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List:       bioc-devel
Subject:    [Bioc-devel] New package HTSFilter
From:       Andrea Rau <andrea.rau () jouy ! inra ! fr>
Date:       2013-02-05 8:48:00
Message-ID: 5110C740.5090001 () jouy ! inra ! fr
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Dear developers,

The package HTSFilter is now available in the Bioc devel branch. =

HTSFilter implements a novel independent filtering procedure using a =

data-based threshold for observations with low, constant levels of =

expression in replicated RNA sequencing data. In particular, it features =

the following:

- Data-driven way to select an appropriate filtering threshold, rather =

than an arbitrarily chosen threshold (e.g., mean counts < 5)
- Filtering of observations that appear to generate an uninformative =

signal and have little chance of being identified as differentially =

expressed, thus reducing the number of tests to be performed
- Seamless integration into the DESeq (S4 class CountDataSet) and edgeR =

(D3 classes DGEList, DGEExact, DGEGLM, DGELRT) pipelines for =

differential analysis

Thanks, and I look forward to hearing your feedback.

Andrea

-- =

_____________________________________________

Dr. Andrea Rau
Institut National de la Recherche Agronomique
(GABI / PSGen)
Domaine de Vilvert, B=E2timent 211
78352 Jouy-en-Josas CEDEX
Tel: (+33) (0) 1.34.65.22.82
Fax: (+33) (0) 1.34.65.22.10
http://www.jouy.inra.fr/gabi

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