Title: Drug Response Prediction from Differential Multi-Omics Networks
Description: While it has been well established that drugs affect and help
patients differently, personalized drug response predictions remain
challenging. Solutions based on single omics measurements have been proposed,
and networks provide means to incorporate molecular interactions into reasoning.
However, how to integrate the wealth of information contained in multiple omics
layers still poses a complex problem.
We present a novel network analysis pipeline, DrDimont, Drug response prediction
from Differential analysis of multi-omics networks. It allows for comparative
conclusions between two conditions and translates them into differential drug
response predictions. DrDimont focuses on molecular interactions. It establishes
condition-specific networks from correlation within an omics layer that are
then reduced and combined into heterogeneous, multi-omics molecular networks.
A novel semi-local, path-based integration step ensures integrative conclusions.
Differential predictions are derived fro [...truncated...]
Author: Katharina Baum [cre] ,
Pauline Hiort [aut] ,
Julian Hugo [aut] ,
Spoorthi Kashyap [aut] ,
Nataniel Mueller [aut] ,
Justus Zeinert [aut]
Maintainer: Katharina Baum <katharina.baum@fu-berlin.de>
Diff between DrDimont versions 0.1.4 dated 2022-09-23 and 0.1.6 dated 2025-11-08
DrDimont-0.1.4/DrDimont/man/calculate_interaction_score.Rd |only DrDimont-0.1.4/DrDimont/man/check_connection.Rd |only DrDimont-0.1.4/DrDimont/man/check_drug_target.Rd |only DrDimont-0.1.4/DrDimont/man/check_drug_targets_in_layers.Rd |only DrDimont-0.1.4/DrDimont/man/check_layer.Rd |only DrDimont-0.1.4/DrDimont/man/check_sensible_connections.Rd |only DrDimont-0.1.4/DrDimont/man/chunk.Rd |only DrDimont-0.1.4/DrDimont/man/chunk_2gether.Rd |only DrDimont-0.1.4/DrDimont/man/combine_graphs.Rd |only DrDimont-0.1.4/DrDimont/man/corPvalueStudentParallel.Rd |only DrDimont-0.1.4/DrDimont/man/create_unique_layer_node_ids.Rd |only DrDimont-0.1.4/DrDimont/man/find_targets.Rd |only DrDimont-0.1.4/DrDimont/man/generate_reduced_graph.Rd |only DrDimont-0.1.4/DrDimont/man/get_layer.Rd |only DrDimont-0.1.4/DrDimont/man/get_layer_setting.Rd |only DrDimont-0.1.4/DrDimont/man/graph_metrics.Rd |only DrDimont-0.1.4/DrDimont/man/inter_layer_edgelist_by_id.Rd |only DrDimont-0.1.4/DrDimont/man/inter_layer_edgelist_by_table.Rd |only DrDimont-0.1.4/DrDimont/man/load_interaction_score_output.Rd |only DrDimont-0.1.4/DrDimont/man/network_reduction_by_p_value.Rd |only DrDimont-0.1.4/DrDimont/man/network_reduction_by_pickHardThreshold.Rd |only DrDimont-0.1.4/DrDimont/man/sample_size.Rd |only DrDimont-0.1.4/DrDimont/man/set_cluster.Rd |only DrDimont-0.1.4/DrDimont/man/shutdown_cluster.Rd |only DrDimont-0.1.4/DrDimont/man/target_edge_list.Rd |only DrDimont-0.1.4/DrDimont/man/write_interaction_score_input.Rd |only DrDimont-0.1.6/DrDimont/DESCRIPTION | 36 DrDimont-0.1.6/DrDimont/LICENSE | 2 DrDimont-0.1.6/DrDimont/MD5 | 148 DrDimont-0.1.6/DrDimont/NAMESPACE | 26 DrDimont-0.1.6/DrDimont/R/checks.R | 48 DrDimont-0.1.6/DrDimont/R/data_documentations.R | 90 DrDimont-0.1.6/DrDimont/R/drug_targets.R | 20 DrDimont-0.1.6/DrDimont/R/graph_combination.R | 10 DrDimont-0.1.6/DrDimont/R/interaction_score.R | 18 DrDimont-0.1.6/DrDimont/R/network_generation.R | 87 DrDimont-0.1.6/DrDimont/R/network_reduction.R | 66 DrDimont-0.1.6/DrDimont/R/pipeline_functions.R | 63 DrDimont-0.1.6/DrDimont/R/settings.R | 34 DrDimont-0.1.6/DrDimont/R/utilities.R | 114 DrDimont-0.1.6/DrDimont/R/utils-pipe.R | 4 DrDimont-0.1.6/DrDimont/build/vignette.rds |binary DrDimont-0.1.6/DrDimont/data/combined_graphs_example.rda |binary DrDimont-0.1.6/DrDimont/data/correlation_matrices_example.rda |binary DrDimont-0.1.6/DrDimont/data/differential_graph_example.rda |binary DrDimont-0.1.6/DrDimont/data/drug_gene_interactions.rda |binary DrDimont-0.1.6/DrDimont/data/drug_response_scores_example.rda |binary DrDimont-0.1.6/DrDimont/data/drug_target_edges_example.rda |binary DrDimont-0.1.6/DrDimont/data/individual_graphs_example.rda |binary DrDimont-0.1.6/DrDimont/data/interaction_score_graphs_example.rda |binary DrDimont-0.1.6/DrDimont/data/layers_example.rda |binary DrDimont-0.1.6/DrDimont/data/metabolite_data.rda |binary DrDimont-0.1.6/DrDimont/data/metabolite_protein_interactions.rda |binary DrDimont-0.1.6/DrDimont/data/mrna_data.rda |binary DrDimont-0.1.6/DrDimont/data/phosphosite_data.rda |binary DrDimont-0.1.6/DrDimont/data/protein_data.rda |binary DrDimont-0.1.6/DrDimont/inst/CITATION | 9 DrDimont-0.1.6/DrDimont/inst/doc/DrDimont_Vignette.R | 407 - DrDimont-0.1.6/DrDimont/inst/doc/DrDimont_Vignette.Rmd | 141 DrDimont-0.1.6/DrDimont/inst/doc/DrDimont_Vignette.html | 2197 +++++----- DrDimont-0.1.6/DrDimont/inst/python_igraph_interaction_score.py | 19 DrDimont-0.1.6/DrDimont/man/check_input.Rd | 2 DrDimont-0.1.6/DrDimont/man/combined_graphs_example.Rd | 6 DrDimont-0.1.6/DrDimont/man/compute_correlation_matrices.Rd | 2 DrDimont-0.1.6/DrDimont/man/compute_drug_response_scores.Rd | 2 DrDimont-0.1.6/DrDimont/man/correlation_matrices_example.Rd | 10 DrDimont-0.1.6/DrDimont/man/determine_drug_targets.Rd | 4 DrDimont-0.1.6/DrDimont/man/differential_graph_example.Rd | 2 DrDimont-0.1.6/DrDimont/man/drdimont_settings.Rd | 33 DrDimont-0.1.6/DrDimont/man/drug_gene_interactions.Rd | 6 DrDimont-0.1.6/DrDimont/man/drug_response_scores_example.Rd | 8 DrDimont-0.1.6/DrDimont/man/drug_target_edges_example.Rd | 8 DrDimont-0.1.6/DrDimont/man/generate_combined_graphs.Rd | 2 DrDimont-0.1.6/DrDimont/man/generate_individual_graphs.Rd | 6 DrDimont-0.1.6/DrDimont/man/generate_interaction_score_graphs.Rd | 4 DrDimont-0.1.6/DrDimont/man/individual_graphs_example.Rd | 10 DrDimont-0.1.6/DrDimont/man/interaction_score_graphs_example.Rd | 4 DrDimont-0.1.6/DrDimont/man/layers_example.Rd | 10 DrDimont-0.1.6/DrDimont/man/make_drug_target.Rd | 2 DrDimont-0.1.6/DrDimont/man/make_layer.Rd | 6 DrDimont-0.1.6/DrDimont/man/metabolite_data.Rd | 8 DrDimont-0.1.6/DrDimont/man/metabolite_protein_interactions.Rd | 6 DrDimont-0.1.6/DrDimont/man/mrna_data.Rd | 4 DrDimont-0.1.6/DrDimont/man/phosphosite_data.Rd | 4 DrDimont-0.1.6/DrDimont/man/pipe.Rd | 4 DrDimont-0.1.6/DrDimont/man/protein_data.Rd | 2 DrDimont-0.1.6/DrDimont/man/run_pipeline.Rd | 4 DrDimont-0.1.6/DrDimont/vignettes/DrDimont_Vignette.Rmd | 141 88 files changed, 1927 insertions(+), 1912 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-10-24 1.6.0
2025-10-08 1.5.5
2025-08-25 1.5.4
2025-08-18 1.5.3
2025-07-24 1.5.2
2025-07-15 1.5.0
2025-07-07 1.4.4
2025-07-07 1.4.5
Title: Plot Null Hypothesis Significance Tests
Description: Illustrate graphically the most common Null Hypothesis Significance Testing procedures. More specifically, this package provides functions to plot Chi-Squared, F, t (one- and two-tailed) and z (one- and two-tailed) tests, by plotting the probability density under the null hypothesis as a function of the different test statistic values. Although highly flexible (color theme, fonts, etc.), only the minimal number of arguments (observed test statistic, degrees of freedom) are necessary for a clear and useful graph to be plotted, with the observed test statistic and the p value, as well as their corresponding value labels. The axes are automatically scaled to present the relevant part and the overall shape of the probability density function. This package is especially intended for education purposes, as it provides a helpful support to help explain the Null Hypothesis Significance Testing process, its use and/or shortcomings.
Author: Nils Myszkowski [aut, cre]
Maintainer: Nils Myszkowski <nilsmyszkowskiscience@gmail.com>
Diff between nhstplot versions 1.4.0 dated 2025-07-30 and 1.4.1 dated 2025-11-08
DESCRIPTION | 6 ++-- MD5 | 16 +++++------ NEWS.md | 5 ++- R/plot.chisqtest.R | 10 +++---- R/plot.ftest.R | 10 +++---- R/plot.ttest.R | 32 +++++++++++------------ R/plot.ztest.R | 34 ++++++++++++------------ build/vignette.rds |binary inst/doc/nhstplot.html | 67 +++++++++++++++++++++++++++---------------------- 9 files changed, 96 insertions(+), 84 deletions(-)
Title: Custom Visualizations & Functions for Streamlined Analyses of
Single Cell Sequencing
Description: Collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using 'R'. 'scCustomize' aims to provide 1) Customized visualizations for aid in ease of use and to create more aesthetic and functional visuals. 2) Improve speed/reproducibility of common tasks/pieces of code in scRNA-seq analysis with a single or group of functions. For citation please use: Marsh SE (2021) "Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing" <doi:10.5281/zenodo.5706430> RRID:SCR_024675.
Author: Samuel Marsh [aut, cre] ,
Ming Tang [ctb],
Velina Kozareva [ctb],
Lucas Graybuck [ctb],
Zoe Clarke [ctb]
Maintainer: Samuel Marsh <sccustomize@gmail.com>
Diff between scCustomize versions 3.2.0 dated 2025-09-10 and 3.2.1 dated 2025-11-08
scCustomize-3.2.0/scCustomize/man/Liger_to_Seurat.Rd |only scCustomize-3.2.0/scCustomize/man/deprecated.Rd |only scCustomize-3.2.1/scCustomize/DESCRIPTION | 10 scCustomize-3.2.1/scCustomize/MD5 | 72 - scCustomize-3.2.1/scCustomize/NAMESPACE | 5 scCustomize-3.2.1/scCustomize/NEWS.md | 33 scCustomize-3.2.1/scCustomize/R/Color_Palettes.R | 11 scCustomize-3.2.1/scCustomize/R/Deprecated.R | 18 scCustomize-3.2.1/scCustomize/R/Generics.R | 3 scCustomize-3.2.1/scCustomize/R/Internal_Utilities.R | 633 ++++++++-- scCustomize-3.2.1/scCustomize/R/LIGER_Internal_Utilities.R | 16 scCustomize-3.2.1/scCustomize/R/LIGER_Plotting.R | 1 scCustomize-3.2.1/scCustomize/R/LIGER_Utilities.R | 56 scCustomize-3.2.1/scCustomize/R/Object_Conversion.R | 483 +++---- scCustomize-3.2.1/scCustomize/R/Object_Utilities.R | 337 ++++- scCustomize-3.2.1/scCustomize/R/Plotting_Nebulosa.R | 7 scCustomize-3.2.1/scCustomize/R/Plotting_QC_Seq_10X.R | 30 scCustomize-3.2.1/scCustomize/R/Plotting_QC_Seurat.R | 2 scCustomize-3.2.1/scCustomize/R/Plotting_Seurat.R | 265 +++- scCustomize-3.2.1/scCustomize/R/Plotting_Seurat_Iterative.R | 14 scCustomize-3.2.1/scCustomize/R/Plotting_Shared.R | 1 scCustomize-3.2.1/scCustomize/R/Plotting_Statistics.R | 8 scCustomize-3.2.1/scCustomize/R/Plotting_Utilities_Internal.R | 39 scCustomize-3.2.1/scCustomize/R/QC_Utilities_Seurat.R | 12 scCustomize-3.2.1/scCustomize/R/Read_&_Write_Data.R | 54 scCustomize-3.2.1/scCustomize/R/Statistics.R | 5 scCustomize-3.2.1/scCustomize/R/Utilities.R | 39 scCustomize-3.2.1/scCustomize/R/zzz.R | 2 scCustomize-3.2.1/scCustomize/man/Clustered_DotPlot.Rd | 6 scCustomize-3.2.1/scCustomize/man/DimPlot_scCustom.Rd | 10 scCustomize-3.2.1/scCustomize/man/ElbowPlot_scCustom.Rd |only scCustomize-3.2.1/scCustomize/man/Extract_Sample_Meta.Rd | 7 scCustomize-3.2.1/scCustomize/man/Fetch_Meta.Rd | 8 scCustomize-3.2.1/scCustomize/man/Map_New_Meta.Rd |only scCustomize-3.2.1/scCustomize/man/NavyAndOrange.Rd | 2 scCustomize-3.2.1/scCustomize/man/Random_Cells_Downsample.Rd | 4 scCustomize-3.2.1/scCustomize/man/Read_CellBender_h5_Multi_Directory.Rd | 3 scCustomize-3.2.1/scCustomize/man/Stacked_VlnPlot.Rd | 4 scCustomize-3.2.1/scCustomize/man/VlnPlot_scCustom.Rd | 2 39 files changed, 1465 insertions(+), 737 deletions(-)
Title: Dental Surface Complexity Measurement Tools
Description: Surface topography calculations of Dirichlet's normal energy,
relief index, surface slope, and orientation patch count for teeth using scans of
enamel caps.
Importantly, for the relief index and orientation patch count calculations to
work, the scanned tooth files must be oriented with the occlusal plane parallel
to the x and y axes, and perpendicular to the z axis. The files should also be
simplified, and smoothed in some other software prior to uploading into R.
Author: James D. Pampush [aut, cre, cph],
Paul E. Morse [aut, cph],
Alexander Q. Vining [aut, cph],
Edward Fuselier [aut, cph]
Maintainer: James D. Pampush <jdpampush@gmail.com>
Diff between molaR versions 5.3 dated 2023-01-26 and 6.0 dated 2025-11-08
molaR-5.3/molaR/R/ARC_Legend.R |only molaR-5.3/molaR/R/DNE_Discard_Legend.R |only molaR-5.3/molaR/R/DNE_Legend.R |only molaR-5.3/molaR/R/OPC_Legend.R |only molaR-5.3/molaR/R/RFI_Legend.R |only molaR-5.3/molaR/R/Slope_Legend.R |only molaR-5.3/molaR/R/molaR_bgplot.R |only molaR-6.0/molaR/DESCRIPTION | 12 molaR-6.0/molaR/MD5 | 61 molaR-6.0/molaR/NAMESPACE | 2 molaR-6.0/molaR/R/ARC3d.R | 310 ++ molaR-6.0/molaR/R/Check2D.R | 218 + molaR-6.0/molaR/R/DNE3d.R | 490 ++-- molaR-6.0/molaR/R/DNE3dDiscard.R | 328 +- molaR-6.0/molaR/R/Face_Normals.R | 2 molaR-6.0/molaR/R/OPC3d.R | 644 +++-- molaR-6.0/molaR/R/RFI3d.R | 462 ++-- molaR-6.0/molaR/R/Slope3d.R | 375 ++- molaR-6.0/molaR/R/clipDisplay.R | 20 molaR-6.0/molaR/R/meshClip.R | 330 +- molaR-6.0/molaR/R/plyPlaneCut.R | 428 +-- molaR-6.0/molaR/R/zzz.R |only molaR-6.0/molaR/build/vignette.rds |binary molaR-6.0/molaR/inst/doc/molaR_vignette.R | 125 - molaR-6.0/molaR/inst/doc/molaR_vignette.Rmd | 45 molaR-6.0/molaR/inst/doc/molaR_vignette.html | 3067 +++++++++------------------ molaR-6.0/molaR/man/ARC3d.Rd | 86 molaR-6.0/molaR/man/Check2D.Rd | 84 molaR-6.0/molaR/man/DNE3d.Rd | 110 molaR-6.0/molaR/man/DNE3dDiscard.Rd | 104 molaR-6.0/molaR/man/OPC3d.Rd | 131 - molaR-6.0/molaR/man/RFI3d.Rd | 113 molaR-6.0/molaR/man/Slope3d.Rd | 91 molaR-6.0/molaR/man/meshClip.Rd |only molaR-6.0/molaR/man/plyPlaneCut.Rd | 151 - molaR-6.0/molaR/vignettes/molaR_vignette.Rmd | 45 36 files changed, 3914 insertions(+), 3920 deletions(-)
Title: Patient-Reported Outcome Data Analysis with Stan
Description: Algorithms and subroutines for patient-reported outcome data analysis.
Author: Bin Wang [aut, cre]
Maintainer: Bin Wang <bwang831@gmail.com>
Diff between prome versions 2.0.1.9 dated 2025-10-08 and 3.0.1.5 dated 2025-11-08
prome-2.0.1.9/prome/R/blindinglogit.R |only prome-2.0.1.9/prome/man/lslogit.Rd |only prome-3.0.1.5/prome/DESCRIPTION | 10 +++++----- prome-3.0.1.5/prome/MD5 | 20 +++++++++++++++----- prome-3.0.1.5/prome/NAMESPACE | 11 +++++++---- prome-3.0.1.5/prome/R/blindingCPE.R |only prome-3.0.1.5/prome/R/blindingTEST.R |only prome-3.0.1.5/prome/R/zzz.R |only prome-3.0.1.5/prome/data/bd010.rda |only prome-3.0.1.5/prome/data/bd011.rda |only prome-3.0.1.5/prome/data/bd012.rda |only prome-3.0.1.5/prome/data/datalist | 3 +++ prome-3.0.1.5/prome/inst/extdata |only prome-3.0.1.5/prome/man/blindingcpe.Rd |only prome-3.0.1.5/prome/man/blindingdata.Rd |only prome-3.0.1.5/prome/man/blindingtest.Rd |only 16 files changed, 30 insertions(+), 14 deletions(-)
Title: Run Any CLI Tool on a 'Conda' Environment
Description: Simplifies the execution of command line interface (CLI)
tools within isolated and reproducible environments. It enables users
to effortlessly manage 'Conda' environments, execute command line
tools, handle dependencies, and ensure reproducibility in their data
analysis workflows.
Author: Lucio Queiroz [aut, cre, cph] ,
Claudio Zanettini [aut, ctb]
Maintainer: Lucio Queiroz <luciorqueiroz@gmail.com>
Diff between condathis versions 0.1.2 dated 2025-06-02 and 0.1.3 dated 2025-11-08
DESCRIPTION | 19 - MD5 | 117 +++---- NAMESPACE | 1 NEWS.md | 70 +++- R/check_micromamba_version.R | 5 R/clean_cache.R | 42 +- R/create_base_env.R | 2 R/create_env.R | 93 +++-- R/define_platform.R | 16 R/env_exists.R | 2 R/format_channels_args.R | 1 R/get_best_micromamba_path.R | 22 + R/get_env_dir.R | 2 R/get_install_dir.R | 8 R/get_sys_arch.R | 2 R/install_micromamba.R | 64 ++- R/install_packages.R | 53 ++- R/list_envs.R | 4 R/list_packages.R | 41 +- R/micromamba_bin_path.R | 8 R/native_cmd.R | 49 +- R/packages_search_native.R | 25 - R/parse_output.R | 63 +++ R/parse_quiet_flag.R | 2 R/parse_strategy_verbose.R | 103 ++++-- R/remove_env.R | 33 + R/rethrow_error_run.R | 14 R/run.R | 146 +++++--- R/run_bin.R | 46 +- R/run_internal_native.R | 44 +- R/symlink_micromamba_bin.R | 8 README.md | 284 +++++------------ build |only inst/doc |only man/clean_cache.Rd |only man/condathis-package.Rd | 1 man/create_env.Rd | 26 + man/env_exists.Rd | 22 + man/get_install_dir.Rd | 8 man/install_micromamba.Rd | 8 man/install_packages.Rd | 24 + man/list_packages.Rd | 33 + man/parse_output.Rd | 25 + man/remove_env.Rd | 27 + man/run.Rd | 84 +++-- man/run_bin.Rd | 54 ++- tests/testthat.R | 2 tests/testthat/test-clean_cache.R |only tests/testthat/test-create_base_env.R | 6 tests/testthat/test-create_env.R | 76 ++-- tests/testthat/test-create_nested_env.R | 10 tests/testthat/test-format_channels_args.R | 5 tests/testthat/test-get_env_dir.R | 2 tests/testthat/test-get_sys_arch.R | 9 tests/testthat/test-is_micromamba_available_for_arch.R | 15 tests/testthat/test-parse_output.R |only tests/testthat/test-parse_strategy_verbose.R | 141 +++++++- tests/testthat/test-rethrow_error.R | 26 + tests/testthat/test-run_bin.R | 20 - tests/testthat/test-run_output_file.R | 26 - tests/testthat/test-run_verbose_levels.R |only vignettes |only 62 files changed, 1338 insertions(+), 701 deletions(-)
Title: Visualization Package for CanvasXpress in R
Description: Enables creation of visualizations using the CanvasXpress framework
in R. CanvasXpress is a standalone JavaScript library for reproducible research
with complete tracking of data and end-user modifications stored in a single
PNG image that can be played back. See <https://www.canvasxpress.org> for more
information.
Author: Isaac Neuhaus [aut],
Connie Brett [aut, cre]
Maintainer: Connie Brett <connie@aggregate-genius.com>
Diff between canvasXpress versions 1.57.4 dated 2025-07-22 and 1.58.7 dated 2025-11-08
DESCRIPTION | 6 ++-- MD5 | 26 +++++++++--------- NEWS.md | 4 ++ build/vignette.rds |binary inst/README-known_issues.md | 2 + inst/doc/additional_examples.html | 4 +- inst/doc/getting_started.html | 4 +- inst/htmlwidgets/canvasXpress.yaml | 2 - inst/htmlwidgets/lib/canvasXpress/canvasXpress.css | 8 ++--- inst/htmlwidgets/lib/canvasXpress/canvasXpress.min.js | 6 ++-- inst/ui-examples/cX-function.R.gz |binary tests/testthat/test-other-decorations.R | 7 ++++ tests/testthat/test-other-piping.R | 1 tests/testthat/test-ui-heatmap.R | 8 +++++ 14 files changed, 48 insertions(+), 30 deletions(-)