Changes in version 1.25.1
FIX
* remove DiscriMiner dependency and functions since it is not available for 3.16
Changes in version 1.21.1
FIX
* rmarkdown dependcies
* fix bug that will create difference with older versions (#19)
Changes in version 1.19.2
FIX
* Add affiliation of GE
* Remove funs from dplyr to avoid future errors
* Fix column_to_names error when there are rownames
Changes in version 1.17.2
FIX
* Fix n() error from dplyr. Now importing in NAMESPACE.
Changes in version 1.17.1
FIX
* Fix error in tibble when selecting a column. Now it needs unlist to coarce to a vector.
Changes in version 1.15.2
FIX
* Fix error for class type when using `counts` method.
Changes in version 1.15.1
FIX
* Fix bug when dataframe is empty at isoSelect: Thanks to @DrHogart. https://github.com/miRTop/mirtop/issues/65#issuecomment-593845084
* Fix class error: using is now.
Changes in version 1.11.4
FEATURES
* Accept files from mirtop tool
Changes in version 1.11.3
FEATURES
* Combined samples and create new object. Useful for technical replicates.
* Add isoAnnotate function to get more information for each isomiR.
* Add isomiR naming and sequences table in metadata of object.
* Remove reference sequences from isoPlot figures.
* Support filtering isomiRs with low % of importance (statistically supported).
* Support isoPLot to use only certain isomiRs.
Changes in version 1.11.2
FIX
* Fix NEWS format.
* Fix documentation typos.
FEATURES
* Filter isomiRs by importance ratio.
* Allow to plot selected isomiRs with isoPlot function.
Changes in version 1.9.4
* Support object creation from rawData of a current IsomirDataSeq object.
Changes in version 1.9.3
* Fix warnings in dosc.
Changes in version 1.9.2
* Fix bug that quantify wrongly the reference sequence.
Changes in version 1.9.1
MAJOR
* Improve clustering in isoNetwork plot.
* Use varianceStabilizingTransformation to normalize counts.
* Use a less common column as ID for samples in isoPLot fns.
* Add updateIsomirDataSeq to be compatible with previous versions.
* Adapt all functions to new object. Fix documentation.
* Reduce object size and structure
Changes in version 1.7.3
FIX
* Fix findTargets to use common groups between miRNA and mRNA data sets.
* Fix mirna2targetscan to accept mmu species.
* Error in isoNetwork example code.
Changes in version 1.7.2
Feature
* Better looking for isoPlotNet function.
* Improve docs for mm isomiR plot. Thanks to @mshadbolt.
* Add option to remove ambiguos reads.
* Add option to get other gene ID when retrieving miRNA targets.
* Improve docs to explain better isoPlot figures. Thanks @mshadbolt.
* Add mirna prediction using targetscan annotation package in BioC.
FIX
* Fix examples for findTargets.
* Error in names columns for isoNetwork analysis.
* Remove sequences with Ns in add column.
* Move correction functions to independent package scounts.
Changes in version 1.7.1
FIX
* Use limma::voom when number of samples is high. Set up by user.
* Fix error when table is empty after filtering bad hits.
Changes in version 1.5.5
FIX
o Migrate vignette to new BiocStyle
o Remove unused function join_all
o Use parameter not integer number
o Using testthat for unit test
Changes in version 1.5.4
FEATURES
o Better documentation for isoCorrection function. Add
proper authors and citation.
Changes in version 1.5.3
FEATURES
o Better colors for polar plot of isomiRs
FIX
o Fix notes during R CHECK for variables inside dplyr/ggplot functions
o Use roxygen2 for NAMESPACE
Changes in version 1.5.2
FIX
o Remove TMB dependency
Changes in version 1.5.1
FEATURES
o Add new polar figure to plot all isomiRs at the same time
o Add NLQO distribution to correct expression knowing sequencing
bias [Argyropoulos et al, 2017]
o Improve data documentation
Changes in version 1.3.5
FEATURES
o Add isomiRs naming to documentation
o Add design to the object to get better usability
o Remove non-template addition with C/G nucleotides by default (canonicalAdd)
o Remove sequences with mutations and more than one miRNA hit
Changes in version 1.3.4
FIXES
o Fix removing false mutations from the raw files. Change sequences
to correct the nucleotide at the specific position.
FEATURES
o Improve code to remove error sequencing from raw data
o Improve code to show the raw data with isoSelect
Changes in version 1.3.3
FIXES
o Fix data with correct headers name
Changes in version 1.3.2
OTHERS
o Preparing migration to new isomiRs naming using mirTOP naming system
Changes in version 1.3.1
OTHERS
o Add option to IsomirDataSeqFromFiles to decide
when to consider mutations as reals
Changes in version 1.1.5
OTHERS
o Suppress message from readr when reading
o Add instruction of how to create DESeq2 object from ids one.
Changes in version 1.1.4
OTHERS
o Add mRNA-miRNA integration
Changes in version 1.1.2
OTHERS
o Update version dependecy for packages
Changes in version 0.99.18
BUG FIXES
o Avoid removing isomiRs with mutation and reference non-detected
Changes in version 0.99.13
NEW FEATURES
o Modify main class to have all the information in metadata
o Improve docs with more information in return values
o Add minimum data to test creation of main class