Flexible analysis of transcriptome assemblies with Ballgown
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Alyssa C. Frazee | Andrew E. Jaffe | Jeffrey T. Leek | Geo Pertea | Steven L. Salzberg | Ben Langmead | S. Salzberg | B. Langmead | G. Pertea | J. Leek | A. Jaffe | Ben Langmead
[1] B. Williams,et al. Mapping and quantifying mammalian transcriptomes by RNA-Seq , 2008, Nature Methods.
[2] Cole Trapnell,et al. The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells , 2014, Nature Biotechnology.
[3] R. Stewart,et al. Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells , 2011, Nature.
[4] Gordon K Smyth,et al. Statistical Applications in Genetics and Molecular Biology Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments , 2011 .
[5] Cole Trapnell,et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. , 2010, Nature biotechnology.
[6] M. Pop,et al. Robust methods for differential abundance analysis in marker gene surveys , 2013, Nature Methods.
[7] W. Huber,et al. which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets , 2011 .
[8] Nadav S. Bar,et al. Landscape of transcription in human cells , 2012, Nature.
[9] John D. Storey,et al. Statistical significance for genomewide studies , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[10] John D. Storey,et al. Significance analysis of time course microarray experiments. , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[11] Charity W. Law,et al. voom: precision weights unlock linear model analysis tools for RNA-seq read counts , 2014, Genome Biology.
[12] D. Reich,et al. Principal components analysis corrects for stratification in genome-wide association studies , 2006, Nature Genetics.
[13] Mark D. Robinson,et al. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data , 2009, Bioinform..
[14] Cole Trapnell,et al. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions , 2013, Genome Biology.
[15] David P. Sexton,et al. Managing and Analyzing Next-Generation Sequence Data , 2009, PLoS Comput. Biol..
[16] Andrey A. Shabalin,et al. Matrix eQTL: ultra fast eQTL analysis via large matrix operations , 2011, Bioinform..
[17] Jeffrey T Leek,et al. Differential expression analysis of RNA-seq data at single-base resolution , 2014, Biostatistics.
[18] J. Davis. Bioinformatics and Computational Biology Solutions Using R and Bioconductor , 2007 .
[19] Matthew D. Schultz,et al. Global Epigenomic Reconfiguration During Mammalian Brain Development , 2013, Science.
[20] David G Hendrickson,et al. Differential analysis of gene regulation at transcript resolution with RNA-seq , 2012, Nature Biotechnology.
[21] B. Graveley. The developmental transcriptome of Drosophila melanogaster , 2010, Nature.
[22] Hugues Bersini,et al. InSilico DB genomic datasets hub: an efficient starting point for analyzing genome-wide studies in GenePattern, Integrative Genomics Viewer, and R/Bioconductor , 2012, Genome Biology.
[23] John D. Storey,et al. Capturing Heterogeneity in Gene Expression Studies by Surrogate Variable Analysis , 2007, PLoS genetics.
[24] Ruiqiang Li,et al. Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells , 2013, Nature Structural &Molecular Biology.
[25] Pora Kim,et al. A High-Dimensional, Deep-Sequencing Study of Lung Adenocarcinoma in Female Never-Smokers , 2013, PloS one.
[26] Günter P. Wagner,et al. Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples , 2012, Theory in Biosciences.
[27] Jean YH Yang,et al. Bioconductor: open software development for computational biology and bioinformatics , 2004, Genome Biology.
[28] L. Stein. The case for cloud computing in genome informatics , 2010, Genome Biology.
[29] Jeroen F. J. Laros,et al. Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories , 2013, Nature Biotechnology.
[30] Colin N. Dewey,et al. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome , 2011, BMC Bioinformatics.
[31] N. Friedman,et al. Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data , 2011, Nature Biotechnology.
[32] Thomas Ragg,et al. The RIN: an RNA integrity number for assigning integrity values to RNA measurements , 2006, BMC Molecular Biology.
[33] Pedro G. Ferreira,et al. Transcriptome and genome sequencing uncovers functional variation in humans , 2013, Nature.
[34] Rafael A. Irizarry,et al. Differential expression analysis of RNA-seq data at single-base resolution , 2014, Biostatistics.
[35] Chris P. Ponting,et al. Identification and Properties of 1,119 Candidate LincRNA Loci in the Drosophila melanogaster Genome , 2012, Genome biology and evolution.
[36] Gonçalo R. Abecasis,et al. The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..
[37] Gordon K. Smyth,et al. limma: Linear Models for Microarray Data , 2005 .