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Transcriptome analysis

This section incorporates all aspects of transcriptomic analysis including but not limited to: methods and applications for the analysis of microarray and RNA-seq data.

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1.

Software   Open Access

BioTile, A Perl based tool for the identification of differentially enriched regions in tiling microarray data

Jerry Guintivano, Michal Arad, Kellie LK Tamashiro, Todd D Gould, Zachary A Kaminsky BMC Bioinformatics 2013, 14:76 (3 March 2013)

Abstract | Provisional PDF

2.

Software   Open Access

virtualArray: a R/bioconductor package to merge raw data from different microarray platforms

Andreas Heider, Rüdiger Alt BMC Bioinformatics 2013, 14:75 (2 March 2013)

Abstract | Provisional PDF

3.

Research article   Open Access

Identification of germ cell-specific genes in mammalian meiotic prophase

Yunfei Li, Debjit Ray, Ping Ye BMC Bioinformatics 2013, 14:72 (27 February 2013)

Abstract | Provisional PDF | PubMed

4.

Methodology article   Open Access

A novel method for cross-species gene expression analysis

Erik Kristiansson, Tobias Österlund, Lina Gunnarsson, Gabriella Arne, D G Joakim Larsson, Olle Nerman BMC Bioinformatics 2013, 14:70 (27 February 2013)

Abstract | Provisional PDF | PubMed

5.

Research article   Open Access

Improved shrunken centroid classifiers for high-dimensional class-imbalanced data

Rok Blagus, Lara Lusa BMC Bioinformatics 2013, 14:64 (23 February 2013)

Abstract | Provisional PDF | PubMed

6.

Methodology article   Open Access Highly Accessed

A new unsupervised gene clustering algorithm based on the integration of biological knowledge into expression data

Marie Verbanck, Sébastien Lê, Jérôme Pagès BMC Bioinformatics 2013, 14:42 (7 February 2013)

Abstract | Provisional PDF | PubMed

7.

Software   Open Access Highly Accessed

puma 3.0: improved uncertainty propagation methods for gene and transcript expression analysis

Xuejun Liu, Zhenzhu Gao, Li Zhang, Magnus Rattray BMC Bioinformatics 2013, 14:39 (5 February 2013)

Abstract | Provisional PDF | PubMed

8.

Software   Open Access

FUSIM: a software tool for simulating fusion transcripts

Andrew E Bruno, Jeffrey C Miecznikowski, Maochun Qin, Jianmin Wang, Song Liu BMC Bioinformatics 2013, 14:13 (16 January 2013)

Abstract | Provisional PDF | PubMed

9.

Software   Open Access Highly Accessed

GSVA: gene set variation analysis for microarray and RNA-Seq data

Sonja Hänzelmann, Robert Castelo, Justin Guinney BMC Bioinformatics 2013, 14:7 (16 January 2013)

Abstract | Provisional PDF | PubMed

10.

Methodology article   Open Access

More powerful significant testing for time course gene expression data using functional principal component analysis approaches

Shuang Wu, Hulin Wu BMC Bioinformatics 2013, 14:6 (16 January 2013)

Abstract | Provisional PDF | PubMed

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