igblastr 0.99.8

Man page for augment_germline_db_*() utilities completed.

Unit tests to follow soon...
 

 Air format.
 

 Update streme test for later version.
 

 Allow parsing xml when evalue metadata is jagged.

When a database uses multiple sources of motifs with varying metadata,
the metadata entries in the tomtom db motifs will be inconsistent. Ex
when using a hybrid database with and without evalue entries. This
resolves #123 where a database was used that lacked a evalue
entries in some db targets.

Also adds a unit test for this behavior.
 

 add drs_nci_crdc to drs_hub documentaiton
 

 Merge pull request #29 from lamortenera/27-bioconductor-error-package-at-risk-of-deprecation-and-affecting-reverse-dependencies

Removing zlibbioc due to deprecation 

 Merge branch 'master' into 27-bioconductor-error-package-at-risk-of-deprecation-and-affecting-reverse-dependencies
 

 Bumping version to reflect bioc bamsignals development version
 

 Bumping version in DESCRIPTION to trigger rebuilt
 

 Incremented version
 

 Start man page for augment_germline_db_*() utilities

(plus various small tweaks)
 

 Merge remote-tracking branch 'origin/devel' into devel
 

 update a typo in code example 

update the code example for extracting novel transcript with at least 1 full length count in any sample 

 Version bump
 

 update SEA
 

 Accidentally confused BPPARAM and BLUSPARAM. Fixed
 

 Update documentation
 

 Update access to SHR and NBC for `runConcordex()`
 

 Update return value to return a list instead of matrix
 

 Update NBC computation to avoid `bplappy()` for serial evaluation
 

 bump to 1.5.1
 

 add within group multiple test correction
 

 version bump 1.21.3
 

 Updated the eminem library.
 

 tests: add additional unit tests
 

 Solve vignette issue

Squashed commit of the following:

commit 060b890d0735c9dc76b180c46e7074be6a8ca7d5
Author: Pierrick Roger <pierrick.rogermele@cea.fr>
Date:   Thu Jun 12 16:12:00 2025 +0200

    Remove some tests

commit fc642a77f77e82370a3b9d75e132e52785a8a8b6
Author: Pierrick Roger <pierrick.rogermele@cea.fr>
Date:   Thu Jun 12 15:52:01 2025 +0200

    Remove old code.
 

 Resolve "Move BiodbRequestScheduler into sched CRAN pkg"
 

 Resolve "Move BiodbRequest into sched CRAN pkg"
 

 Move BiodbUrl to sched::URL
 

 chore: appease lintr
 

 Update R/utils.R

Co-authored-by: j-smola <31825957+j-smola@users.noreply.github.com> 

 Update R/utils.R

Co-authored-by: j-smola <31825957+j-smola@users.noreply.github.com> 

 doc: reoxygenate
 

 refactor: update fun parent name
 

 chore: bump version and update NEWS.md
 

 refactor: extend loop function
 

 Merge pull request #89 from fgcz/use-pak-for-ci

Fix and optimize CI 

 Correctly name the package
 

 use pak for ci
 

 Update r.yml 

 update pipeline steps: respect paths in object
TODO: quantify_transcript. Optional args for create_sce_from_dir as well?
 

 Merge pull request #56 from gdrplatform/GDR-2981

Gdr 2981 

 chore: bump v+c
 

 bump to 1.17.7
 

 version bump in devel to 1.1.2
 

 Updated NEWS.md, tidying up GHA
 

 add orcid
 

 Updates to DESCRIPTION to comply with BiocCheck()
 

 bugfix
 

 version bump to 1.1.1 in devel
 

 Peer review fix: completed #1
 

 Partial peer review fixes
 

 Fix issue #229
 

 add @param in description
 

 fix deprecated ggplot note
 

 remove unnecesary dt conversion
 

 Delayed Instantiation
 

 versioning
 

 Merge branch 'devel' of github.com:GilbertHan1011/linkSet into devel
 

 version
 

 solve warning2
 

 20250611_fail_chicane
 

 20250405
 

 Version bump

bug fixes or
minor enhancements.
 

 fix a note generated during build

markdown format was wrong
 

 Merge pull request #78 from rformassspectrometry/bioc_submission

Use virtualenvs by default 

 Update NAMESPACE
 

 ci: disable miniconda installation on macOS
 

 merge
 

 Updated to latest BioTIP release, removed large files
 

 Update myplotIc.R

corrected typo in line 13 if() sentence 

 Update myplotIc.R

add the parameter p.IC to the function myplotIc.R 

 fix typo in BioTIP wrap
 

 fix typo in BioTIP wrap
 

 added temporarily removed files
 

 added multiple-sample in assignment out
 

 improved read assignment out format
 

 Updated paths from YARN
 

 Merge pull request #204 from MangiolaLaboratory/patch-19

Update `prepare_replicate_data` to use `original_formula_composition`… 

 Merge branch 'patch-19' of https://github.com/MangiolaLaboratory/sccomp into patch-19
 

 Update `prepare_replicate_data` to use `original_formula_composition` for grouping names

- Modified the `prepare_replicate_data` function to accept `original_formula_composition` as a parameter.
- Updated the calculation of `original_grouping_names` to utilize `original_formula_composition` instead of `formula_composition`.
- Enhanced the `replicate_data` function to pass the original formula composition from the data attributes.
 

 Add `original_formula_composition` to `replicate_data` tests

- Updated multiple test cases in `test-replicate_data.R` to include `original_formula_composition` as a parameter.
- Ensured consistency in testing by passing the original formula composition across various scenarios, enhancing the robustness of the tests.
 

 Update `prepare_replicate_data` to use `original_formula_composition` for grouping names

- Modified the `prepare_replicate_data` function to accept `original_formula_composition` as a parameter.
- Updated the calculation of `original_grouping_names` to utilize `original_formula_composition` instead of `formula_composition`.
- Enhanced the `replicate_data` function to pass the original formula composition from the data attributes.
 

 Merge pull request #201 from MangiolaLaboratory/print-method

Add print method for sccomp objects and related functionality 

 Merge branch 'print-method' of https://github.com/MangiolaLaboratory/sccomp into print-method
 

 fix result description in README
 

 Add SeuratObject to DESCRIPTION and update GitHub Actions workflow to install R dependencies

This commit includes the addition of the `SeuratObject` package to the DESCRIPTION file and enhances the GitHub Actions workflow by adding a step to install R dependencies, ensuring that all necessary packages are available for the build process.
 

 fix data attribute
 

 fix for generic column
 

 Add prettydoc package to GitHub Actions workflow dependencies

This update includes the addition of the `prettydoc` package to the list of dependencies in the GitHub Actions workflow for R-CMD-check with CmdStan integration, enhancing documentation capabilities.
 

 Rename .github/workflow_with_cmdstanr.yml to .github/workflows/workflow_with_cmdstanr.yml 

 Add GitHub Actions workflow for R-CMD-check with CmdStan integration

This commit introduces a new GitHub Actions workflow to automate R package checks using CmdStan. The workflow supports multiple operating systems and R versions, ensuring comprehensive testing. It includes steps for setting up the environment, installing CmdStan, and checking R package dependencies.
 

 Refactor count_data handling in plotting and estimation functions

Updated the handling of count_data across multiple functions to use attributes instead of nested data frames. This change improves efficiency and consistency in data access. Additionally, enhanced documentation to clarify the attributes attached to results, including count_data, model_input, and formulas used for modeling. Adjusted test cases to reflect the updated argument names and improve clarity.
 

 Merge pull request #200 from MangiolaLaboratory/reorganise-methods

Reorganise methods 

 Bring stan common functions out of the scripts
 

 Standardize argument names in replicate_data tests

Updated the test cases in test-replicate_data.R to replace deprecated argument names (.sample, .cell_type, .count) with standardized names (sample, cell_group, count). This change enhances consistency and clarity across the test suite, aligning with recent updates to the sccomp functions.
 

 Merge pull request #198 from MangiolaLaboratory/improve-args-type

Improve args type 

 Standardize argument names in documentation and examples across sccomp functions

Updated the README, vignettes, and test cases to replace deprecated argument names (.sample, .cell_group, .abundance) with standardized names (sample, cell_group, abundance). This change enhances clarity and consistency in the usage of sccomp functions. Additionally, updated the citation format in the introduction vignette and improved the formatting of tables in the README for better readability.
 

 Refactor test cases in test-sccomp_ to use n_iterations for max_sampling_iterations

Updated the test cases in test-sccomp_ to replace hardcoded max_sampling_iterations values with a new variable, n_iterations. This change enhances code maintainability and consistency across tests, ensuring that the sampling iterations can be easily adjusted in one place.
 

 Refactor sccomp functions to standardize argument names and improve seed handling

Updated the sccomp functions to replace deprecated argument names (.sample, .cell_group, .abundance) with standardized names (sample, cell_group, abundance). Introduced a new sample_seed function for consistent random seed generation. Adjusted documentation and test cases to reflect these changes, ensuring clarity and improved usability.
 

 Refactor sccomp_estimate functions to improve quosure handling and deprecation warnings

Updated the sccomp_estimate functions to utilize quosures for .count, .sample, .cell_group, and .abundance arguments, ensuring proper validation and error handling. Deprecated arguments now trigger appropriate warnings, and test cases have been adjusted to reflect these changes, enhancing overall robustness and clarity in the function's usage.
 

 Add validation for column types in sccomp_estimate function

Enhance the sccomp_estimate function to check that sample_column, cell_group_column, and abundance_column are of character type. Introduce the 'not' function from magrittr and 'quo_get_expr' from rlang for improved quosure handling. Add tests to ensure proper error handling when non-character values or symbols are provided for these arguments. Update documentation to reflect these changes.
 

 Merge pull request #195 from MangiolaLaboratory/improve-random-effects

Improve random effects 

 Remove @noRd tags from documentation for multipanel_theme and no_significance_df to allow their export. This change ensures that the relevant datasets are properly documented and accessible for users.
 

 Enhance tests for get_random_effect_design3 and replicate_data by adding skip_cmdstan() to all relevant test cases. This adjustment improves test execution control when using CmdStan, ensuring smoother testing processes for scenarios involving NA values and complex designs.
 

 Update version to 1.99.19 and enhance sccomp_remove_outliers.sccomp_tbl function with initialization of unseen random effect variables. Adjust tests to include tidyr library and modify data handling in replicate_data for improved sample selection.
 

 Update tests for replicate_data to improve NA handling and enhance design matrix evaluations. Refactor data preparation steps to utilize sccomp:::.subset for original_count_data. Introduce accept_NA_as_average_effect parameter in random effect elements for better NA management across various test scenarios.
 

 Refactor sccomp_glm_data_frame_counts function to improve data integrity checks. Replace rectangular data frame validation with a call to make_rectangular_data for consistent sample/cell group pairing. Introduce check_if_NAs_in_count to ensure count data does not contain NAs.
 

 Update tests for get_random_effect_design3 to use scaled continuous variables for age and weight. Enhance test cases to ensure proper handling of complex formulas and interactions with NAs. Adjust expected values in assertions to reflect the new scaling approach.
 

 Enhance get_random_effect_design2 function to accept NA values as average effects. Update related calls in prepare_replicate_data to ensure consistent handling of NA scenarios. Improve design matrix generation by incorporating new parameter for NA handling.
 

 Add debugging prints and tests for handling NA values in random effects within replicate_data function. Enhance test coverage for scenarios with missing group information and ensure correct design matrix outputs.
 

 Enhance replicate_data function to support unseen random effects and improve data preparation. Update Stan model to incorporate random effects for unseen groups. Add comprehensive tests for replicate_data functionality, including scenarios with random intercepts and slopes.
 

 Refactor group assignment handling in get_random_effect_design2 function to improve clarity and efficiency. Introduce a mask for design matrix and streamline filtering of empty groupings.
 

 ignore DS store files
 

 adapt function to new
 

 Merge branch 'check-columns-of-tidy-eval' of https://github.com/MangiolaLaboratory/sccomp into check-columns-of-tidy-eval
 

 use base pipe
 

 avoid conversion to quo_names
 

 use characters as column names
 

 use characters as column names
 

 use characters as column names
 

 use base pipe
 

 avoid conversion to quo_names
 

 avoid conversion to quo_names
 

 avoid conversion to quo_names
 

 use characters as column names
 

 implement unknown group for random intercept. I still need to limit to not random effect
 

 Merge branch 'increase-significant-figures' into check-columns-of-tidy-eval
 

 Merge branch 'check-columns-of-tidy-eval' of https://github.com/MangiolaLaboratory/sccomp into check-columns-of-tidy-eval
 

 use characters as column names
 

 use characters as column names
 

 use characters as column names
 

 use base pipe
 

 avoid conversion to quo_names
 

 use characters as column names
 

 use base pipe
 

 avoid conversion to quo_names
 

 use base pipe
 

 avoid conversion to quo_names
 

 use base pipe
 

 avoid conversion to quo_names
 

 baslisk fixing
 

 bug fixed in cc_server()
 

 getMetaboLights: Information on ion mode and other improvements to importing (#43)

 

 Fix issue related to facets and points (#194)

 

 plotBoxplot fixes (#190)

 

 plotBoxplot: bugfixes (#187)

 

 plotBoxplot (#184)

 

 Improve plotHistogram (#186)

 

 Fix plot*Tree (#178)

 

 update DESCRIPTION file (#731)

Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com> 

 Minor fix to internal function (#728)

 

 raise version
 

 raise version
 

 Integrated dynamic BugSigDB loading and removed static signatures. Fixed bug in fetching NCBI IDs
 

 fix minor bugs
 

 version bump 1.29.3
 

 use isScalarCharacter isScalarNumber in oncoPrintTCGA
 

 import selectSome and setSlots from BiocBaseUtils
 

 remove mirbase.db dep

- rm GenomicFeatures::microRNAs
- defunct mirToRanges