Changes in version 1.39.1 FIX o Fix ggplot2 compatibility issues with labs() function - removed deprecated list() syntax o Fix ggplot2 deprecation warning by replacing aes_string() with modern aes() and tidy evaluation Changes in version 1.37.1 o Remove functions that were using targetScan since it is not available anymore. Changes in version 1.33.1 o fix isoAnnotate error due to duplicates lines https://github.com/lpantano/isomiRs/issues/18 Changes in version 1.31.2 o remove `assertive.sets` o Add gitactions o Add color to PCA plot by `isoTop` function o Fix depreciated dplyr code o Many other fixes Changes in version 1.25.1 FIX o remove DiscriMiner dependency and functions since it is not available for 3.16 Changes in version 1.22.1 FIX o error with betther message when freq column = 0 https://github.com/lpantano/isomiRs/issues/20 Changes in version 1.21.1 FIX o rmarkdown dependcies o fix bug that will create difference with older versions (#19) Changes in version 1.19.2 FIX o Add affiliation of GE o Remove funs from dplyr to avoid future errors o Fix column_to_names error when there are rownames Changes in version 1.17.2 FIX o Fix n() error from dplyr. Now importing in NAMESPACE. Changes in version 1.17.1 FIX o Fix error in tibble when selecting a column. Now it needs unlist to coarce to a vector. Changes in version 1.15.2 FIX o Fix error for class type when using `counts` method. Changes in version 1.15.1 FIX o Fix bug when dataframe is empty at isoSelect: Thanks to @DrHogart. https://github.com/miRTop/mirtop/issues/65#issuecomment-593845084 o Fix class error: using is now. Changes in version 1.11.4 FEATURES o Accept files from mirtop tool Changes in version 1.11.3 FEATURES o Combined samples and create new object. Useful for technical replicates. o Add isoAnnotate function to get more information for each isomiR. o Add isomiR naming and sequences table in metadata of object. o Remove reference sequences from isoPlot figures. o Support filtering isomiRs with low % of importance (statistically supported). o Support isoPLot to use only certain isomiRs. Changes in version 1.11.2 FIX o Fix NEWS format. o Fix documentation typos. FEATURES o Filter isomiRs by importance ratio. o Allow to plot selected isomiRs with isoPlot function. Changes in version 1.9.4 o Support object creation from rawData of a current IsomirDataSeq object. Changes in version 1.9.3 o Fix warnings in dosc. Changes in version 1.9.2 o Fix bug that quantify wrongly the reference sequence. Changes in version 1.9.1 MAJOR o Improve clustering in isoNetwork plot. o Use varianceStabilizingTransformation to normalize counts. o Use a less common column as ID for samples in isoPLot fns. o Add updateIsomirDataSeq to be compatible with previous versions. o Adapt all functions to new object. Fix documentation. o Reduce object size and structure Changes in version 1.7.3 FIX o Fix findTargets to use common groups between miRNA and mRNA data sets. o Fix mirna2targetscan to accept mmu species. o Error in isoNetwork example code. Changes in version 1.7.2 Feature o Better looking for isoPlotNet function. o Improve docs for mm isomiR plot. Thanks to @mshadbolt. o Add option to remove ambiguos reads. o Add option to get other gene ID when retrieving miRNA targets. o Improve docs to explain better isoPlot figures. Thanks @mshadbolt. o Add mirna prediction using targetscan annotation package in BioC. FIX o Fix examples for findTargets. o Error in names columns for isoNetwork analysis. o Remove sequences with Ns in add column. o Move correction functions to independent package scounts. Changes in version 1.7.1 FIX o Use limma::voom when number of samples is high. Set up by user. o 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