ops.R R/maxcol_strict.R R/metaprograms.R R/msigdb.R R/nSigGenes.R R/ntop.R R/ohmySNNclusters.R R/ohmyqc.R R/ohmytsne.R R/outliers.R R/pairup.R R/pal19-data.R R/pal28-data.R R/palBuRd-data.R R/palG34R-data.R R/pca.R R/plot_hierarchy.R R/program_variability.R R/programs.R R/qc.R R/range_rowmeans.R R/row_subset.R R/rowttests-methods.R R/sample_strict.R R/scdata.R R/score.R R/setColNames.R R/setRowNames.R R/sigScores.R R/simpsons-data.R R/state_fractions.R R/state_high_genes.R R/subsplit.R R/substri.R

R/sysdata.rda

R/textxy.R R/theme_scalop.R R/tpm.R R/unique_sample_names.R R/unlogcpm.R R/unlogtpm.R R/utils-bin.R R/utils-fitBimodal.R R/utils-grombine.R R/utils-hca.R R/utils.R R/vannomap.R R/volcano_plot.R R/wilcoxtest.R

data/MGH136.rda

data/Markers_Normal.rda

data/NormalBrainSignatures.rda

data/NormalBrainSignatures2.rda

data/NormalBrainSignatures3.rda

data/NormalSignatures.rda

data/SignaturesList.rda

data/Signatures_Campbell2017.rda

data/Signatures_GBM.rda

data/Signatures_Gavish2023.rda

data/Signatures_H3_K27M.rda

data/Signatures_Habib2016.rda

data/Signatures_IDH_A.rda

data/Signatures_IDH_O.rda

data/Signatures_Melanoma.rda

data/Signatures_Pollen2015.rda

data/Signatures_TCGA_GBM.rda

data/Signatures_TabulaMuris2016.rda

data/cluster.methods.rda

data/cor.methods.rda

data/discrete_colours.rda

data/dist.methods.rda

data/ensembl2symbol.rda

data/futurama.rda

data/ggpubr.rda

data/pal19.rda

data/pal28.rda

data/palBuRd.rda

data/palG34R.rda

data/scdata.rda

data/simpsons.rda

data/skG34R.HTAPP.rda

data/skG34R.rda

docs/.nojekyll

docs/404.html

docs/LICENSE-text.html

docs/LICENSE.html

docs/articles/01_intra_tumour_programs.html

docs/articles/02_MGH136_programs_the_real_deal.html

docs/articles/index.html

docs/articles/old_01.html

docs/articles/old_01_files/figure-html/unnamed-chunk-7-1.png

docs/articles/recreate_gbm_metaprograms.html

docs/articles/recreate_gbm_metaprograms_files/figure-html/unnamed-chunk-7-1.png

docs/authors.html

docs/bootstrap-toc.css

docs/bootstrap-toc.js

docs/docsearch.css

docs/docsearch.js

docs/index.html

docs/link.svg

docs/pkgdown.css

docs/pkgdown.js

docs/pkgdown.yml

docs/reference/GeneInfo.html

docs/reference/MGH136.html

docs/reference/Markers_Normal.html

docs/reference/NormalBrainSignatures.html

docs/reference/NormalBrainSignatures2.html

docs/reference/NormalBrainSignatures3.html

docs/reference/NormalSignatures.html

docs/reference/Rplot001.png

docs/reference/Sapply.html

docs/reference/Unlist.html

docs/reference/add_to_dataframe.html

docs/reference/aggr_gene_expr.html

docs/reference/alias2ensembl.html

docs/reference/alias2entrez.html

docs/reference/alias2refseq.html

docs/reference/alias2symbol.html

docs/reference/alias2ucsc.html

docs/reference/allowedExons.html

docs/reference/annomap.html

docs/reference/as_bulk.html

docs/reference/as_bulk_samples.html

docs/reference/as_four_state_gbm.html

docs/reference/assign_bulk_states.html

docs/reference/baseScores.html

docs/reference/bin.html

docs/reference/binmatch.html

docs/reference/bootstrap_summary.html

docs/reference/bootstrapped_state_fractions.html

docs/reference/cluster.methods.html

docs/reference/col_subset.html

docs/reference/colcenter.html

docs/reference/coldetected.html

docs/reference/combine_group2_dea.html

docs/reference/comply.html

docs/reference/cor.methods.html

docs/reference/cpm.html

docs/reference/dea.html

docs/reference/dims.html

docs/reference/discrete_colours-1.png

docs/reference/discrete_colours.html

docs/reference/dist.methods.html

docs/reference/doubletCells.html

docs/reference/enricher.html

docs/reference/ensembl2symbol.html

docs/reference/entrez2alias.html

docs/reference/entrez2ensembl.html

docs/reference/entrez2refseq.html

docs/reference/entrez2symbol.html

docs/reference/entrez2ucsc.html

docs/reference/expr_housekeeping.html

docs/reference/filter_signatures.html

docs/reference/filter_sigs.html

docs/reference/fitBimodal.html

docs/reference/flip.html

docs/reference/foldchange.html

docs/reference/frac_mito.html

docs/reference/futurama-1.png

docs/reference/futurama.html

docs/reference/geneLength.html

docs/reference/genericModel.html

docs/reference/getGRCh.html

docs/reference/get_ensembl.html

docs/reference/get_entrez.html

docs/reference/get_genes.html

docs/reference/get_refseq.html

docs/reference/get_signatures.html

docs/reference/get_snn_graph_clusters.html

docs/reference/get_symbols.html

docs/reference/get_ucsc.html

docs/reference/ggDensity.html

docs/reference/ggmap.html

docs/reference/ggoutliers.html

docs/reference/ggpubr-1.png

docs/reference/ggpubr.html

docs/reference/ggvolcano.html

docs/reference/gmap.html

docs/reference/graster.html

docs/reference/grombine.html

docs/reference/grouped_reorder.html

docs/reference/grouped_rowcenter.html

docs/reference/hca.html

docs/reference/headl.html

docs/reference/headr.html

docs/reference/hierarchy.html

docs/reference/hms_span.html

docs/reference/index.html

docs/reference/is_accnum.html

docs/reference/is_alias.html

docs/reference/is_annotation.html

docs/reference/is_ensembl.html

docs/reference/is_entrez.html

docs/reference/is_refseq.html

docs/reference/is_symbol.html

docs/reference/is_ucsc.html

docs/reference/jacFilt.html

docs/reference/jaccard.html

docs/reference/jacmap.html

docs/reference/ldcast.html

docs/reference/logRowMeans.html

docs/reference/logcpm.html

docs/reference/map_alias.html

docs/reference/map_ensembl.html

docs/reference/map_entrez.html

docs/reference/map_genes.html

docs/reference/map_refseq.html

docs/reference/map_symbol.html

docs/reference/markerScores.html

docs/reference/mat01.html

docs/reference/maxcol_strict.html

docs/reference/metaprograms.html

docs/reference/msigdb.html

docs/reference/nSigGenes.html

docs/reference/ncols.html

docs/reference/nrows.html

docs/reference/ntop.html

docs/reference/ohmySNNclusters.html

docs/reference/ohmyqc.html

docs/reference/ohmytsne.html

docs/reference/outliers.html

docs/reference/overlap.html

docs/reference/pairup.html

docs/reference/pal19-1.png

docs/reference/pal19.html

docs/reference/pal28-1.png

docs/reference/pal28.html

docs/reference/palG34R-1.png

docs/reference/palG34R.html

docs/reference/pca.html

docs/reference/pipe.html

docs/reference/plot_hierarchy.html

docs/reference/programs.html

docs/reference/range_rowmeans.html

docs/reference/refseq2alias.html

docs/reference/refseq2ensembl.html

docs/reference/refseq2entrez.html

docs/reference/refseq2symbol.html

docs/reference/refseq2ucsc.html

docs/reference/row_subset.html

docs/reference/rowcenter.html

docs/reference/rowdetected.html

docs/reference/sample_strict.html

docs/reference/scdata.html

docs/reference/score.html

docs/reference/setColNames.html

docs/reference/setRowNames.html

docs/reference/sigScores.html

docs/reference/simpsons-1.png

docs/reference/simpsons.html

docs/reference/state_fractions.html

docs/reference/state_high_genes.html

docs/reference/subsplit.html

docs/reference/substri.html

docs/reference/symbol2alias.html

docs/reference/symbol2ensembl.html

docs/reference/symbol2entrez.html

docs/reference/symbol2refseq.html

docs/reference/symbol2ucsc.html

docs/reference/taill.html

docs/reference/tailr.html

docs/reference/theme_scalop.html

docs/reference/totalExons.html

docs/reference/tpm.html

docs/reference/ucsc2alias.html

docs/reference/ucsc2ensembl.html

docs/reference/ucsc2entrez.html

docs/reference/ucsc2refseq.html

docs/reference/ucsc2symbol.html

docs/reference/unique_sample_names.html

docs/reference/unlogcpm.html

docs/reference/unlogtpm.html

docs/reference/unpack-assign-back.html

docs/reference/unpack-assign.html

docs/reference/vannomap.html

docs/reference/which_annotation.html

docs/reference/wilcoxtest.html

docs/reference/x2y.html

docs/sitemap.xml

extdata/Brain_Non-Myeloid_Marker_Genes.R

extdata/README

img/DEA.jpg

img/DEA.pdf img/MGH136_clustersNoCutoff.pdf img/Picture1.pdf

inst/CITATION

man/GeneInfo.Rd man/MGH136.Rd man/Markers_Normal.Rd man/NormalBrainSignatures2.Rd man/NormalBrainSignatures3.Rd man/NormalSignatures.Rd man/Sapply.Rd man/Unlist.Rd man/add_to_dataframe.Rd man/aggr_dup_genes.Rd man/aggr_gene_expr.Rd man/alias2ensembl.Rd man/alias2entrez.Rd man/alias2refseq.Rd man/alias2symbol.Rd man/alias2ucsc.Rd man/allowedExons.Rd man/annomap.Rd man/as_bulk.Rd man/as_bulk_samples.Rd man/as_four_state_gbm.Rd man/assign_bulk_states.Rd man/baseScores.Rd man/bin.Rd man/binmatch.Rd man/bootstrap_summary.Rd man/bootstrapped_state_fractions.Rd man/cluster.methods.Rd man/col_subset.Rd man/colcenter.Rd man/coldetected.Rd man/combine_group2_dea.Rd man/comply.Rd man/cor.methods.Rd man/cpm.Rd man/dea.Rd man/dims.Rd man/discrete_colours.Rd man/dist.methods.Rd man/doubletCells.Rd man/enricher.Rd man/ensembl2symbol.Rd man/entrez2alias.Rd man/entrez2ensembl.Rd man/entrez2refseq.Rd man/entrez2symbol.Rd man/entrez2ucsc.Rd man/expr_housekeeping.Rd man/filter_signatures.Rd man/filter_sigs.Rd man/fitBimodal.Rd man/flip.Rd man/foldchange.Rd man/frac_mito.Rd man/futurama.Rd man/geneLength.Rd man/genericModel.Rd man/getGRCh.Rd man/get_ensembl.Rd man/get_entrez.Rd man/get_genes.Rd man/get_refseq.Rd man/get_signatures.Rd man/get_snn_graph_clusters.Rd man/get_symbols.Rd man/get_ucsc.Rd man/ggDensity.Rd man/ggmap.Rd man/ggoutliers.Rd man/ggpubr.Rd man/ggvolcano.Rd man/gmap.Rd man/graster.Rd man/grombine.Rd man/grouped_reorder.Rd man/grouped_rowcenter.Rd man/hca.Rd man/headl.Rd man/headr.Rd man/hierarchy.Rd man/hms_span.Rd man/is_accnum.Rd man/is_alias.Rd man/is_annotation.Rd man/is_ensembl.Rd man/is_entrez.Rd man/is_refseq.Rd man/is_symbol.Rd man/is_ucsc.Rd man/jacFilt.Rd man/jaccard.Rd man/jacmap.Rd man/ldcast.Rd man/logRowMeans.Rd man/logcpm.Rd man/map_alias.Rd man/map_ensembl.Rd man/map_entrez.Rd man/map_genes.Rd man/map_refseq.Rd man/map_symbol.Rd man/markerScores.Rd man/mat01.Rd man/maxcol_strict.Rd man/metaprograms.Rd man/msigdb.Rd man/nSigGenes.Rd man/ncols.Rd man/nrows.Rd man/ntop.Rd man/ohmySNNclusters.Rd man/ohmyqc.Rd man/ohmytsne.Rd man/outliers.Rd man/overlap.Rd man/pairup.Rd man/pal19.Rd man/pal28.Rd man/palG34R.Rd man/pca.Rd man/pipe.Rd man/plot_hierarchy.Rd man/programs.Rd man/range_rowmeans.Rd man/refseq2alias.Rd man/refseq2ensembl.Rd man/refseq2entrez.Rd man/refseq2symbol.Rd man/refseq2ucsc.Rd man/row_subset.Rd man/rowcenter.Rd man/rowdetected.Rd man/sample_strict.Rd man/scdata.Rd man/score.Rd man/setColNames.Rd man/setRowNames.Rd man/sigScores.Rd man/simpsons.Rd man/state_fractions.Rd man/state_high_genes.Rd man/subsplit.Rd man/substri.Rd man/symbol2alias.Rd man/symbol2ensembl.Rd man/symbol2entrez.Rd man/symbol2refseq.Rd man/symbol2ucsc.Rd man/taill.Rd man/tailr.Rd man/theme_scalop.Rd man/totalExons.Rd man/tpm.Rd man/ucsc2alias.Rd man/ucsc2ensembl.Rd man/ucsc2entrez.Rd man/ucsc2refseq.Rd man/ucsc2symbol.Rd man/unique_sample_names.Rd man/unlogcpm.Rd man/unlogtpm.Rd man/unpack-assign-back.Rd man/unpack-assign.Rd man/vannomap.Rd man/which_annotation.Rd man/wilcoxtest.Rd man/x2y.Rd

src/.gitignore

src/init.c

src/nd.c

src/rowttests.c

src/scalop.h

vignettes/.01_intra_tumour_programs.Rmd.swo

vignettes/.gitignore

vignettes/01_intra_tumour_programs.Rmd vignettes/02_MGH136_programs_the_real_deal.Rmd vignettes/old_01.Rmd

jlaffy/scalop documentation built on March 24, 2024, 9 a.m.