DTUrtle v1.0.2

• 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.
• styled R code with styler-package for better code readability.

DTUrtle v1.0.1

• filtering confusing DRIMSeq computation time messages.
  • implemented a message filtering function filter_messages().
• plot_transcripts_view(): added include_ID_in_title parameter.
• plot_proportion_barplot(): added label_angle parameter.
• added lifecycle and R build status badges.
  • added automatic R CMD check via GitHub actions.
• moved general package code from zzz.R to DTUrtle-package.R.
• new Suggests: lifecycle

DTUrtle v1.0.0

• DTUrtle manuscript got published in Bioinformatics:
  • added citation information.
  • added DOI in Readme.

DTUrtle v0.8.1

• remodeled a lot of code - preserving functionality if not stated otherwise.
• added basic DGE-calling methods:
  • import_dge_counts(): import quantification data and summarize to gene-level.
  • run_deseq2(): perform DGE analysis with DESeq2.
• added priming_bias_detection_probability() functionality, to estimate the potential influence of a prime-biased sequencing protocol on the DTU detection ability.
• added Vignettes for a Smart-seq2 single-cell data set from Wuidart et al.
• Vignettes: added sections showcasing DGE calling and priming bias detection probability calculation.
• new Dependency: DESeq2
• new Suggests: glmGamPoi, apeglm

DTUrtle v0.7.3

• readded "GenomicFeatures" as dependency - eases installation.
• measure and show computation time in vignettes.
• extended vignettes.
• extended README.
• 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.
• removed dependency of 'stringi'.
• added 'sparseDRIMSeq' to depending packages, to get rid of sometimes not-occuring package load.
• fixed some smaller bugs.

DTUrtle v0.7.1

• add new vignette for Tabula Muris (Mouse) data set.
• 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.
• extended checks for provided file paths.
• safer BiocParallel starting and stopping.
• made whole package documentation searchable via docsearch.
• README: fixed typo and added link to vignettes.
• set GenomeInfoDb as standard Imports.
• minor improvements.

DTUrtle v0.2.6

Changes

• add 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.
• minor update of function documentation.
• plot_dtu_table(): add min_page_length parameter.
• plot_dtu_table(): slightly change icon and heading alignment.
• added conditional vignette evaluation.
• added knitr in Suggests for vignette building.

Initial first version

Initial first full working version.