
                RELEASE HISTORY OF HTSFilter PACKAGE
             ========================================

		CHANGES in HTSFilter VERSION 1.31.1

-- Remove all references and functionality related to the
deprecated DESeq package.
-- Vignette has been updated to Rmarkdown from Sweave.

		CHANGES in HTSFilter VERSION 1.23.1

-- Add ImmunoOncology to biocViews in DESCRIPTION

		CHANGES in HTSFilter VERSION 1.19.3

—- Fixed bug for the DESeqDataSet class when there are additional columns in the
colData of the object beyond those used in the design (thanks to Stephanie Durand
for finding the bug!)
-- Keep rownames and colnames on filtered data for matrix and data.frame class

		CHANGES in HTSFilter VERSION 1.14.1

-- Fixed bug for missing parallel option when a CountDataSet is used with
HTSFilter

		CHANGES in HTSFilter VERSION 1.13.1

-- Fixed bug in vignette causing error message on dev (related to new
estimateDisp function in edgeR package)
-- All documentation now automatically done through Roxygen
-- Functionality for DESeq pipeline (CountDataSet objects) now deprecated
-- Add possibility for parallel computing via BiocParallel
-- Recorrect multiple testing correction of p-values in DESeq2 framework (only
correct p-values for genes that pass filter) using pAdjustMethod argument in
HTSFilter and HTSBasicFilter functions
-- Started adding unit testing framework


		CHANGES in HTSFilter VERSION 1.7.1

-- Minor bug fix for integration in edgeR pipeline
-- Minor updates in vignette and documentation
-- Removed IRanges and GenomicRanges from imports (hard-coded
the mcols and colData functions for use in DESeq2 pipeline instead)
-- Add BiocStyle to Suggests for vignette style

		CHANGES in HTSFilter VERSION 1.2.1

-- Minor bug fix for integeration in DESeq2 pipeline (which now has automatic
independent
filtering available)

-- HTSFilter now accepts data with multi-factor designs for all input types


		CHANGES in HTSFilter VERSION 1.0.1

-- Updated citation information, minor updates to vignette

-- DESeq2, IRanges, and GenomicRanges added to Imports field, and HTSFilter and HTSFilterBasic

methods written for objects of with DESeqDataSet signature (from DESeq2 pipeline).
Examples
illustrating the use of HTSFilter have also been added in the documentation and vignettes.
-- DESeq and edgeR moved to Imports field (thanks to Denis Laloë for the suggestion)

-- Warning message added when gene ID's are included as a column in the data frame

(thanks to Luc Jouneau for the suggestion)

		CHANGES in HTSFilter VERSION 0.99.3-0.99.8

-- Fixed minor bugs in HTSBasicFilter function for rpkm calculation
-- Minor changes to vignette

		CHANGES in HTSFilter VERSION 0.99.2

-- Small updates to vignette, fixed small bug in HTSBasicFilter function and doc

		CHANGES in HTSFilter VERSION 0.99.1

-- Vignette updated
-- New method HTSBasicFilter for all classes handled by HTSFilter
-- Made normalizeData a visible function
-- Changes to dependencies (include classes and methods for DESeq, include
additional classes for edgeR pipeline: DGEExact, DGEGLM, DGELRT)
-- Slight changes/additions to man pages and citation info (paper in revision)
-- Inclusion of methods for CountDataSet S4 objects
-- Inclusion of methods for additional edgeR objects: DGEList, DGEExact,
DGEGLM, and DGELRT now supported
-- Minor change in .perConditionSimilarityIndex() to use mean rather than sum
(in case of unbalanced experiments)

		CHANGES in HTSFilter VERSION 0.99.0

-- Version bumped for submission to Bioconductor.

		CHANGES in HTSFilter VERSION 0.1.1

-- Some additional documentation about the HTSFilter output
-- Small changes to vignette: typos, name changed to HTSFilter.pdf to
   allow calls to vignette("HTSFilter"), added .onAttach function to
   zzz.R to add HTSFilter vignette to Windows toolbar.
-- Added HTSFilter method for signature "data.frame"

		CHANGES in HTSFilter VERSION 0.1.0

This is the first release (29 October 2012).
