Changes in version 1.39.1

FIX

* Fix ggplot2 compatibility issues with labs() function - removed deprecated list() syntax
* Fix ggplot2 deprecation warning by replacing aes_string() with modern aes() and tidy evaluation

Changes in version 1.37.1

* Remove functions that were using targetScan since it is not available anymore.

Changes in version  1.33.1

* fix isoAnnotate error due to duplicates lines https://github.com/lpantano/isomiRs/issues/18

Changes in version  1.31.2 (Ömer An)

* remove `assertive.sets`
* Add gitactions
* Add color to PCA plot by `isoTop` function
* Fix depreciated dplyr code
* Many other fixes

Changes in version  1.25.1

FIX

* remove DiscriMiner dependency and functions since it is not available for 3.16

Changes in version  1.22.1

FIX

* error with betther message when freq column = 0
  https://github.com/lpantano/isomiRs/issues/20

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
