Files in jianhaizhang/spatialHeatmap
spatialHeatmap

.Rbuildignore

.gitignore

DESCRIPTION

NAMESPACE

NEWS

R/AllClasses.R R/AllGenerics.R R/adj_mod.R R/aggr_rep.R R/cache.R R/cell_group.R R/check_data.R R/cluster_cell.R R/coclus_opt.R R/cocluster.R R/col_bar.R R/com_factor.R R/covis.R R/custom_shiny.R R/cut_dendro.R R/cvt_id.R R/data_ref.R R/database.R R/deseq2.R R/desired_bulk_shiny.R R/detect_cluster.R R/dim_color.R R/dim_color2cell.R R/dim_color_coclus.R R/dim_color_idp.R R/dim_decon.R R/dim_opt.R R/dim_srsc.R R/edgeR.R R/edit_tar.R R/filter_asg.R R/filter_cell.R R/filter_data.R R/gg_2lgd.R R/gg_lgd.R R/helper.R R/html_ly.R R/lay_shm.R R/limma.R R/list_shm.R R/matrix_hm.R R/network.R R/nn_graph.R R/nod_lin.R R/norm_cell.R R/norm_data.R R/norm_srsc.R R/opt_bar.R R/opt_setting.R R/opt_violin.R R/optimal_k.R R/path_br.R R/path_br_all.R R/plot_dim.R R/plot_kmeans.R R/process_cell_meta.R R/qc_cell.R R/read_fr.R R/read_svg.R R/reduce_dim.R R/reduce_rep.R R/refine_asg.R R/remote_asvg_data.R R/return_feature.R R/sc_qc_plot.R R/sce_sub.R R/shiny_shm.R R/shm.R R/sort_gen_con.R R/spatial_enrich.R R/spatial_hm.R R/sphm_class.R R/sphm_methods.R R/sub_na.R R/submatrix.R R/svg.R R/svg_attr.R R/svg_df.R R/svg_methods.R R/true_bulk.R R/up_dn.R R/update_feature.R R/video.R R/wng.R R/write_svg.R README.md

data/aSVG.remote.repo.rda

inst/CITATION

inst/extdata/cocluster/data/bulk_cocluster.rds

inst/extdata/cocluster/data/sc10_cocluster.rds

inst/extdata/cocluster/data/sc11_cocluster.rds

inst/extdata/cocluster/data/true_match_arab_root_cocluster.txt

inst/extdata/cocluster/slurm.tmpl

inst/extdata/cocluster/true_match_mouse_brain_cocluster.txt

inst/extdata/cocluster/true_match_mouse_kidney_cocluster.txt

inst/extdata/shinyApp/bookmarks.db

inst/extdata/shinyApp/config/config.yaml

inst/extdata/shinyApp/config/dummyfile

inst/extdata/shinyApp/data/aSVGs_shm.tar

inst/extdata/shinyApp/data/arab_organ.rds

inst/extdata/shinyApp/data/arab_root.rds

inst/extdata/shinyApp/data/arab_root_tip.rds

inst/extdata/shinyApp/data/arab_shoot.rds

inst/extdata/shinyApp/data/arab_shoot_root.rds

inst/extdata/shinyApp/data/arabidopsis.thaliana_organ_shm.svg

inst/extdata/shinyApp/data/arabidopsis.thaliana_organ_shm1.svg

inst/extdata/shinyApp/data/arabidopsis.thaliana_organ_shm2.svg

inst/extdata/shinyApp/data/arabidopsis.thaliana_root.cross_shm.svg

inst/extdata/shinyApp/data/arabidopsis.thaliana_root.ebi_shm.svg

inst/extdata/shinyApp/data/arabidopsis.thaliana_root.roottip_shm.svg

inst/extdata/shinyApp/data/arabidopsis.thaliana_shoot.root_shm.svg

inst/extdata/shinyApp/data/arabidopsis.thaliana_shoot_shm.svg

inst/extdata/shinyApp/data/bulk_mouse_cocluster.rds

inst/extdata/shinyApp/data/bulk_mouse_cocluster.txt

inst/extdata/shinyApp/data/bulk_sp.rds

inst/extdata/shinyApp/data/cell_mouse_brain.rds

inst/extdata/shinyApp/data/cell_mouse_cocluster.rds

inst/extdata/shinyApp/data/cell_mouse_cocluster.txt

inst/extdata/shinyApp/data/chicken_organ.rds

inst/extdata/shinyApp/data/count_chicken.txt

inst/extdata/shinyApp/data/count_chicken_simple.txt

inst/extdata/shinyApp/data/dat_overlay.txt

inst/extdata/shinyApp/data/data_shm.tar

inst/extdata/shinyApp/data/dummyfile

inst/extdata/shinyApp/data/expr_chicken.txt

inst/extdata/shinyApp/data/expr_mouse.txt

inst/extdata/shinyApp/data/gallus_gallus.svg

inst/extdata/shinyApp/data/homo.sapiens_brain.shiny_shm.svg

inst/extdata/shinyApp/data/homo_sapiens.brain.svg

inst/extdata/shinyApp/data/human_brain.rds

inst/extdata/shinyApp/data/maize_leaf_shm1.png

inst/extdata/shinyApp/data/maize_leaf_shm1.svg

inst/extdata/shinyApp/data/maize_leaf_shm2.png

inst/extdata/shinyApp/data/maize_leaf_shm2.svg

inst/extdata/shinyApp/data/manual_cluster_mouse_brain.txt

inst/extdata/shinyApp/data/match_mouse_brain_cocluster.txt

inst/extdata/shinyApp/data/mouse_organ.rds

inst/extdata/shinyApp/data/mouse_organ_reference.txt

inst/extdata/shinyApp/data/mus_brain_vars.txt

inst/extdata/shinyApp/data/mus_brain_vars_se.rds

inst/extdata/shinyApp/data/mus_brain_vars_se_shiny.rds

inst/extdata/shinyApp/data/mus_musculus.brain.svg

inst/extdata/shinyApp/data/mus_musculus.brain_sp.svg

inst/extdata/shinyApp/data/mus_musculus.male.svg

inst/extdata/shinyApp/data/random_data_multiple_aSVGs.txt

inst/extdata/shinyApp/data/selected_cells_with_desired_bulk.txt

inst/extdata/shinyApp/data/shiny_covis_bulk_cell_mouse_brain.rds

inst/extdata/shinyApp/data/target_arab.txt

inst/extdata/shinyApp/data/target_chicken.txt

inst/extdata/shinyApp/data/target_human.txt

inst/extdata/shinyApp/data/target_mouse.txt

inst/extdata/shinyApp/data/true_match_mouse_brain_cocluster.txt

inst/extdata/shinyApp/desired_bulk_app.R

inst/extdata/shinyApp/mouse_organ_reference.txt

inst/extdata/shinyApp/www/html/about.html

inst/extdata/shinyApp/www/html/gallery.html

inst/extdata/shinyApp/www/html/landing.html

inst/extdata/shinyApp/www/html/shm_shiny_manual.html

inst/extdata/shinyApp/www/image/ann_quick.jpg

inst/extdata/shinyApp/www/image/brain_hum.png

inst/extdata/shinyApp/www/image/busy.gif

inst/extdata/shinyApp/www/image/chicken.png

inst/extdata/shinyApp/www/image/coclus_quick.jpg

inst/extdata/shinyApp/www/image/data_svg.png

inst/extdata/shinyApp/www/image/dataset.jpg

inst/extdata/shinyApp/www/image/enrich_quick.jpg

inst/extdata/shinyApp/www/image/logo.png

inst/extdata/shinyApp/www/image/mouse.png

inst/extdata/shinyApp/www/image/mus_multi_dim.png

inst/extdata/shinyApp/www/image/organ_arab.png

inst/extdata/shinyApp/www/image/root_arab.png

inst/extdata/shinyApp/www/image/select.jpg

inst/extdata/shinyApp/www/image/shoot_arab.png

inst/extdata/shinyApp/www/image/stage_arab.png

inst/extdata/shinyApp/www/image/tailoring.jpg

inst/extdata/shinyApp/www/logo.png

inst/extdata/shinyApp/www/script.js

inst/extdata/shinyApp/www/style.css

inst/extdata/shinyApp/www/video/dummyfile

inst/script/cocluster_data.R inst/script/fun_cocluster.R inst/script/sc_spatial_data.R inst/script/shm_data.R inst/unitTests/test_adj_mod.R inst/unitTests/test_filter_data.R man/SPHM.Rd man/SPHMMethods.Rd man/SVG.Rd man/SVGMethods.Rd man/SpatialEnrichment.Rd man/aSVG.remote.repo.Rd man/adj_mod.Rd man/aggr_rep.Rd man/cell_group.Rd man/cluster_cell.Rd man/coclus_opt.Rd man/cocluster.Rd man/com_factor.Rd man/covis.Rd man/custom_shiny.Rd man/cut_dendro.Rd man/cvt_id.Rd man/data_ref.Rd man/database.Rd man/edit_tar.Rd man/filter_data.Rd man/matrix_hm.Rd man/network.Rd man/norm_cell.Rd man/norm_data.Rd man/norm_srsc.Rd man/opt_bar.Rd man/opt_setting.Rd man/opt_violin.Rd man/optimal_k.Rd man/plot_dim.Rd man/plot_kmeans.Rd man/plot_meta.Rd man/process_cell_meta.Rd man/qc_cell.Rd man/read_cache.Rd man/read_fr.Rd man/read_svg.Rd man/reduce_dim.Rd man/reduce_rep.Rd man/return_feature.Rd man/save_cache.Rd man/shiny_shm.Rd man/shm.Rd man/spatialHeatmap-package.Rd man/spatial_hm.Rd man/submatrix.Rd man/true_bulk.Rd man/update_feature.Rd man/write_svg.Rd tests/runTests.R

vignettes/bibtex.bib

vignettes/covisualize.Rmd vignettes/custom_SVGs.Rmd

vignettes/file/custom.css

vignettes/file/spatial_hm_arg.txt

vignettes/img/assign_bulk.png

vignettes/img/coclustering.jpg

vignettes/img/data_str.jpg

vignettes/img/graphical_overview_shm.jpg

vignettes/img/group_color.jpg

vignettes/img/shiny.jpg

vignettes/img/shiny.png

vignettes/img/shiny_covis.jpg

vignettes/spatialHeatmap.Rmd

jianhaizhang/spatialHeatmap documentation built on July 31, 2024, 2:59 a.m.

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jianhaizhang/spatialHeatmap
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Files in jianhaizhang/spatialHeatmap
spatialHeatmap

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jianhaizhang/spatialHeatmap spatialHeatmap

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jianhaizhang/spatialHeatmap
spatialHeatmap

Files in jianhaizhang/spatialHeatmap
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