Version 0.7.3

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README.Rmd

NEWS.Rmd

Package: DTUrtle

Type: Package

URL: https://github.com/TobiTekath/DTUrtle, https://tobitekath.github.io/DTUrtle

Title: Differential Transcript Usage analysis

Version: 0.7.1

Authors@R: c(person(given = "Tobias", family = "Tekath", role = c("aut", "cre"), email = "tobias.tekath@gmail.com"))

Description: Easily perform Differential Transcript Usage (DTU) analysis for bulk or single-cell RNAseq data utilizing transcript level quantification counts.

License: GPL (>= 3)

Title: Differential Transcript Usage analysis of bulk and single-cell RNA-seq data

Version: 0.7.3

Authors@R: c(person(given = "Tobias", family = "Tekath", role = c("aut", "cre"), email = "tobias.tekath@wwu.de", comment = c(ORCID = "0000-0002-9315-5452")))

Description: Easily perform and visualize Differential Transcript Usage (DTU) analysis for bulk or single-cell RNA-seq data, utilizing transcript level quantification counts.

License: GPL (>= 3) + file LICENSE

Encoding: UTF-8

LazyData: true

Depends: R (>= 3.4.0)

Imports: Matrix, tximport, sparseDRIMSeq, stageR, rtracklayer, formattable, DT, Gviz, assertthat, scales, ggplot2, reshape2, BiocParallel, Matrix.utils, pheatmap, methods, GenomicRanges, GenomeInfoDb, htmltools, htmlwidgets, knitr, stringi 

Depends: R (>= 3.4.0), sparseDRIMSeq

Imports: Matrix, tximport, stageR, rtracklayer, GenomicFeatures, formattable, DT, Gviz, assertthat, scales, ggplot2, reshape2, BiocParallel, Matrix.utils, pheatmap, methods, GenomicRanges, GenomeInfoDb, htmltools, htmlwidgets, knitr 

Suggests: Seurat (>= 3.0.0), webshot, webshot2, magick

Remotes: github::TobiTekath/sparseDRIMSeq, bioc::BiocParallel, bioc::GenomicRanges, bioc::Gviz, bioc::rtracklayer, bioc::stageR, bioc::tximport

Remotes: github::TobiTekath/sparseDRIMSeq, bioc::BiocParallel, bioc::GenomicRanges, bioc::Gviz, bioc::rtracklayer, bioc::stageR, bioc::tximport, github::rstudio/webshot2

RoxygenNote: 7.1.1

Roxygen: list(markdown = TRUE)

VignetteBuilder: knitr

export(combine_to_matrix)

export(create_dtu_table)

export(dataframe_to_partitioning)

export(get_by_partition)

export(get_proportion_matrix)

export(import_counts)

export(import_gtf)

export(move_columns_to_front)

export(one_to_one_mapping)

export(partitioning_to_dataframe)

export(plot_dimensional_reduction)

export(plot_dtu_table)

export(plot_proportion_barplot)

export(summarize_to_gene)

export(table_percentage_bar)

export(table_pval_tile)

import(sparseDRIMSeq)

---

title: "DTUrtle News"

output: github_document

---

```{r setup, include=FALSE}

knitr::opts_chunk$set(echo = TRUE)

```

# DTUrtle 0.7.1

 - 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 0.2.6

## 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.

# DTUrtle 0.2.5

## Changes

- initial first version.