Files in saezlab/liana
LIANA: a LIgand-receptor ANalysis frAmework
.Rbuildignore
.github/.gitignore
.github/workflows/R-CMD-check.yaml
.github/workflows/pkgdown.yaml
.gitignore
DESCRIPTION
LICENSE
NAMESPACE
NEWS.md
R/cellchat_pipe.R
R/connectome_pipe.R
R/crosstalk_funs.R
R/get_omnipath.R
R/italk_pipe.R
R/liana_aggregate.R
R/liana_call.R
R/liana_defaults.R
R/liana_ortho.R
R/liana_pipe.R
R/liana_plot.R
R/liana_prep.R
R/liana_recomplexify.R
R/liana_specs.R
R/liana_tensor.R
R/liana_utils.R
R/liana_wrapper.R
R/natmi_pipe.R
R/nonperm_funs.R
R/perm_funs.R
R/sca_pipe.R
R/squidpy_pipe.R
README.md
configure
configure.win
inst/CITATION
inst/LRdb.rda
inst/example_elbow.csv
inst/figures/liana_logo.png
inst/human_mouse_orthologues.RDS
inst/omni_resources.rds
inst/squidpy_pipe.py
inst/testdata/input/converted_seurat.rds
inst/testdata/input/sce_conv.rds
inst/testdata/input/seurat_conv.rds
inst/testdata/input/testdata.rds
inst/testdata/input/testsce.rds
inst/testdata/input/wrap_sce.rds
inst/testdata/output/cc_res.RDS
inst/testdata/output/conn_res.RDS
inst/testdata/output/conn_score.RDS
inst/testdata/output/conn_score.RDS.orig
inst/testdata/output/context_df_test.RDS
inst/testdata/output/decomp.RDS
inst/testdata/output/italk_res.RDS
inst/testdata/output/liana_agg_decomplex.RDS
inst/testdata/output/liana_aggr.RDS
inst/testdata/output/liana_constrained.RDS
inst/testdata/output/liana_cpdb.RDS
inst/testdata/output/liana_cytotalk.RDS
inst/testdata/output/liana_def_args.RDS
inst/testdata/output/liana_def_res.RDS
inst/testdata/output/liana_dotplot_out.RDS
inst/testdata/output/liana_freq_out.RDS
inst/testdata/output/liana_house_aggr.RDS
inst/testdata/output/liana_pipe.RDS
inst/testdata/output/liana_res.RDS
inst/testdata/output/liana_res_plus.RDS
inst/testdata/output/liana_spec_out.RDS
inst/testdata/output/logfc_score.RDS
inst/testdata/output/natmi_res.RDS
inst/testdata/output/natmi_score.RDS
inst/testdata/output/op_ortho.RDS
inst/testdata/output/rank_mag_example.RDS
inst/testdata/output/rank_spec_example.RDS
inst/testdata/output/recomplex.RDS
inst/testdata/output/sca_res.RDS
inst/testdata/output/sca_score.RDS
inst/testdata/output/squidpy_res.RDS
liana_env.yml
man/FormatConnectome.Rd
man/FormatNatmi.Rd
man/FormatSCA.Rd
man/FormatiTALK.Rd
man/ScoreSpecifics-class.Rd
man/assign_ligrecs.Rd
man/assign_lr_weights.Rd
man/calculate_gini.Rd
man/call_cellchat.Rd
man/call_connectome.Rd
man/call_italk.Rd
man/call_natmi.Rd
man/call_sca.Rd
man/call_squidpy.Rd
man/cellchat_formatDB.Rd
man/cellphonedb_score.Rd
man/check_if_dissociated.Rd
man/chord_freq.Rd
man/compile_ligrec.Rd
man/compute_mi_dist.Rd
man/compute_nst_from_matrix.Rd
man/compute_nst_scores.Rd
man/compute_pem_scores.Rd
man/conn_formatDB.Rd
man/cytotalk_score.Rd
man/decomplexify.Rd
man/decompose_tensor.Rd
man/dot-antilog1m.Rd
man/dot-rank_matrix.Rd
man/dot-sp_costrain.Rd
man/filter_nonabundant_celltypes.Rd
man/generate_homologs.Rd
man/generate_lr_geneset.Rd
man/generate_orthologs.Rd
man/genesymbol_to_uniprot.Rd
man/get_abundance_summary.Rd
man/get_c2c_factors.Rd
man/get_cellcall.Rd
man/get_cellchat_missing.Rd
man/get_connectome.Rd
man/get_curated_omni.Rd
man/get_homologene_dict.Rd
man/get_logfc.Rd
man/get_lr_resources.Rd
man/get_natmi.Rd
man/get_partners.Rd
man/get_permutations.Rd
man/get_sca.Rd
man/get_up_dict.Rd
man/heat_freq.Rd
man/join_means.Rd
man/liana_aggregate.Rd
man/liana_bysample.Rd
man/liana_call.Rd
man/liana_defaults.Rd
man/liana_dotplot.Rd
man/liana_heatmap.Rd
man/liana_message.Rd
man/liana_pipe.Rd
man/liana_prep.Rd
man/liana_scores.Rd
man/liana_tensor_c2c.Rd
man/liana_wrap.Rd
man/map_custom.Rd
man/mean0.Rd
man/mean_permute.Rd
man/min0.Rd
man/minmax.Rd
man/omnipath_partners.Rd
man/plot_abundance_summary.Rd
man/plot_c2c_cells.Rd
man/plot_c2c_overview.Rd
man/plot_context_boxplot.Rd
man/plot_context_heat.Rd
man/plot_lr_heatmap.Rd
man/preprocess_scores.Rd
man/rank_aggregate.Rd
man/rank_method.Rd
man/recode.character2.Rd
man/recomplexify.Rd
man/sca_formatDB.Rd
man/select_resource.Rd
man/show_homologene.Rd
man/show_methods.Rd
man/show_resources.Rd
pkgdown/_pkgdown.yml
pkgdown/extra.css
pkgdown/favicon/android-chrome-192x192.png
pkgdown/favicon/android-chrome-512x512.png
pkgdown/favicon/apple-touch-icon.png
pkgdown/favicon/browserconfig.xml
pkgdown/favicon/favicon-16x16.png
pkgdown/favicon/favicon-32x32.png
pkgdown/favicon/favicon.ico
pkgdown/favicon/favicon.svg
pkgdown/favicon/mstile-150x150.png
pkgdown/favicon/safari-pinned-tab.svg
pkgdown/favicon/site.webmanifest
tests/testthat.R
tests/testthat/test-call_cellchat.R
tests/testthat/test-call_connectome.R
tests/testthat/test-call_italk.R
tests/testthat/test-call_natmi.R
tests/testthat/test-call_sca.R
tests/testthat/test-call_squidpy.R
tests/testthat/test-liana_aggr.R
tests/testthat/test-liana_cpdb.R
tests/testthat/test-liana_cytotalk.R
tests/testthat/test-liana_pipe.R
tests/testthat/test-liana_plot.R
tests/testthat/test-liana_prep.R
tests/testthat/test-liana_tensor.R
tests/testthat/test-liana_utils.R
tests/testthat/test-liana_wrap.R
vignettes/liana_cc2tensor.Rmd
vignettes/liana_custom_op.Rmd
vignettes/liana_devel.Rmd
vignettes/liana_nichenet.Rmd
vignettes/liana_nichenet.svg
vignettes/liana_ortho.Rmd
vignettes/liana_tutorial.Rmd
vignettes/ligrec_pipe.png
