7c5952c (HEAD -> devel, origin/devel, origin/HEAD) bump x.y.z version to odd y following creation of RELEASE_3_20 branch by
J Wokaty <jennifer.wokaty@sph.cuny.edu>2024-10-29 11:28:52 -0400;
311fdc5 (origin/RELEASE_3_20, RELEASE_3_20) bump x.y.z version to even y prior to creation of RELEASE_3_20 branch by
J Wokaty <jennifer.wokaty@sph.cuny.edu>2024-10-29 11:28:52 -0400;
5d0c81b (origin/RELEASE_3_19, RELEASE_3_19) Version bump in release by
almeidasilvaf <fabricio_almeidasilva@hotmail.com>2024-09-05 07:16:01 +0100;
6b4d85c bugfix: pca_plot() now works when shape_by = NULL by
almeidasilvaf <fabricio_almeidasilva@hotmail.com>2024-09-05 07:14:10 +0100;
585f31b Version bump in devel by
almeidasilvaf <fabricio_almeidasilva@hotmail.com>2024-09-05 07:14:52 +0100;
ec9fd98 bugfix: pca_plot() now works when shape_by = NULL by
almeidasilvaf <fabricio_almeidasilva@hotmail.com>2024-09-05 07:14:10 +0100;
3fbdc87 bump x.y.z version to odd y following creation of RELEASE_3_19 branch by
J Wokaty <jwokaty@users.noreply.github.com>2024-04-30 11:55:08 -0400;
ecf95e5 bump x.y.z version to even y prior to creation of RELEASE_3_19 branch by
J Wokaty <jwokaty@users.noreply.github.com>2024-04-30 11:55:07 -0400;
881cd7e Set LazyData to FALSE by
almeidasilvaf <fabricio_almeidasilva@hotmail.com>2024-02-23 12:04:46 +0100;
5c114fe Revised text in vignette by
almeidasilvaf <fabricio_almeidasilva@hotmail.com>2024-02-23 11:46:08 +0100;
52424c9 Added helper functions for input data validation by
almeidasilvaf <fabricio_almeidasilva@hotmail.com>2024-02-23 11:45:54 +0100;
d1ddd59 Added package-level documentation by
almeidasilvaf <fabricio_almeidasilva@hotmail.com>2024-02-23 10:46:06 +0100;
7f84f16 Remove redundancy in x axis of schematic line plots by
almeidasilvaf <fabricio_almeidasilva@hotmail.com>2024-02-15 18:47:21 +0100;
9294786 Fixed example for get_deg_list() to remove unused parameter by
almeidasilvaf <fabricio_almeidasilva@hotmail.com>2024-02-02 10:56:51 +0100;
a698140 Moved the size factor calculation to a dedicated function named `add_size_factors()` and updated vignettes and tests accordingly by
almeidasilvaf <fabricio_almeidasilva@hotmail.com>2024-02-02 10:42:41 +0100;
81e81ae Simplified pkgdown configs by
almeidasilvaf <fabricio_almeidasilva@hotmail.com>2024-01-12 22:33:37 +0100;
618cc55 Updated lifecycle badge by
almeidasilvaf <fabricio_almeidasilva@hotmail.com>2023-12-12 11:42:37 +0100;
a054823 Added pkgdown/extra.css by
almeidasilvaf <fabricio_almeidasilva@hotmail.com>2023-12-12 11:22:51 +0100;
87e8868 Added parameter labels to plot_expression_partitions and plot_expression_frequencies where users can specify labels for each generation by
almeidasilvaf <fabricio_almeidasilva@hotmail.com>2023-11-28 17:00:25 +0100;
f6d5859 Added logo by
almeidasilvaf <fabricio_almeidasilva@hotmail.com>2023-11-28 16:34:33 +0100;
5246079 Included a `plotdata` attribute to the output of `get_deg_list()` with log2 fold changes for all genes by
almeidasilvaf <fabricio_almeidasilva@hotmail.com>2023-11-28 16:28:38 +0100;
a46b1c5 Fixed bug in axis label in `plot_partition_frequencies()` by
almeidasilvaf <fabricio_almeidasilva@hotmail.com>2023-11-28 16:27:34 +0100;
f35c30b Added option to plot PCA with only colors (no shapes mapped to variables) by
almeidasilvaf <fabricio_almeidasilva@hotmail.com>2023-11-17 15:18:01 +0100;
9725b09 Added option to specify level for midparent values by
almeidasilvaf <fabricio_almeidasilva@hotmail.com>2023-11-17 15:17:40 +0100;
a84abdc Include note on how to handle ERCC counts when users do not want to use spike-in normalization by
almeidasilvaf <fabricio_almeidasilva@hotmail.com>2023-11-17 15:17:07 +0100;
76105e9 Added section on ORA with examples + added FAQ item on SummarizedExperiment objects by
almeidasilvaf <fabricio_almeidasilva@hotmail.com>2023-11-04 21:22:37 +0100;
44ee042 Added functions to perform overrepresentation analyses with unit tests and example data set by
almeidasilvaf <fabricio_almeidasilva@hotmail.com>2023-11-04 20:16:23 +0100;
0aa59b4 Updated affiliations in vignette to use only one (for better display in pkgdown website) by
almeidasilvaf <fabricio_almeidasilva@hotmail.com>2023-11-04 19:16:36 +0100;
f650047 Modified GHA workflow to run BiocCheck and unset --as-cran by
almeidasilvaf <fabricio_almeidasilva@hotmail.com>2023-11-04 19:11:16 +0100;
b79b26f Added Bioc-like configs for pkgdown by
almeidasilvaf <fabricio_almeidasilva@hotmail.com>2023-11-04 19:10:04 +0100;
8adf884 Fixed bug in `get_deg_list()` and `get_deg_counts()` when NAs were present in variables padj and log2FoldChange by
almeidasilvaf <fabricio_almeidasilva@hotmail.com>2023-11-04 19:09:40 +0100;
a2151b0 Updated vignette section on "Expression-based gene classification" by
almeidasilvaf <fabricio_almeidasilva@hotmail.com>2023-11-03 20:59:46 +0100;
ce15ed4 Fixed bug in Category-to-Class mapping by
almeidasilvaf <fabricio_almeidasilva@hotmail.com>2023-11-03 20:59:06 +0100;
92e2d67 Wrote vignette up to "Expression-based gene classification" by
almeidasilvaf <fabricio_almeidasilva@hotmail.com>2023-11-03 14:30:41 +0100;
74e1531 Replaced a single occurrence of m:n with seq_len() by
almeidasilvaf <fabricio_almeidasilva@hotmail.com>2023-11-03 13:45:27 +0100;
5fe1c68 Added option to specify correlation method in `plot_samplecor()` by
almeidasilvaf <fabricio_almeidasilva@hotmail.com>2023-11-02 22:27:10 +0100;
be5fc31 Updated README with short description of the package's features by
almeidasilvaf <fabricio_almeidasilva@hotmail.com>2023-11-02 20:18:28 +0100;
c810fc2 Added GHA workflow with {rworkflows} by
almeidasilvaf <fabricio_almeidasilva@hotmail.com>2023-11-02 19:48:23 +0100;
6712b22 Added vignette skeleton by
almeidasilvaf <fabricio_almeidasilva@hotmail.com>2023-11-02 19:40:50 +0100;
93544ab Added biocViews and package description in DESCRIPTION by
almeidasilvaf <fabricio_almeidasilva@hotmail.com>2023-11-02 19:39:17 +0100;
8d83f96 Renamed variable "Group" (expression groups, 1-12) to "Category" by
almeidasilvaf <fabricio_almeidasilva@hotmail.com>2023-11-02 19:19:11 +0100;
8ebe6d0 Added options to create midparent values by using sum or weighted mean of parents by
almeidasilvaf <fabricio_almeidasilva@hotmail.com>2023-11-02 14:10:31 +0100;
069a4e0 Added functions to plot PCA and heatmap of sample correlations by
almeidasilvaf <fabricio_almeidasilva@hotmail.com>2023-11-02 13:27:07 +0100;
4a6d1ed Fixed unit test for pca_plot() by
almeidasilvaf <fabricio_almeidasilva@hotmail.com>2023-10-27 08:49:25 +0200;
5f86197 Updated example of pca_plot() by
almeidasilvaf <fabricio_almeidasilva@hotmail.com>2023-10-26 20:50:16 +0200;
e6a59db Added pca_plot() + included option to specify custom color palette for all graphical functions by
almeidasilvaf <fabricio_almeidasilva@hotmail.com>2023-10-26 20:38:24 +0200;
56e9940 Added functions to visualize expression partitionsas barplots or scatterplots of log fold change by
almeidasilvaf <fabricio_almeidasilva@hotmail.com>2023-10-25 19:23:20 +0200;
58a92fa Added function to perform expression partitioning into 12 groups and 5 classes by
almeidasilvaf <fabricio_almeidasilva@hotmail.com>2023-10-25 19:22:31 +0200;
ee50124 Modified reference and test levels in contrasts for DGE analyses by
almeidasilvaf <fabricio_almeidasilva@hotmail.com>2023-10-25 19:21:34 +0200;
a8426cd Updated list names in `deg_list` by
almeidasilvaf <fabricio_almeidasilva@hotmail.com>2023-10-25 19:20:24 +0200;
3f85732 Added patchwork to Imports by
almeidasilvaf <fabricio_almeidasilva@hotmail.com>2023-10-25 19:19:46 +0200;
5b56c00 Updated documentation for data acquisition by
almeidasilvaf <fabricio_almeidasilva@hotmail.com>2023-10-21 20:11:50 +0200;
1d78a93 Added plot_expression_triangle() with utils and unit tests by
almeidasilvaf <fabricio_almeidasilva@hotmail.com>2023-10-21 20:11:21 +0200;
09d5d90 Added functions to perform DGE analyses and get DEG counts by
almeidasilvaf <fabricio_almeidasilva@hotmail.com>2023-10-21 20:10:47 +0200;
fb1f497 Fixed assay name in add_midparent_expression() by
almeidasilvaf <fabricio_almeidasilva@hotmail.com>2023-10-21 20:10:04 +0200;
26797a6 Added example data sets with documentation by
almeidasilvaf <fabricio_almeidasilva@hotmail.com>2023-10-21 20:09:12 +0200;
635f7aa Added required packages to imports by
almeidasilvaf <fabricio_almeidasilva@hotmail.com>2023-10-21 20:08:03 +0200;
59dcc0e Added add_midparent_expression() with unit tests and example data by
almeidasilvaf <fabricio_almeidasilva@hotmail.com>2023-10-19 08:47:23 +0200;
bec6d13 Added package's core structure by
almeidasilvaf <fabricio_almeidasilva@hotmail.com>2023-10-17 14:07:58 +0200;
b3ed5f4 Initial commit by
almeidasilvaf <fabricio_almeidasilva@hotmail.com>2023-10-17 09:26:11 +0200;
