Bioinformatics

RAX2: genome-wide detection of condition-associated transcription variation
Yuan-De Tan, Jixin Deng, Joel R. Neilson

bioRxiv 013201; doi: https://doi.org/10.1101/013201

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Polyester: Simulating RNA-Seq Datasets With Differential Transcript Expression
Alyssa C. Frazee, Andrew E. Jaffe, Ben Langmead, Jeffrey T. Leek

bioRxiv 006015; doi: https://doi.org/10.1101/006015

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QuASAR: Quantitative Allele Specific Analysis of Reads
Chris T. Harvey, Gregory A. Moyerbrailean, Gordon O. Davis, Xiaoquan Wen, Francesca Luca, Roger Pique-Regi

bioRxiv 007492; doi: https://doi.org/10.1101/007492

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SpeedSeq: Ultra-fast personal genome analysis and interpretation
Colby Chiang, Ryan M Layer, Gregory G Faust, Michael R Lindberg, David B Rose, Erik P Garrison, Gabor T Marth, Aaron R Quinlan, Ira M Hall

bioRxiv 012179; doi: https://doi.org/10.1101/012179

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Searching and Indexing Genomic Databases via Kernelization
Travis Gagie, Simon J. Puglisi

bioRxiv 012161; doi: https://doi.org/10.1101/012161

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Reveel: large-scale population genotyping using low-coverage sequencing data
Lin Huang, Bo Wang, Ruitang Chen, Sivan Bercovici, Serafim Batzoglou

bioRxiv 011882; doi: https://doi.org/10.1101/011882

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FlexAID: Revisiting docking on non native-complex structures
F. Gaudreault, R. Najmanovich

bioRxiv 011791; doi: https://doi.org/10.1101/011791 New Results

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CNVkit: Copy number detection and visualization for targeted sequencing using off-target reads
Eric Talevich, A. Hunter Shain, Thomas Botton, Boris C. Bastian

bioRxiv 010876; doi: https://doi.org/10.1101/010876

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CLASS: Accurate and Efficient Splice Variant Annotation from RNA-seq Reads
Li Song, Sarven Sabunciyan, Liliana Florea

bioRxiv 011718; doi: https://doi.org/10.1101/011718

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FusionCatcher – a tool for finding somatic fusion genes in paired-end RNA-sequencing data
Daniel Nicorici, Mihaela Şatalan, Henrik Edgren, Sara Kangaspeska, Astrid Murumägi, Olli Kallioniemi, Sami Virtanen, Olavi Kilkku

bioRxiv 011650; doi: https://doi.org/10.1101/011650

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Bioinformatics

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