NEWS.md

In 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

circRNAprofiler documentation built on March 6, 2021, 2 a.m.