
                RELEASE HISTORY OF coseq PACKAGE
             ========================================

    coseq VERSION 1.15.1 - 1.15.6

-- Improved documentation in vignette, especially FAQs. (Thanks to Florian Rocher,
David Roux, and Jessica Keffer for questions leading to these clarifications.)
-- Fixed non-reproducibility observed when seed argument is provided for
Poisson mixture model and K-means with parallel computing. (Thanks to Océane
Cassan for the bug report.)

    coseq VERSION 1.13.1 - 1.13.2

-- Adjust plotting function to remove ggplot2 warning. (Thanks to Praveen Kumar for the pull request.)
-- Add option to remove red lines from boxplots with add_lines argument. (Thanks to
Marie-Laure Martin-Magniette for the suggestion.)
-- Fix behavior when seed is to be set for reproducible results for the Normal
mixture model via the new seed argument.

		coseq VERSION 1.7.1 - 1.7.3

-- Add ImmunoOncology to biocViews in DESCRIPTION
-- Add informative error message when a subset of estimated Gaussian mixture models
have singular covariance matrices.
-- Add generic for plot function.
-- Specify UTF-8 encoding in DESCRIPTION.
-- Minor updates to vignette and documentation.

		coseq VERSION 1.5.2

-- Fix use of n_row and n_col in plotting function, and fix bug in coseq plotting
when data feature an unbalanced number of replicates per condition. (Thanks to
Yuguo Xiao for the bug report.)
-- Remove dependency on gridExtra package (previously the use of n_row and n_col
In plotting used marrangeGrob, but this is now directly dealt with using ggplot2).
-- Update vignette to illustrate how to customize coseq plots via ggplot2.

		coseq VERSION 1.5.1

-- Clarify in documentation that normalization can be suppressed by setting
normFactors = "none" in coseq. (Thanks to David Rangel for many helpful discussions.)
-- K-means can now be run for less than 10 models without provoking an error;
however, a message appears to inform user that model selection via capushe is not
possible (and the largest model is automatically selected).
-- Updated citations.
-- The coseq plot function now has the argument collapse_rows, which can take the
values c("none", "sum", "average"). When collapse_rows = "sum", the plot behaves
the same as when average_over_conds = TRUE , and profiles for replicates within a
condition are summed. When collapse_rows = "average", values for replicates are
averaged; this behavior may be preferable for highly unbalanced designs. (Thanks to
Gosia Komor for the idea.)



		coseq VERSION 1.3.2

-- Added some clarification in the documentation of coseq, especially to
clarify that genes should be in rows and samples in columns.
-- Added some checks/warnings for “normal” vs “Normal”, applying transformations
to profiles
-- Updated maintainer email

		coseq VERSION 1.1.3

-- Corrected error causing failing test for compareARI function when a matrix
of non-discrete and/or non-positive values was provided.

		coseq VERSION 0.99.8 - 0.99.12

-- Add Fietz et al. (2012) data to package
-- Add in K-means algorithm functionality and conditional probability
calculation.
-- Add flexibility in graph options (output ggplot object from function,
xlab, ylab, use_sample_names, optional facet labeling)
-- Updated vignette and citation info.


		coseq VERSION 0.99.5

-- Add unit tests, remove static vignette.

		coseq VERSION 0.99.1

-- Fairly significant changes to address Bioconductor reviewer comments. In
particular, the package now makes use of S4 classes and methods: a new S4 class,
coseqResults, has been created to extend the RangedSummarizedExperiment S4 class
from the SummarizedExperiment package.

		coseq VERSION 0.1.x - 0.99.0

-- Initial development version of coseq.

