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NEWS.Rmd
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NEWS.Rmd
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---
output: md_document
---
# 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()