NEWS.md

In Aufiero/circRNAprofiler: circRNAprofiler: An R-Based Computational Framework for the Downstream Analysis of Circular RNAs

Version 1.0.0 (Oct 29, 2019)

• First release on bioconductor

Version 1.1.2 (development version) (Dic 15, 2019)

• Improved vignettes

• In plotMotifs function:

  • To avoid infinity as a value for fold change, 1 was added to number of occurences of each motif found in the foreground and background target sequences before the normalization.

  • Added angle param for the rotation angle of the axis labels.

  • Added removeNegLog2FC param to remove the RBPs having a negative log2FC.

• volcanoPlot function:

  • Added geneSet param that allows to show only specified host gene names.

• In getMotifs function:

  • Included possibilities to use motifs of RBPs from MEME database

Version 1.1.3 (development version) (Dic 19, 2019)

• In plotMotifs function:
  • Added n param for filtering the motifs.

Version 1.1.4 (development version) (Jen 08, 2020)

• In getMotifs function:
  • Fixed a bug when trimming the BSJ sequences. E.g. by setting width = 6, the BSJ sequences are trimmed so that only 5 nucleotides are left at each side of the BSJ. If width = 7, then 6 nucleotides are left at each side of the BSJ etc.

Version 1.1.5 (development version) (Jen 09, 2020)

• In plotMotifs function:
  • Before only motifs found in the foreground sequences were reported. Now also motifs found in the background are reported in the output.

Version 1.1.14 (development version) (Jen 09, 2020)

• In mergeBSJunctions function:
  • Since different detection tools can report sligtly different coordinates before grouping the back-spliced junctions, it is now possible to fix the latter using the gtf file. See param fixBSJsWithGTF.

Version 1.2.0 (April 27, 2020)

• Second release on bioconductor

Version 1.3.1 (development version)

• Added files to fix bugs

Version 1.4.0 (October 27, 2020)

• Third release on bioconductor

Version 1.5.3 (development version)

• Removed citr package from DESCRIPTION

Version 1.8.0 (October 27, 2021)

• Fifth release on bioconductor

Version 1.15.2 (October 10, 2023)

• Possibility to use a maximum of 3 unsupported/‘other’ tools.

Version 1.15.3 (October 24, 2023)

• Fixed bug due to dplyr::bind_rows()

Aufiero/circRNAprofiler documentation built on Nov. 3, 2024, 10:12 a.m.