相关参考文献
注意：仅列出部分参考文献，下载原文获取全部文献信息。Omics Pipe: a community-based framework for reproducible multi-omics data analysis
Kathleen M. Fisch et al.
BIOINFORMATICS (2015)
RAP: RNA-Seq Analysis Pipeline, a new cloud-based NGS web application
Mattia D'Antonio et al.
BMC GENOMICS (2015)
sRNAtoolbox: an integrated collection of small RNA research tools
Antonio Rueda et al.
NUCLEIC ACIDS RESEARCH (2015)
miRGate: a curated database of human, mouse and rat miRNA-mRNA targets
Eduardo Andres-Leon et al.
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION (2015)
Single-cell RNA-seq transcriptome analysis of linear and circular RNAs in mouse preimplantation embryos
Xiaoying Fan et al.
GENOME BIOLOGY (2015)
CIRI: an efficient and unbiased algorithm for de novo circular RNA identification
Yuan Gao et al.
GENOME BIOLOGY (2015)
BioVLAB-MMIA-NGS: microRNA-mRNA integrated analysis using high-throughput sequencing data
Heejoon Chae et al.
BIOINFORMATICS (2015)
QuasR: quantification and annotation of short reads in R
Dimos Gaidatzis et al.
BIOINFORMATICS (2015)
featureCounts: an efficient general purpose program for assigning sequence reads to genomic features
Yang Liao et al.
BIOINFORMATICS (2014)
MAP-RSeq: Mayo Analysis Pipeline for RNA sequencing
Krishna R. Kalari et al.
BMC BIOINFORMATICS (2014)
eRNA: a graphic user interface-based tool optimized for large data analysis from high-throughput RNA sequencing
Tiezheng Yuan et al.
BMC GENOMICS (2014)
CAP-miRSeq: a comprehensive analysis pipeline for microRNA sequencing data
Zhifu Sun et al.
BMC GENOMICS (2014)
Integrated analysis of microRNA and mRNA expression and association with HIF binding reveals the complexity of microRNA expression regulation under hypoxia
Carme Camps et al.
MOLECULAR CANCER (2014)
RNA-Seq Transcriptome Profiling Identifies CRISPLD2 as a Glucocorticoid Responsive Gene that Modulates Cytokine Function in Airway Smooth Muscle Cells
Blanca E. Himes et al.
PLOS ONE (2014)
RNA-Seq Gene Profiling - A Systematic Empirical Comparison
Nuno A. Fonseca et al.
PLOS ONE (2014)
Grape RNA-Seq analysis pipeline environment
David G. Knowles et al.
BIOINFORMATICS (2013)
iMir: An integrated pipeline for high-throughput analysis of small non-coding RNA data obtained by smallRNA-Seq
Giorgio Giurato et al.
BMC BIOINFORMATICS (2013)
Detecting miRNAs in deep-sequencing data: a software performance comparison and evaluation
Vernell Williamson et al.
BRIEFINGS IN BIOINFORMATICS (2013)
Circular RNAs are a large class of animal RNAs with regulatory potency
Sebastian Memczak et al.
NATURE (2013)
Kraken: A set of tools for quality control and analysis Of high-throughput sequence data
Matthew P. A. Davis et al.
METHODS (2013)
The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote
Yang Liao et al.
NUCLEIC ACIDS RESEARCH (2013)
TCW: Transcriptome Computational Workbench
Carol Soderlund et al.
PLOS ONE (2013)
mirTools 2.0 for non-coding RNA discovery, profiling and functional annotation based on high-throughput sequencing
Jinyu Wu et al.
RNA BIOLOGY (2013)
TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
Daehwan Kim et al.
GENOME BIOLOGY (2013)
Fast gapped-read alignment with Bowtie 2
Ben Langmead et al.
NATURE METHODS (2012)
miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades
Marc R. Friedlaender et al.
NUCLEIC ACIDS RESEARCH (2012)
A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae
Intawat Nookaew et al.
NUCLEIC ACIDS RESEARCH (2012)
RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics
Marc Lohse et al.
NUCLEIC ACIDS RESEARCH (2012)
wapRNA: a web-based application for the processing of RNA sequences
Wenming Zhao et al.
BIOINFORMATICS (2011)
Differential expression in RNA-seq: A matter of depth
Sonia Tarazona et al.
GENOME RESEARCH (2011)
RNA sequencing: advances, challenges and opportunities
Fatih Ozsolak et al.
NATURE REVIEWS GENETICS (2011)
miRanalyzer: an update on the detection and analysis of microRNAs in high-throughput sequencing experiments
Michael Hackenberg et al.
NUCLEIC ACIDS RESEARCH (2011)
GENE-Counter: A Computational Pipeline for the Analysis of RNA-Seq Data for Gene Expression Differences
Jason S. Cumbie et al.
PLOS ONE (2011)
ExpressionPlot: a web-based framework for analysis of RNA-Seq and microarray gene expression data
Brad A. Friedman et al.
GENOME BIOLOGY (2011)
edgeR: a Bioconductor package for differential expression analysis of digital gene expression data
Mark D. Robinson et al.
BIOINFORMATICS (2010)
miRNAkey: a software for microRNA deep sequencing analysis
Roy Ronen et al.
BIOINFORMATICS (2010)
Fast and accurate long-read alignment with Burrows-Wheeler transform
Heng Li et al.
BIOINFORMATICS (2010)
DSAP: deep-sequencing small RNA analysis pipeline
Po-Jung Huang et al.
NUCLEIC ACIDS RESEARCH (2010)
Gene ontology analysis for RNA-seq: accounting for selection bias
Matthew D. Young et al.
GENOME BIOLOGY (2010)
Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites
Doron Betel et al.
GENOME BIOLOGY (2010)
miRExpress: Analyzing high-throughput sequencing data for profiling microRNA expression
Wei-Chi Wang et al.
BMC BIOINFORMATICS (2009)
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
Ben Langmead et al.
GENOME BIOLOGY (2009)
Mapping and quantifying mammalian transcriptomes by RNA-Seq
Ali Mortazavi et al.
NATURE METHODS (2008)
A bioinformatics tool for linking gene expression profiling results with public databases of microRNA target predictions
Chad J. Creighton et al.
RNA (2008)
The role of site accessibility in microRNA target recognition
Michael Kertesz et al.
NATURE GENETICS (2007)
RNAhybrid:: microRNA target prediction easy, fast and flexible
Jan Krueger et al.
NUCLEIC ACIDS RESEARCH (2006)
MicroTar: predicting microRNA targets from RNA duplexes
Rahul Thadani et al.
BMC BIOINFORMATICS (2006)
分享论文
