NEWS

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isomiRs 1.33.1

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

isomiRs 1.31.2

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

isomiRs 1.25.1

FIX

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

isomiRs 1.22.1

FIX

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

isomiRs 1.21.1

FIX

• rmarkdown dependcies
• fix bug that will create difference with older versions (#19)

isomiRs 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

isomiRs 1.17.2

FIX

• Fix n() error from dplyr. Now importing in NAMESPACE.

isomiRs 1.17.1

FIX

• Fix error in tibble when selecting a column. Now it needs unlist to coarce to a vector.

isomiRs 1.15.2

FIX

• Fix error for class type when using 'counts' method.

isomiRs 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.

isomiRs 1.11.4

FEATURES

• Accept files from mirtop tool

isomiRs 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.

isomiRs 1.11.2

FIX

• Fix NEWS format.
• Fix documentation typos.

FEATURES

• Filter isomiRs by importance ratio.
• Allow to plot selected isomiRs with isoPlot function.

isomiRs 1.9.4

• Support object creation from rawData of a current IsomirDataSeq object.

isomiRs 1.9.3

• Fix warnings in dosc.

isomiRs 1.9.2

• Fix bug that quantify wrongly the reference sequence.

isomiRs 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

isomiRs 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.

isomiRs 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.

isomiRs 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.

isomiRs 1.5.5

FIX

• Migrate vignette to new BiocStyle
• Remove unused function join_all
• Use parameter not integer number
• Using testthat for unit test

isomiRs 1.5.4

FEATURES

• Better documentation for isoCorrection function. Add proper authors and citation.

isomiRs 1.5.3

FEATURES

• Better colors for polar plot of isomiRs

FIX

• Fix notes during R CHECK for variables inside dplyr/ggplot functions
• Use roxygen2 for NAMESPACE

isomiRs 1.5.2

FIX

• Remove TMB dependency

isomiRs 1.5.1

FEATURES

• Add new polar figure to plot all isomiRs at the same time
• Add NLQO distribution to correct expression knowing sequencing bias [Argyropoulos et al, 2017]
• Improve data documentation

isomiRs 1.3.5

FEATURES

• Add isomiRs naming to documentation
• Add design to the object to get better usability
• Remove non-template addition with C/G nucleotides by default (canonicalAdd)
• Remove sequences with mutations and more than one miRNA hit

isomiRs 1.3.4

FIXES

• Fix removing false mutations from the raw files. Change sequences to correct the nucleotide at the specific position.

FEATURES

• Improve code to remove error sequencing from raw data
• Improve code to show the raw data with isoSelect

isomiRs 1.3.3

FIXES

• Fix data with correct headers name

isomiRs 1.3.2

OTHERS

• Preparing migration to new isomiRs naming using mirTOP naming system

isomiRs 1.3.1

OTHERS

• Add option to IsomirDataSeqFromFiles to decide when to consider mutations as reals

isomiRs 1.1.5

OTHERS

• Suppress message from readr when reading
• Add instruction of how to create DESeq2 object from ids one.

isomiRs 1.1.4

OTHERS

• Add mRNA-miRNA integration

isomiRs 1.1.2

OTHERS

• Update version dependecy for packages

isomiRs 0.99.18

BUG FIXES

• Avoid removing isomiRs with mutation and reference non-detected

isomiRs 0.99.13

NEW FEATURES

• Modify main class to have all the information in metadata
• Improve docs with more information in return values
• Add minimum data to test creation of main class