NEWS.md

In sebastian-gregoricchio/Rseb: An R-package for NGS data managing and visualization

title: "changeLog"

Rseb

v0.3.4 - June 12th 2024

• Improved the multiplot visualization of the output from evaluate.heterogeneity function.
• Added possibility of sample clustering for evaluate.heterogeneity function.
• Updated the dependencies to be compatible with new functions/features: patchwork, ggh4x, Hmisc.
• Bug fixed in the incucyte function.
• Performance optimized for DE.status function
• Bug fixed in ggplot2 function calling in plot.NES
• Bug fixed in plot.gsea and plot.multi.gsea

v0.3.3 - January 28th 2024

• Bug fixing in incucyte function
• Added functions plot.multi.gsea, plot.NES
• Solved issue for incompatibility between files with and without 'chr' in evaluate.heterogeneity functions
• Dot strokes automatically removed in the volcano function in order to reduce the plot size for publications

v0.3.2 - September 18th 2023

• Update of evaluate.heterogeneity to enable the log1p signal in the heatmap and avoid scientific annotation of the rank numbers
• Minor bug-fixing in the evaluate.heterogeneity
• Added new function plot.gsea
• Dependencies update to include enrichplot and RColorBrewer required for plot.gsea

v0.3.1 - December 10th 2022

• New functions added: evaluate.heterogeneity, incucyte, read.computeMatrix.file, intersect.regions, venn.overlap and closest.regions
• Updated the dependencies to be compatible with new functions: scales, grDevices, R.utils, eulerr, IRanges and pryr
• Added the possibility to export a file with the session info in the function pkg.version
• Bug fixing for abs(number) < 1 in floating.floor and floating.ceiling
• Optimized alignment of the plot for plot.density.differences, plot.density.profile, plot.density.profile.smooth and plot.density.summary

v0.3.0 - August 15th 2022

• Improvement of sort.bed usage: a) removed redundant "export.bed" option (now it is sufficient to add a file name in the "export.file.name" parameter if exporting is wished), b) added the "unique.regions" option, c) minor bug fixed in sort.bed for input class check
• Added option 'verbose' for sort.bed and collapse.bed functions
• Added citation file to cite the article associated to this package
• Improvement of the vignette
• Changed the default value for command string parameter for intersect.bed and computeMatrix.deeptools functions
• Bug-fixing for the handling of data.frames inputs in the function density.matrix
• Bug-fixing for the handling of bigWig inputs that do not contain 'chr' in the seqnames/chromosome names for the function density.matrix
• Added stranded option in the function density.matrix, allowing the possibility to reverse the signal of strand '-' regions
• Addition of diffloop dependence used to handle bigWig inputs that do not contain 'chr' in the seqnames for the function density.matrix
• Added new function get.single.base.score.bw
• Added new function plot.density.profile.smooth
• Added new function genomic.tracks
• Added new function qPCR.rna.exp
• Added new function qPCR.results example
• Updated dependencies to satisfy genomic.tracks and qPCR.rna.exp requirements: colorspace, ggbio, ggforce, GenomicRanges, AnnotationFilter, EnsDb.Hsapiens.v75, EnsDb.Hsapiens.v86, EnsDb.Mmusculus.v79, openssl, readxl, jpeg

v0.2.0 - April 13th 2021

• Updated information in DESCRIPTION file (new suggested: ggpmisc, prettydoc, knitr, rmarkdown, stats)
• Added vignette to describe the main functions of the package
• Added function density.matrix (alternative to computeMatrix.deeptools)
• Added example datasets RNAseq, deeptools.matrix, CNV.table
• New function plot.density.differences
• Updtate actualize function to build vignettes and bugs fixed
• Optimized the plot.density.summary and plot.density.profile functions in order to not interfer with other packages
• Optimized the plot.density.summary and plot.density.profile functions in order to keep the input order of the samples and groups in the plots colors/legend
• Updated plot.density.profile to change legend title when 'plot.by.group==FALSE'
• Updated plot.density.summary to compute the means comparisons even when not required to show on the plot and indicate whether the statistical test performed was paired or not
• Bug fixed in matrix loading for plot.density.summary function
• Better handling of Rseb version visualization in pkg.version output

v0.1.7 - February 20th 2021

• Updated information in DESCRIPTION file
• Updated the dependencies to require an R version >= 4.0.0
• Moved all "depending" packages in "imports" to avoid attaching of all packages. Morover, added ggpubr and removed labeling
• Bug fixing in actualize and uniform.x.axis functions
• Optimization for better definition of the breaks in the functions uniform.x.axis and uniform.y.axis
• Optimization of package handling for plot.density.summary and plot.density.profile
• Optimized color handling for summary plots in plot.density.summary function
• Now computation and plot of the statistical mean comparisons is available for plot.density.summary
• In the plot.density.summary function a density profile corresponding to the summary plot subset range is generated
• The data.table of plot.density.summary now contains also the orignal positions used to generate the matrix
• Optimization of IGVsnap function and improvment of relative manual information
• IGVsnap allows the addiction of a delay time between snap generation

v0.1.6 - February 10th 2021

• Added the function actualize and integrated in each function to check everytime if Rseb package is up-to-date
• New functions plot.density.summary, floating.ceiling, floating.floor
• Updated the dependencies to add rvcheck and curl
• Optimization for different labeling and better handle of Y-axis autoscale in plot.density.profile function
• Optimization of uniform.x.axis and uniform.y.axis with the new functions floating.ceiling and floating.floor and to support a given number of digits

v0.1.5 - January 29th 2021

• DE.status now supports also NAs for the FoldChange
• Added functions color.gradient and is.color
• Bugs fixed in volcano

v0.1.4 - January 15th 2021

• Bugs fixed in plot.density.profile
• Bugs fixed in build.bed
• Bugs fixed in intersect.bedtools
• Updated dependencies required (labeling)
• Added functions uniform.x.axis and uniform.y.axis

v0.1.3 - January 11th 2021

• Optimization of volcano function: parameter 'font_size' added
• Bugs fixed in computeMatrix.deeptools
• Added function build.bed
• Added R version dependence (set to R >= 3.2.0) to be compatible with dplyr

v0.1.2 - January 7th 2021

• Optimization of IGVsnap function
• Added the function pkg.check

v0.1.1 - January 6th 2021

• Some bug-fixing
• Added the function read.computeMatrix.file
• Optimized function plot.density.profile to be compatibile with outputs from read.computeMatrix.file

v0.1.0 - January 5th 2021

First release.

Contributors

sebastian-gregoricchio/Rseb documentation built on June 14, 2024, 12:22 p.m.