NEWS.md
plot_transcripts_view(): now creates missing save folder, like other plotting functions.check_unique_by_partition(): now handles columns with only NA values.get_by_partition(): correctly retains factor columns.styler-package for better code readability.filter_messages().plot_transcripts_view(): added include_ID_in_title parameter.plot_proportion_barplot(): added label_angle parameter.lifecycle and R build status badges.
R CMD check via GitHub actions.zzz.R to DTUrtle-package.R.lifecycle
import_dge_counts(): import quantification data and summarize to gene-level.run_deseq2(): perform DGE analysis with DESeq2.priming_bias_detection_probability() functionality, to estimate the potential influence of a prime-biased sequencing protocol on the DTU detection ability.DESeq2
glmGamPoi, apeglm
plot_transcripts_view(): added tested_transcripts_only parameter, to allow better control which transcripts of a gene should be displayed. Also allows to create plot for genes which have been excluded from the analysis.plot_transcripts_view(): changed default value of reduce_introns_fill to ‘white’ to get visually more appealing plots by default.plot_proportion_barplot(): define data and mapping already in general ggplot function, to ease editability.plot_proportion_barplot(): added global ‘text_size’ parameter.plot_dimensional_reduction(): added ‘plot_scale’ parameter, allowing for free x- or y-axis of facets, or both.plot_dimensional_reduction(): added global ‘text_size’ parameter.plot_transcripts_view(): added ‘arrow_start’ parameter, to allow adjustment of the transcript annotation start position.plot_transcripts_view(): changed default parameters and resolution, to get visually more appealing high quality plots.import_gtf(): generalized function and added parameter for returned feature type and return format. Now can create fitting plot_transcripts_view() GTF input.run_drimseq(): added susbet_feature and subset_sample parameters, replacing subset_counts. Now samples and features can be excluded from analysis on the fly.run_drimseq(): added add_pseudocount parameter, to enable comparisons of features with zero expression in one comparison group.run_drimseq(): added filter_only parameter, to return (sparse) count matrix after group-based filtering.combine_to_matrix(): added ability to infer Seurat cellname extension.combine_to_matrix(): added cell_extension_side parameter to choose label append or prepend.plot_dimensional_reduction(): added functionality to plot in dimensional reduction space.plot_transcripts_view(): safer and more specific IdeoGram track generation.plot_transcripts_view(): improved handling of non-UCSC chromosome identifiers.run_drimseq(): added check for matching names of counts and tx2gene.run_drimseq(): added subset_counts parameter - ability to force subset the count matrix to matching tx2gene features only.plot_dtu_table(): disable warning for server side rendering.plot_proportion_pheatmap(): plots names are now run through make.names(), as all other plots.create_dtu_table(): changed default column names and added description of column meaning.add_to_table parameter to plotting functions, to add plot savepaths directly to dtu_table.run_drimseq(): added description of predefined filter strategies.run_drimseq(): added check if two sample groups are left after excluding unused samples.plot_dtu_table(): add min_page_length parameter.plot_dtu_table(): slightly change icon and heading alignment.knitr in Suggests for vignette building.