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

	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).