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