Title: Multiple Time Series Scanner
Description: Generate interactive html reports that enable quick visual review of multiple related time series stored in a data frame. For static datasets, this can help to identify any temporal artefacts that may affect the validity of subsequent analyses. For live data feeds, regularly scheduled reports can help to pro-actively identify data feed problems or unexpected trends that may require action. The reports are self-contained and shareable without a web server.
Author: T. Phuong Quan [aut, cre] ,
University of Oxford [cph],
National Institute for Health Research [fnd]
Maintainer: T. Phuong Quan <phuong.quan@ndm.ox.ac.uk>
Diff between mantis versions 0.4.2 dated 2025-07-28 and 0.4.3 dated 2025-08-01
DESCRIPTION | 6 MD5 | 25 +-- NAMESPACE | 3 NEWS.md | 23 +- R/construct.R | 279 ++++++++++++++++++++++++++++++++++ build/vignette.rds |binary inst/doc/bespoke-reports.R |only inst/doc/bespoke-reports.Rmd |only inst/doc/bespoke-reports.html |only inst/doc/mantis.R | 66 -------- inst/doc/mantis.Rmd | 69 -------- man/bespoke_rmd_alert_results.Rd |only man/bespoke_rmd_initialise_widgets.Rd |only man/bespoke_rmd_output.Rd |only tests/testthat/test-construct.R | 6 vignettes/bespoke-reports.Rmd |only vignettes/mantis.Rmd | 69 -------- 17 files changed, 321 insertions(+), 225 deletions(-)
Title: GLCM Textures of Raster Layers
Description: Calculates grey level co-occurrence matrix (GLCM) based texture measures (Hall-Beyer (2017) <https://prism.ucalgary.ca/bitstream/handle/1880/51900/texture%20tutorial%20v%203_0%20180206.pdf>; Haralick et al. (1973) <doi:10.1109/TSMC.1973.4309314>) of raster layers using a sliding rectangular window. It also includes functions to quantize a raster into grey levels as well as tabulate a glcm and calculate glcm texture metrics for a matrix.
Author: Alexander Ilich [aut, cre]
Maintainer: Alexander Ilich <ailich@usf.edu>
Diff between GLCMTextures versions 0.6.2 dated 2025-05-22 and 0.6.3 dated 2025-08-01
DESCRIPTION | 6 +- MD5 | 8 +-- R/make_glcm.R | 84 ++++++++++++++++++------------------ inst/doc/README.html | 12 ++--- tests/testthat/test-glcm_textures.R | 35 ++++++++++++++- 5 files changed, 89 insertions(+), 56 deletions(-)
Title: An Interpretable Machine Learning-Based Automatic Clinical Score
Generator
Description: A novel interpretable machine learning-based framework to automate the development of a clinical scoring model for predefined outcomes. Our novel framework consists of six modules: variable ranking with machine learning, variable transformation, score derivation, model selection, domain knowledge-based score fine-tuning, and performance evaluation.The details are described in our research paper<doi:10.2196/21798>. Users or clinicians could seamlessly generate parsimonious sparse-score risk models (i.e., risk scores), which can be easily implemented and validated in clinical practice. We hope to see its application in various medical case studies.
Author: Feng Xie [aut, cre] ,
Yilin Ning [aut] ,
Han Yuan [aut] ,
Mingxuan Liu [aut] ,
Siqi Li [aut] ,
Ehsan Saffari [aut] ,
Bibhas Chakraborty [aut] ,
Nan Liu [aut]
Maintainer: Feng Xie <xief@u.duke.nus.edu>
This is a re-admission after prior archival of version 1.0.0 dated 2022-10-15
Diff between AutoScore versions 1.0.0 dated 2022-10-15 and 1.1.0 dated 2025-08-01
AutoScore-1.0.0/AutoScore/vignettes/Figure1.png |only AutoScore-1.1.0/AutoScore/DESCRIPTION | 35 AutoScore-1.1.0/AutoScore/MD5 | 182 AutoScore-1.1.0/AutoScore/NAMESPACE | 162 AutoScore-1.1.0/AutoScore/NEWS.md |only AutoScore-1.1.0/AutoScore/R/AutoScore.R | 1916 +++++----- AutoScore-1.1.0/AutoScore/R/AutoScore_Ordinal.R | 1730 ++++----- AutoScore-1.1.0/AutoScore/R/AutoScore_Survival.R | 1698 ++++---- AutoScore-1.1.0/AutoScore/R/bca.R |only AutoScore-1.1.0/AutoScore/R/common.R | 1808 ++++----- AutoScore-1.1.0/AutoScore/README.md |only AutoScore-1.1.0/AutoScore/build/vignette.rds |binary AutoScore-1.1.0/AutoScore/inst/CITATION | 69 AutoScore-1.1.0/AutoScore/inst/doc/brief_intro.R | 20 AutoScore-1.1.0/AutoScore/inst/doc/brief_intro.Rmd | 210 - AutoScore-1.1.0/AutoScore/inst/doc/brief_intro.html | 976 ++--- AutoScore-1.1.0/AutoScore/man/AutoScore_fine_tuning.Rd | 100 AutoScore-1.1.0/AutoScore/man/AutoScore_fine_tuning_Ordinal.Rd | 132 AutoScore-1.1.0/AutoScore/man/AutoScore_fine_tuning_Survival.Rd | 112 AutoScore-1.1.0/AutoScore/man/AutoScore_impute.Rd |only AutoScore-1.1.0/AutoScore/man/AutoScore_parsimony.Rd | 192 - AutoScore-1.1.0/AutoScore/man/AutoScore_parsimony_Ordinal.Rd | 214 - AutoScore-1.1.0/AutoScore/man/AutoScore_parsimony_Survival.Rd | 204 - AutoScore-1.1.0/AutoScore/man/AutoScore_rank.Rd | 88 AutoScore-1.1.0/AutoScore/man/AutoScore_rank_Ordinal.Rd | 96 AutoScore-1.1.0/AutoScore/man/AutoScore_rank_Survival.Rd | 98 AutoScore-1.1.0/AutoScore/man/AutoScore_testing.Rd | 102 AutoScore-1.1.0/AutoScore/man/AutoScore_testing_Ordinal.Rd | 128 AutoScore-1.1.0/AutoScore/man/AutoScore_testing_Survival.Rd | 116 AutoScore-1.1.0/AutoScore/man/AutoScore_weighting.Rd | 98 AutoScore-1.1.0/AutoScore/man/AutoScore_weighting_Ordinal.Rd | 158 AutoScore-1.1.0/AutoScore/man/AutoScore_weighting_Survival.Rd | 144 AutoScore-1.1.0/AutoScore/man/add_baseline.Rd | 38 AutoScore-1.1.0/AutoScore/man/assign_score.Rd | 38 AutoScore-1.1.0/AutoScore/man/bca.Rd |only AutoScore-1.1.0/AutoScore/man/change_reference.Rd | 38 AutoScore-1.1.0/AutoScore/man/check_data.Rd | 44 AutoScore-1.1.0/AutoScore/man/check_data_ordinal.Rd | 46 AutoScore-1.1.0/AutoScore/man/check_data_survival.Rd | 46 AutoScore-1.1.0/AutoScore/man/check_link.Rd | 32 AutoScore-1.1.0/AutoScore/man/check_predictor.Rd | 34 AutoScore-1.1.0/AutoScore/man/compute_auc_val.Rd | 74 AutoScore-1.1.0/AutoScore/man/compute_auc_val_ord.Rd | 86 AutoScore-1.1.0/AutoScore/man/compute_auc_val_survival.Rd | 74 AutoScore-1.1.0/AutoScore/man/compute_descriptive_table.Rd | 60 AutoScore-1.1.0/AutoScore/man/compute_final_score_ord.Rd | 56 AutoScore-1.1.0/AutoScore/man/compute_mauc_ord.Rd | 46 AutoScore-1.1.0/AutoScore/man/compute_multi_variable_table.Rd | 44 AutoScore-1.1.0/AutoScore/man/compute_multi_variable_table_ordinal.Rd | 58 AutoScore-1.1.0/AutoScore/man/compute_multi_variable_table_survival.Rd | 42 AutoScore-1.1.0/AutoScore/man/compute_prob_observed.Rd | 68 AutoScore-1.1.0/AutoScore/man/compute_prob_predicted.Rd | 68 AutoScore-1.1.0/AutoScore/man/compute_score_table.Rd | 42 AutoScore-1.1.0/AutoScore/man/compute_score_table_ord.Rd | 52 AutoScore-1.1.0/AutoScore/man/compute_score_table_survival.Rd | 42 AutoScore-1.1.0/AutoScore/man/compute_uni_variable_table.Rd | 44 AutoScore-1.1.0/AutoScore/man/compute_uni_variable_table_ordinal.Rd | 60 AutoScore-1.1.0/AutoScore/man/compute_uni_variable_table_survival.Rd | 42 AutoScore-1.1.0/AutoScore/man/conversion_table.Rd | 56 AutoScore-1.1.0/AutoScore/man/conversion_table_ordinal.Rd | 82 AutoScore-1.1.0/AutoScore/man/conversion_table_survival.Rd | 56 AutoScore-1.1.0/AutoScore/man/estimate_p_mat.Rd | 44 AutoScore-1.1.0/AutoScore/man/eva_performance_iauc.Rd | 36 AutoScore-1.1.0/AutoScore/man/evaluate_model_ord.Rd | 52 AutoScore-1.1.0/AutoScore/man/extract_or_ci_ord.Rd | 34 AutoScore-1.1.0/AutoScore/man/find_one_inds.Rd | 28 AutoScore-1.1.0/AutoScore/man/find_possible_scores.Rd | 38 AutoScore-1.1.0/AutoScore/man/get_cut_vec.Rd | 56 AutoScore-1.1.0/AutoScore/man/group_score.Rd | 48 AutoScore-1.1.0/AutoScore/man/induce_informative_missing.Rd | 70 AutoScore-1.1.0/AutoScore/man/induce_median_missing.Rd | 38 AutoScore-1.1.0/AutoScore/man/inv_cloglog.Rd | 28 AutoScore-1.1.0/AutoScore/man/inv_logit.Rd | 28 AutoScore-1.1.0/AutoScore/man/inv_probit.Rd | 28 AutoScore-1.1.0/AutoScore/man/make_design_mat.Rd | 32 AutoScore-1.1.0/AutoScore/man/plot_auc.Rd | 68 AutoScore-1.1.0/AutoScore/man/plot_importance.Rd | 34 AutoScore-1.1.0/AutoScore/man/plot_predicted_risk.Rd | 80 AutoScore-1.1.0/AutoScore/man/plot_roc_curve.Rd | 42 AutoScore-1.1.0/AutoScore/man/plot_survival_km.Rd | 90 AutoScore-1.1.0/AutoScore/man/print_performance_ci_survival.Rd | 54 AutoScore-1.1.0/AutoScore/man/print_performance_ordinal.Rd | 58 AutoScore-1.1.0/AutoScore/man/print_performance_survival.Rd | 50 AutoScore-1.1.0/AutoScore/man/print_roc_performance.Rd | 52 AutoScore-1.1.0/AutoScore/man/print_scoring_table.Rd | 44 AutoScore-1.1.0/AutoScore/man/sample_data.Rd | 38 AutoScore-1.1.0/AutoScore/man/sample_data_ordinal.Rd | 56 AutoScore-1.1.0/AutoScore/man/sample_data_ordinal_small.Rd | 36 AutoScore-1.1.0/AutoScore/man/sample_data_small.Rd | 38 AutoScore-1.1.0/AutoScore/man/sample_data_survival.Rd | 46 AutoScore-1.1.0/AutoScore/man/sample_data_survival_small.Rd | 46 AutoScore-1.1.0/AutoScore/man/sample_data_with_missing.Rd | 38 AutoScore-1.1.0/AutoScore/man/split_data.Rd | 84 AutoScore-1.1.0/AutoScore/man/transform_df_fixed.Rd | 38 AutoScore-1.1.0/AutoScore/vignettes/brief_intro.Rmd | 210 - 95 files changed, 7025 insertions(+), 6993 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-07-29 3.0
2024-11-14 2.0
2022-12-22 1.0
Title: Interactive Analysis of UCSC Xena Data
Description: Provides functions and a Shiny application for downloading,
analyzing and visualizing datasets from UCSC Xena
(<http://xena.ucsc.edu/>), which is a collection of UCSC-hosted public
databases such as TCGA, ICGC, TARGET, GTEx, CCLE, and others.
Author: Shixiang Wang [aut, cre] ,
Shensuo Li [aut],
Yi Xiong [aut] ,
Longfei Zhao [aut] ,
Kai Gu [aut] ,
Yin Li [aut],
Fei Zhao [aut]
Maintainer: Shixiang Wang <w_shixiang@163.com>
Diff between UCSCXenaShiny versions 2.1.0 dated 2024-05-15 and 2.2.0 dated 2025-08-01
UCSCXenaShiny-2.1.0/UCSCXenaShiny/inst/shinyapp/helper/batch_ids.md |only UCSCXenaShiny-2.1.0/UCSCXenaShiny/inst/shinyapp/helper/home_query.md |only UCSCXenaShiny-2.1.0/UCSCXenaShiny/inst/shinyapp/helper/sur_initial_group.md |only UCSCXenaShiny-2.2.0/UCSCXenaShiny/DESCRIPTION | 25 UCSCXenaShiny-2.2.0/UCSCXenaShiny/MD5 | 266 +-- UCSCXenaShiny-2.2.0/UCSCXenaShiny/NAMESPACE | 4 UCSCXenaShiny-2.2.0/UCSCXenaShiny/NEWS.md | 17 UCSCXenaShiny-2.2.0/UCSCXenaShiny/R/GeomSplitViolin.R | 5 UCSCXenaShiny-2.2.0/UCSCXenaShiny/R/analyze_gene_drug_response.R | 25 UCSCXenaShiny-2.2.0/UCSCXenaShiny/R/ccle.R | 8 UCSCXenaShiny-2.2.0/UCSCXenaShiny/R/ezcor.R | 3 UCSCXenaShiny-2.2.0/UCSCXenaShiny/R/get_pancan_value.R | 139 - UCSCXenaShiny-2.2.0/UCSCXenaShiny/R/load_data.R | 13 UCSCXenaShiny-2.2.0/UCSCXenaShiny/R/query_custom_value.R | 2 UCSCXenaShiny-2.2.0/UCSCXenaShiny/R/query_general.R | 747 +++++----- UCSCXenaShiny-2.2.0/UCSCXenaShiny/R/query_tcga_group.R | 323 ++-- UCSCXenaShiny-2.2.0/UCSCXenaShiny/R/query_value.R | 54 UCSCXenaShiny-2.2.0/UCSCXenaShiny/R/run.R | 149 + UCSCXenaShiny-2.2.0/UCSCXenaShiny/R/tcga_surv.R | 9 UCSCXenaShiny-2.2.0/UCSCXenaShiny/R/utils.R | 4 UCSCXenaShiny-2.2.0/UCSCXenaShiny/R/vis_cross.R |only UCSCXenaShiny-2.2.0/UCSCXenaShiny/R/vis_dim_dist.R | 83 - UCSCXenaShiny-2.2.0/UCSCXenaShiny/R/vis_gene_pw_cor.R | 29 UCSCXenaShiny-2.2.0/UCSCXenaShiny/R/vis_identifier.R | 23 UCSCXenaShiny-2.2.0/UCSCXenaShiny/R/vis_identifier_dim_dist.R | 316 ++-- UCSCXenaShiny-2.2.0/UCSCXenaShiny/R/vis_pancan_value.R | 210 +- UCSCXenaShiny-2.2.0/UCSCXenaShiny/R/vis_pcawg_value.R | 119 - UCSCXenaShiny-2.2.0/UCSCXenaShiny/R/vis_toil_Mut.R | 8 UCSCXenaShiny-2.2.0/UCSCXenaShiny/R/xenashiny.R | 4 UCSCXenaShiny-2.2.0/UCSCXenaShiny/R/zzz.R | 15 UCSCXenaShiny-2.2.0/UCSCXenaShiny/README.md | 30 UCSCXenaShiny-2.2.0/UCSCXenaShiny/build/vignette.rds |binary UCSCXenaShiny-2.2.0/UCSCXenaShiny/data/tcga_genome_instability.rda |binary UCSCXenaShiny-2.2.0/UCSCXenaShiny/inst/doc/api.R | 9 UCSCXenaShiny-2.2.0/UCSCXenaShiny/inst/doc/api.Rmd | 1 UCSCXenaShiny-2.2.0/UCSCXenaShiny/inst/doc/api.html | 50 UCSCXenaShiny-2.2.0/UCSCXenaShiny/inst/shinyapp/App.R | 47 UCSCXenaShiny-2.2.0/UCSCXenaShiny/inst/shinyapp/PGdata.R | 2 UCSCXenaShiny-2.2.0/UCSCXenaShiny/inst/shinyapp/app_preset.R |only UCSCXenaShiny-2.2.0/UCSCXenaShiny/inst/shinyapp/helper/add_signature.md | 6 UCSCXenaShiny-2.2.0/UCSCXenaShiny/inst/shinyapp/helper/analyze_comp_1.md | 15 UCSCXenaShiny-2.2.0/UCSCXenaShiny/inst/shinyapp/helper/analyze_comp_2.md | 11 UCSCXenaShiny-2.2.0/UCSCXenaShiny/inst/shinyapp/helper/analyze_comp_3.md | 11 UCSCXenaShiny-2.2.0/UCSCXenaShiny/inst/shinyapp/helper/analyze_cor_1.md | 16 UCSCXenaShiny-2.2.0/UCSCXenaShiny/inst/shinyapp/helper/analyze_cor_2.md | 15 UCSCXenaShiny-2.2.0/UCSCXenaShiny/inst/shinyapp/helper/analyze_cor_3.md | 14 UCSCXenaShiny-2.2.0/UCSCXenaShiny/inst/shinyapp/helper/analyze_sur_1.md | 18 UCSCXenaShiny-2.2.0/UCSCXenaShiny/inst/shinyapp/helper/analyze_sur_2.md | 6 UCSCXenaShiny-2.2.0/UCSCXenaShiny/inst/shinyapp/helper/analyze_sur_3.md | 6 UCSCXenaShiny-2.2.0/UCSCXenaShiny/inst/shinyapp/helper/choose_samples.md | 4 UCSCXenaShiny-2.2.0/UCSCXenaShiny/inst/shinyapp/helper/cross_gene.md |only UCSCXenaShiny-2.2.0/UCSCXenaShiny/inst/shinyapp/helper/cross_pw.md |only UCSCXenaShiny-2.2.0/UCSCXenaShiny/inst/shinyapp/helper/custom_metadata.md | 5 UCSCXenaShiny-2.2.0/UCSCXenaShiny/inst/shinyapp/helper/data_origin.md | 6 UCSCXenaShiny-2.2.0/UCSCXenaShiny/inst/shinyapp/helper/get_batch_data.md | 6 UCSCXenaShiny-2.2.0/UCSCXenaShiny/inst/shinyapp/helper/get_batch_data_set_groups.md | 6 UCSCXenaShiny-2.2.0/UCSCXenaShiny/inst/shinyapp/helper/get_one_data.md | 6 UCSCXenaShiny-2.2.0/UCSCXenaShiny/inst/shinyapp/helper/set_groups.md | 6 UCSCXenaShiny-2.2.0/UCSCXenaShiny/inst/shinyapp/modules/01_general/modules-ga-dim-distribution.R | 6 UCSCXenaShiny-2.2.0/UCSCXenaShiny/inst/shinyapp/modules/02_quick/modules-1-tcga-01-TN.R | 7 UCSCXenaShiny-2.2.0/UCSCXenaShiny/inst/shinyapp/modules/02_quick/modules-1-tcga-02-Anatomy.R | 8 UCSCXenaShiny-2.2.0/UCSCXenaShiny/inst/shinyapp/modules/02_quick/modules-1-tcga-03-Cor.R | 8 UCSCXenaShiny-2.2.0/UCSCXenaShiny/inst/shinyapp/modules/02_quick/modules-1-tcga-04-TIL.R | 7 UCSCXenaShiny-2.2.0/UCSCXenaShiny/inst/shinyapp/modules/02_quick/modules-1-tcga-05-Immune.R | 13 UCSCXenaShiny-2.2.0/UCSCXenaShiny/inst/shinyapp/modules/02_quick/modules-1-tcga-06-Idx.R | 10 UCSCXenaShiny-2.2.0/UCSCXenaShiny/inst/shinyapp/modules/02_quick/modules-1-tcga-07-PW.R | 7 UCSCXenaShiny-2.2.0/UCSCXenaShiny/inst/shinyapp/modules/02_quick/modules-1-tcga-08-Mut.R | 7 UCSCXenaShiny-2.2.0/UCSCXenaShiny/inst/shinyapp/modules/02_quick/modules-1-tcga-09-KM.R | 27 UCSCXenaShiny-2.2.0/UCSCXenaShiny/inst/shinyapp/modules/02_quick/modules-1-tcga-10-Cox.R | 12 UCSCXenaShiny-2.2.0/UCSCXenaShiny/inst/shinyapp/modules/02_quick/modules-1-tcga-11-Dim.R | 13 UCSCXenaShiny-2.2.0/UCSCXenaShiny/inst/shinyapp/modules/02_quick/modules-2-pcawg-01-TN.R | 7 UCSCXenaShiny-2.2.0/UCSCXenaShiny/inst/shinyapp/modules/02_quick/modules-2-pcawg-02-Cor.R | 15 UCSCXenaShiny-2.2.0/UCSCXenaShiny/inst/shinyapp/modules/02_quick/modules-2-pcawg-03-KM.R | 7 UCSCXenaShiny-2.2.0/UCSCXenaShiny/inst/shinyapp/modules/02_quick/modules-2-pcawg-04-Cox.R | 8 UCSCXenaShiny-2.2.0/UCSCXenaShiny/inst/shinyapp/modules/02_quick/modules-3-ccle-01-Dist.R | 7 UCSCXenaShiny-2.2.0/UCSCXenaShiny/inst/shinyapp/modules/02_quick/modules-3-ccle-02-Cor.R | 17 UCSCXenaShiny-2.2.0/UCSCXenaShiny/inst/shinyapp/modules/02_quick/modules-3-ccle-03-DrugT.R | 63 UCSCXenaShiny-2.2.0/UCSCXenaShiny/inst/shinyapp/modules/02_quick/modules-3-ccle-04-DrugR.R | 48 UCSCXenaShiny-2.2.0/UCSCXenaShiny/inst/shinyapp/modules/03_tcga/modules-pancan-comp-m2o.R | 5 UCSCXenaShiny-2.2.0/UCSCXenaShiny/inst/shinyapp/modules/03_tcga/modules-pancan-comp-o2m.R | 4 UCSCXenaShiny-2.2.0/UCSCXenaShiny/inst/shinyapp/modules/03_tcga/modules-pancan-comp-o2o.R | 8 UCSCXenaShiny-2.2.0/UCSCXenaShiny/inst/shinyapp/modules/03_tcga/modules-pancan-cor-m2o.R | 4 UCSCXenaShiny-2.2.0/UCSCXenaShiny/inst/shinyapp/modules/03_tcga/modules-pancan-cor-o2m.R | 11 UCSCXenaShiny-2.2.0/UCSCXenaShiny/inst/shinyapp/modules/03_tcga/modules-pancan-cor-o2o.R | 4 UCSCXenaShiny-2.2.0/UCSCXenaShiny/inst/shinyapp/modules/03_tcga/modules-pancan-cross-gene-o2m.R |only UCSCXenaShiny-2.2.0/UCSCXenaShiny/inst/shinyapp/modules/03_tcga/modules-pancan-cross-pw-o2m.R |only UCSCXenaShiny-2.2.0/UCSCXenaShiny/inst/shinyapp/modules/03_tcga/modules-pancan-sur-m2o.R | 4 UCSCXenaShiny-2.2.0/UCSCXenaShiny/inst/shinyapp/modules/03_tcga/modules-pancan-sur-o2m.R | 4 UCSCXenaShiny-2.2.0/UCSCXenaShiny/inst/shinyapp/modules/03_tcga/modules-pancan-sur-o2o.R | 4 UCSCXenaShiny-2.2.0/UCSCXenaShiny/inst/shinyapp/modules/04_pcawg/modules-pcawg-sur-m2o.R | 5 UCSCXenaShiny-2.2.0/UCSCXenaShiny/inst/shinyapp/modules/04_pcawg/modules-pcawg-sur-o2m.R | 5 UCSCXenaShiny-2.2.0/UCSCXenaShiny/inst/shinyapp/modules/04_pcawg/modules-pcawg-sur-o2o.R | 4 UCSCXenaShiny-2.2.0/UCSCXenaShiny/inst/shinyapp/modules/06_tpc_func/modules-z-download-feat.R | 71 UCSCXenaShiny-2.2.0/UCSCXenaShiny/inst/shinyapp/modules/06_tpc_func/modules-z-download-res.R | 2 UCSCXenaShiny-2.2.0/UCSCXenaShiny/inst/shinyapp/modules/06_tpc_func/modules-z-filter-sample.R | 11 UCSCXenaShiny-2.2.0/UCSCXenaShiny/inst/shinyapp/modules/06_tpc_func/modules-z-multi-upload.R | 3 UCSCXenaShiny-2.2.0/UCSCXenaShiny/inst/shinyapp/modules/07_PharmacoGenomics/DrugOmicPair.R | 8 UCSCXenaShiny-2.2.0/UCSCXenaShiny/inst/shinyapp/modules/07_PharmacoGenomics/FeatureAcrossType.R | 14 UCSCXenaShiny-2.2.0/UCSCXenaShiny/inst/shinyapp/modules/07_PharmacoGenomics/FeatureDatabaseSig_singlethread.R | 10 UCSCXenaShiny-2.2.0/UCSCXenaShiny/inst/shinyapp/modules/07_PharmacoGenomics/ProfileDrugSens.R | 9 UCSCXenaShiny-2.2.0/UCSCXenaShiny/inst/shinyapp/modules/08_other_page/home-pancan-search.R | 27 UCSCXenaShiny-2.2.0/UCSCXenaShiny/inst/shinyapp/modules/08_other_page/modules-z-download-2-dataset.R | 2 UCSCXenaShiny-2.2.0/UCSCXenaShiny/inst/shinyapp/server/general-analysis.R | 2 UCSCXenaShiny-2.2.0/UCSCXenaShiny/inst/shinyapp/server/home.R | 75 - UCSCXenaShiny-2.2.0/UCSCXenaShiny/inst/shinyapp/server/modules.R | 37 UCSCXenaShiny-2.2.0/UCSCXenaShiny/inst/shinyapp/server/repository.R | 2 UCSCXenaShiny-2.2.0/UCSCXenaShiny/inst/shinyapp/shiny-doc/citation2.md | 28 UCSCXenaShiny-2.2.0/UCSCXenaShiny/inst/shinyapp/shiny-doc/datasets.md | 2 UCSCXenaShiny-2.2.0/UCSCXenaShiny/inst/shinyapp/shiny-doc/intro_personal_pips.md | 12 UCSCXenaShiny-2.2.0/UCSCXenaShiny/inst/shinyapp/shiny-doc/intro_quick_mods.md | 8 UCSCXenaShiny-2.2.0/UCSCXenaShiny/inst/shinyapp/ui/PharmacoGenomics.R | 12 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