NEWS
inferCSN 1.2.3
-
func:
- Optimize
check_parameters() for check input parameters.
-
docs:
- Updated documentation across multiple functions.
inferCSN 1.2.2
-
func:
- Removed
network_sift() and weight_sift() functions.
- Removed S4 method for
data.frame.
-
docs:
- Updated documentation across multiple functions.
inferCSN 1.2.1
-
func:
- Fixed warning on Windows platform for better compatibility.
-
docs:
- Updated documentation across multiple functions.
inferCSN 1.2.0 (2025-10-16)
-
func:
- Removed
srm related functions and files.
- Removed
RcppArmadillo dependency.
- Removed
Makevars files for simplified build process.
- Reorganized package structure by moving and removing files.
-
refactor:
- Updated package template structure.
- Cleaned up package dependencies and build configuration.
-
docs:
- Updated package logo.
- Improved documentation formatting.
inferCSN 1.1.9
-
func:
- Enhanced logo printing functionality.
-
docs:
- Updated documentation across multiple functions.
inferCSN 1.1.8
-
func:
- Added
inferCSN_logo() function for displaying package logo.
- Added new parameters for
log_message() function.
- Modified
.cores_detect() function for better CPU core detection.
- Removed
PKG_LIBS from Makevars and Makevars.win files.
- Moved utility functions to
thisutils package.
-
refactor:
- Updated
pkgdown webpage theme.
- Fixed warnings and errors in GCC compilation.
- Optimized document structure.
-
docs:
- Added examples in README.
- Updated package description.
- Updated
renv configuration files.
inferCSN 1.1.7 (2025-03-30)
- func:
- Added
sparse_cov_cor() function for sparse covariance and correlation computation.
- Removed deprecated
sparseCovCor function.
- Updated documentation for
sparse_cor() function.
inferCSN 1.1.6 (2025-03-27)
-
func:
- Fixed error in
table_to_matrix() function.
- Optimized performance for matrix operations.
-
bugs:
- Fixed error in pkgdown build process.
-
docs:
- Added example for
calculate_accuracy() function.
- Modified examples for
plot_network_heatmap() function.
- Updated badge display.
- Updated ProjectId.
inferCSN 1.1.3
-
func:
- Added new network evaluation functions for assessing network quality.
- Updated import records for better dependency management.
-
docs:
- Edited documentation for multiple functions.
- Modified documentation for
plot_network_heatmap() function.
- Updated
test-coverage.yaml file.
- Renamed files for better organization.
-
refactor:
- Added check workflow for automated testing.
- Modified import statements.
inferCSN 1.1.2
-
func:
- Renamed
fit_sparse_regression() to fit_srm() for shorter function name.
- Modified parameters for multiple functions.
-
docs:
- Updated package logo.
- Updated badge display.
inferCSN 1.1.1
- func:
- Renamed function
fit_sparse_regression() to fit_srm().
inferCSN 1.1.0
- func:
- Modified
algorithm parameter to non-exported for internal use.
inferCSN 1.0.9
-
func:
- Added new utility functions including
%s%, matrix_to_table(), pearson_correlation(), simulate_sparse_matrix(), plot_coefficients(), split_indices(), subsampling_fun(), and weight_sift().
- Added new C++ functions including
network_format(), prepare_calculate_metrics() for improved performance.
- Added
CITATION file for proper citation.
- Renamed function from
percent_samples to subsampling.
- Imported native R pipe operator
|> for better compatibility with R >= 4.1.0.
-
refactor:
- Renamed function
%s% to %ss%.
- Renamed functions to
calculate_metrics().
- Modified structure of
sparse_regression() output.
- Modified normalization method implementation.
- Updated
log_message() function.
- Improved documentation across multiple functions.
-
bugs:
- Fixed multiple coding style issues.
- Fixed error in various functions.
- Fixed warning when package installation.
- Fixed download badge display.
-
docs:
- Optimized function documentation.
- Updated
.gitignore.
- Updated packages record information.
-
deps:
- Deleted suggests packages that are no longer needed.
- Deleted useless packages from dependencies.
inferCSN 1.0.8 (2024-08-24)
-
func:
- Added
log_message() function for consistent logging across package.
- Added export of
log_message() for user access.
- Modified documentation for multiple functions.
-
deps:
- Added import of
cli package for better message formatting.
- Modified Imports section.
- Removed exports for internal functions.
-
docs:
- Updated README.
- Improved documentation consistency.
-
refactor:
- Coding style improvements.
inferCSN 1.0.7
-
func:
- Removed export of
prepare_network_data() as internal function.
- Modified documentation for multiple functions.
-
bugs:
- Fixed error for
normalization() when setting method to softmax.
inferCSN 1.0.6
-
func:
- Added new visualization functions:
plot_embedding() and plot_weight_distribution().
- Added new parameters for
plot_weight_distribution().
- Added
asMatrixParallel() for parallel matrix operations.
- Added
RcppParallel support for improved performance.
- Added
PKG_LIBS information in Makevars.
- Added new function
check_sparsity() for sparsity checking.
- Added new global variables.
- Renamed
performance_evaluation functions.
- Renamed files and functions for better organization.
- Support for sparse matrix operations.
- Updated R version requirement.
- Reduced computation complexity for better performance.
- Removed export of
check_parameters().
-
bugs:
- Fixed error for
.weight_sift().
- Fixed error and improved coding style in
plot_scatter().
- Fixed document issues.
-
docs:
- Modified documentation for multiple functions.
- Modified examples, parameters, and documentation.
- Updated
renv files.
- Updated
Makevars files.
- Updated document for some parameters.
-
refactor:
- Coding style improvements.
- Renamed functions and files.
inferCSN 1.0.5 (2024-06-26)
-
func:
- Added
entropy to filter edges in network.
- Added new function
as_matrix() for matrix conversion.
- Added new function
plot_scatter() for scatter plot visualization.
- Added new parameter for
plot_scatter().
- Added new function
network_sift() for network filtering (renamed from previous version).
- Added new functions:
r_square(), plot_contrast_networks(), plot_dynamic_networks().
- Added new function
map_parallel() and parallelize_fun() for parallel processing.
- Added
.softmax() function.
- Added new parameter
heatmap_size_lock for network.heatmap().
- Modified S4 method for
inferCSN.
- Removed
dynamic.networks, contrast.networks functions (renamed/replaced).
- Renamed
net.format to network_format().
- Renamed
dynamic.networks to plot_static_networks().
- Fixed errors and added new parameters for
network_sift().
- Deleted unnecessary functions.
- Modified import functions and packages.
- Using
as_matrix() instead of as.matrix() for better performance.
-
deps:
- Removed
progress package and added pbapply package.
- Added new packages for enhanced functionality.
- Updated imports.
-
bugs:
- Fixed error in
check.parameters().
- Fixed multiple errors.
- Fixed warning.
- Fixed note info.
-
docs:
- Updated
badges.
- Modified examples.
- Updated
_pkgdown.yml.
- Modified examples and figure style.
- Updated
renv file.
- Modified parameter description of functions.
- Updated
.gitignore.
- Updated README.
-
refactor:
- Coding style improvements across multiple files.
- Improved function organization.
inferCSN 1.0.3 (2024-04-17)
-
func:
- Added new function
weight_filter() for filtering weights.
- Added new parameters for
network.heatmap().
- Set
crossweight example to \dontrun{} for CRAN compatibility.
-
docs:
- Updated NAMESPACE and import records.
inferCSN 1.0.2
-
func:
- Added new function
normalization() for data normalization.
- Added new function
crossweight() for cross-weight analysis.
- Added new function
crossweight_params().
- Added new function
extract_net() (later deleted).
- Added new example data
example_meta_data.
- Updated
crossweight and related functions.
- Updated example data.
- Added new parameters for
calculate.gene.rank().
- Renamed function to
filter_sort.matrix to handle CRAN warning.
- Renamed multiple functions for consistency.
- Deleted function
extract_net().
-
bugs:
- Fixed error when
sample.
- Fixed multiple errors.
- Fixed pkgdown error.
-
docs:
- Updated README.
- Updated
crossweight.Rd.
- Updated
_pkgdown.yml.
- Updated NAMESPACE.
- Updated
renv.lock.
- Modified examples.
- Formatted progress information.
-
refactor:
- Fixed coding style issues.
inferCSN 1.0.1 (2024-03-15)
-
func:
- Added new function
filter.sort.matrix() for efficient matrix filtering and sorting.
- Optimized memory consumption for handling large datasets.
- Modified function used to handle data.
- Modified parameter
k_folds.
- Modified parameter
regulators_num.
- Renamed multiple functions for consistency:
calculate.gene.rank(), sub.model.fit(), model.fit(), single.network().
- Added examples for multiple functions including
network.heatmap(), dynamic.networks().
- Added new parameter for
net.format().
- Modified some functions for better performance.
- Fixed error code.
-
bugs:
-
docs:
- Updated README with improved examples.
- Updated
_pkgdown.yml.
- Updated
.gitignore.
- Updated
cran_release.R.
- Updated
.Rbuildignore.
- Modified parameter information.
- Added test examples for
table_to_matrix().
- Updated logo.svg.
-
refactor:
- Removed test files.
- Updated NAMESPACE.
- Updated renv file.
- Added examples throughout.
inferCSN 1.0.0 (2024-02-09)
-
feat:
- First major release of inferCSN package.
- Core functionality for inferring cell-specific gene regulatory networks.
- Sparse regression-based network inference algorithm.
- Support for single-cell RNA-seq data.
- Network visualization and analysis functions.
- Performance evaluation metrics.
-
docs:
- Complete documentation for all exported functions.
- Comprehensive README with usage examples.
- Package website with pkgdown.
inferCSN 0.99.9 (2024-01-10)
-
func:
- Updated
table_to_matrix.cpp for improved performance.
- Updated version to 0.99.9 in preparation for CRAN submission.
-
docs:
- Updated
cran_release.R.
- Fixed example information.
- Added new function and renamed files.
inferCSN 0.99.8 (2023-12-04)
-
func:
- Updated
inferCSN() function with improvements.
- Updated C++ functions for better performance.
- Updated and formatted code across multiple files.
- Updated example data.
-
bugs:
-
docs:
- Fixed error and modified documentation.
- Updated
renv.lock.
- Updated
requirements.sh.
inferCSN 0.99.7 (2023-10-30)
-
func:
- Fixed error when compiling on CentOS system.
- Updated
requirements.sh.
-
refactor:
- Version update for CRAN submission preparation.
inferCSN 0.1.1
-
func:
- Initial package development.
- Basic sparse regression implementation.
- C++ integration for performance.
-
docs:
- Basic documentation structure.
- Initial README.
inferCSN 0.1.0