Changes in version 1.0 - Bug fix in subsetting logic affecting predict and test_de. The problem occured if a fit object was subsetted with indices or gene names and the order changed, and resulted in a wrong order of the predictions. Changes in version 0.99.1-0.99.8 - Submission to Bioconductor, thus the jump in version number. - Adjusted internal code to handle breaking changes in harmony v1.0.0. - Multiple small fixes to comply with Bioconductor guidelines (see https://github.com/Bioconductor/Contributions/issues/3152) Changes in version 0.0.27 - Instead of include_complement, the find_de_neighborhoods function gains a add_diff_in_diff argument. If it is true, the function calculates the difference between the DE results inside the neighborhood vs. outside. - Change indices columns to neighborhood and store list of cell name vectors in output of find_de_neighborhoods. - Enforce unique column and row names. Changes in version 0.0.26 - Make the neighborhoods more consistent: (1) include cells which are connected to many cells inside the neighborhood, (2) exclude cells from the neighborhood which are not well connected to the other cells in the neighborhood. - Add a control_parameters argument to find_de_neighborhoods. - Add BiocNeighbor as a dependency. Changes in version 0.0.25 - Detect problematic neighborhoods and skip them. - Replace test_data_cell_size_factors by size_factor_method, which is more flexibel. Setting size_factor_method = "ratio" uses the size factor method described in the original DESeq paper Changes in version 0.0.24 - Fix bug in find_de_neighborhoods that meant that accidentally additionally zeros where included in each neighborhood pseudobulk. The test should have more power now. - Expose min_neighborhood_size argument in find_de_neighborhoods. - Add test_data_cell_size_factors argument to find_de_neighborhoods which is useful if the function is called with a subsetted fit argument. Changes in version 0.0.23 - Improve alignment functions: simplify algorithm, find linear approximation to Harmony's steps, include an intercept. - Avoid calling private methods from harmony. - Convert character columns in colData to factors to avoid problems when dividing data into test and training data. - Fix bug in find_de_neighborhoods where I didn't embrace an argument. - Remove BiocNeighbors dependency. Changes in version 0.0.21 - Minor bug fix in find_de_neighborhoods. The function threw an error if alignment_design != design. - Better error messages if find_de_neighborhoods is called without having called test_de before. Changes in version 0.0.20 - Change defaults for find_de_neighborhoods. Increase the ridge_penalty and add a min_neighborhood_size = 10 argument to avoid creation of very small neighborhoods. Changes in version 0.0.19 - Add new test_fraction argument to lemur() function. It automatically defines a hold-out datasets for the fitting step. These hold-out data is used to infer the differential expression of the neighborhoods in find_de_neighborhoods. This change addresses the double-dipping problem, where it was previously left to the user to provide an independent matrix for the find_de_neighborhoods function. - As a consequence of these changes, the structure of lemur_fit objects has changed. They gain three new fields called fit$test_data, fit$training_data, and fit$is_test_data. - The order and names of the arguments for find_de_neighborhoods has changed. Changes in version 0.0.18 - Remove alignment_method field from lemur_fit objects as it was not used for anything. Changes in version 0.0.17 - Rename argument name for align_by_template from alignment_template to template - Tweak algorithm for alignment to take cluster sizes into account during optimization Changes in version 0.0.13 - Change in the alignment model. Previously, the method tried to align cells using rotations and / or stretching, however, the method could not represent reflections! To fix this, I now allow arbitrary linear transformations where $R(x) = (I + sum_k x_k V_k)^{-1}$. The new alignment is more flexible and easier to infer. The downside is the term inside the parantheses can be singular which would lead to an error. - Skip iteration step: first infer centering and then infer latent space. Previously, I iterated between these steps but that either didn't add anything or actually degraded the results. - Set center = FALSE in find_base_point. Centering the data before fitting the base point caused problems and made the data look less integrated in some cases. - Remove ambient PCA step. This was originally conceived as an performance optimization, however it had detrimental effects on the inference. Since a few version it was skipped per default, so removing it should not change the inference. - Add linear_coefficient_estimator to give more flexibility how or if the conditions are centered. - Reduce the minimum_cluster_membership default to 0.001 in align_harmony to make it more sensitive. - Make test_global an internal function again until further more extensive testing. - Remove base_point argument from lemur(). It wasn't used anyways. - Refactor find_de_neighborhoods: the function can now combine the results of different directions, selection criteria, and pseudobulk test (on counts or continuous values). To implement this, I changed the names of the arguments and added parameters. - Remove many superfluous method generics and only provide the accession via $ - Fix documentation warnings - Rename class from 'lemur_fit_obj' to 'lemur_fit' - Store 'contrast' in lemur_fit after calling test_de - Add option to fit count model in find_de_neighborhoods with edgeR