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StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

http://www.wikidata.org/entity/Q34463372

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Analysis of Whole Transcriptome Sequencing Data: Workflow and Software A survey of best practices for RNA-seq data analysis TAF1 Variants Are Associated with Dysmorphic Features, Intellectual Disability, and Neurological Manifestations OSG-GEM: Gene Expression Matrix Construction Using the Open Science Grid The Role of microRNAs in the Repeated Parallel Diversification of Lineages of Midas Cichlid Fish from Nicaragua RASER: reads aligner for SNPs and editing sites of RNA Genetic linkage of distinct adaptive traits in sympatrically speciating crater lake cichlid fish Identification and function annotation of long intervening noncoding RNAs.Benchmark analysis of algorithms for determining and quantifying full-length mRNA splice forms from RNA-seq data BinPacker: Packing-Based De Novo Transcriptome Assembly from RNA-seq Data -Omic and Electronic Health Record Big Data Analytics for Precision Medicine.CoSpliceNet: a framework for co-splicing network inference from transcriptomics data High-throughput interpretation of gene structure changes in human and nonhuman resequencing data, using ACE.The U6 snRNA m6A Methyltransferase METTL16 Regulates SAM Synthetase Intron Retention.Modulation of nonsense mediated decay by rapamycin Recycler: an algorithm for detecting plasmids from de novo assembly graphs.BASIC: BCR assembly from single cells.An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations Radiogenomic Analysis of Oncological Data: A Technical Survey.FEELnc: a tool for long non-coding RNA annotation and its application to the dog transcriptome A Comprehensive Analysis of Alternative Splicing in Paleopolyploid Maize Paternal Induction of Hybrid Dysgenesis in Drosophila melanogaster Is Weakly Correlated with Both P-Element and hobo Element Dosage.Genome-wide characterization and expression analyses of superoxide dismutase (SOD) genes in Gossypium hirsutum.A high quality Arabidopsis transcriptome for accurate transcript-level analysis of alternative splicing.Natural antisense transcripts are significantly involved in regulation of drought stress in maize.Genome-Wide Transcriptome Analysis Reveals Extensive Alternative Splicing Events in the Protoscoleces of Echinococcus granulosus and Echinococcus multilocularis Massive expansion and differential evolution of small heat shock proteins with wheat (Triticum aestivum L.) polyploidization.HopBase: a unified resource for Humulus genomics Genome-wide gene expression patterns in dikaryon of the basidiomycete fungus Pleurotus ostreatus.Insight into the Recent Genome Duplication of the Halophilic Yeast Hortaea werneckii: Combining an Improved Genome with Gene Expression and Chromatin Structure Morphological and transcriptomic evidence for ammonium induction of sexual reproduction in Thalassiosira pseudonana and other centric diatoms.Whole transcriptome sequencing of Pseudomonas syringae pv. actinidiae-infected kiwifruit plants reveals species-specific interaction between long non-coding RNA and coding genes.Regulatory evolution of innate immunity through co-option of endogenous retroviruses.Profile of microRNA in Giant Panda Blood: A Resource for Immune-Related and Novel microRNAs.CANTATAdb: A Collection of Plant Long Non-Coding RNAs.Systematic Identification and Characterization of Long Non-Coding RNAs in the Silkworm, Bombyx mori.RNAontheBENCH: computational and empirical resources for benchmarking RNAseq quantification and differential expression methods Genome-wide annotation of microRNA primary transcript structures reveals novel regulatory mechanisms ISOexpresso: a web-based platform for isoform-level expression analysis in human cancer ExSurv: A Web Resource for Prognostic Analyses of Exons Across Human Cancers Using Clinical Transcriptomes.

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StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

http://www.wikidata.org/entity/Q34463372

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2015 nî lūn-bûn

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2015 թվականի փետրվարին հրատարակված գիտական հոդված

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2015年の論文

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StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

@ast

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

@en

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

@nl

type

label

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

@ast

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

@en

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

@nl

prefLabel

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

@ast

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

@en

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

@nl

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Nature Biotechnology

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StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

@en

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Corina M Antonescu

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Geo M Pertea

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Joshua T Mendell

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Tsung-Cheng Chang

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P2860

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

An integrated encyclopedia of DNA elements in the human genome

Full-length transcriptome assembly from RNA-Seq data without a reference genome

Biases in Illumina transcriptome sequencing caused by random hexamer priming

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

Alternative isoform regulation in human tissue transcriptomes

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses

Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs

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290-295

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10.1038/NBT.3122

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3

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33

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Steven Salzberg

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2015-02-18T00:00:00Z

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1045760294

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25690850

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4643835

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