Cargando…

Chimira: analysis of small RNA sequencing data and microRNA modifications

Summary: Chimira is a web-based system for microRNA (miRNA) analysis from small RNA-Seq data. Sequences are automatically cleaned, trimmed, size selected and mapped directly to miRNA hairpin sequences. This generates count-based miRNA expression data for subsequent statistical analysis. Moreover, it...

Descripción completa

Detalles Bibliográficos
Autores principales:	Vitsios, Dimitrios M., Enright, Anton J.
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Oxford University Press 2015
Materias:	Applications Notes
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4595902/ https://www.ncbi.nlm.nih.gov/pubmed/26093149 http://dx.doi.org/10.1093/bioinformatics/btv380

Ejemplares similares

The UEA sRNA workbench: a suite of tools for analysing and visualizing next generation sequencing microRNA and small RNA datasets
por: Stocks, Matthew B., et al.
Publicado: (2012)

Oasis: online analysis of small RNA deep sequencing data
por: Capece, Vincenzo, et al.
Publicado: (2015)

Mirnovo: genome-free prediction of microRNAs from small RNA sequencing data and single-cells using decision forests
por: Vitsios, Dimitrios M., et al.
Publicado: (2017)

Large-scale analysis of microRNA expression, epi-transcriptomic features and biogenesis
por: Vitsios, Dimitrios M., et al.
Publicado: (2017)

MIO: microRNA target analysis system for immuno-oncology
por: Monfort-Lanzas, Pablo, et al.
Publicado: (2022)

P-SAMS: a web site for plant artificial microRNA and synthetic trans-acting small interfering RNA design
por: Fahlgren, Noah, et al.
Publicado: (2016)

mirPub: a database for searching microRNA publications
por: Vergoulis, Thanasis, et al.
Publicado: (2015)

CPSS 2.0: a computational platform update for the analysis of small RNA sequencing data
por: Wan, Changlin, et al.
Publicado: (2017)

DRUMMER—rapid detection of RNA modifications through comparative nanopore sequencing
por: Abebe, Jonathan S, et al.
Publicado: (2022)

shortran: a pipeline for small RNA-seq data analysis
por: Gupta, Vikas, et al.
Publicado: (2012)

Interactive Web-based Annotation of Plant MicroRNAs with iwa-miRNA
por: Zhang, Ting, et al.
Publicado: (2022)

MAGI: a Node.js web service for fast microRNA-Seq analysis in a GPU infrastructure
por: Kim, Jihoon, et al.
Publicado: (2014)

iMotifs: an integrated sequence motif visualization and analysis environment
por: Piipari, Matias, et al.
Publicado: (2010)

viRome: an R package for the visualization and analysis of viral small RNA sequence datasets
por: Watson, Mick, et al.
Publicado: (2013)

RNA-MATE: a recursive mapping strategy for high-throughput RNA-sequencing data
por: Cloonan, Nicole, et al.
Publicado: (2009)

miRcode: a map of putative microRNA target sites in the long non-coding transcriptome
por: Jeggari, Ashwini, et al.
Publicado: (2012)

piPipes: a set of pipelines for piRNA and transposon analysis via small RNA-seq, RNA-seq, degradome- and CAGE-seq, ChIP-seq and genomic DNA sequencing
por: Han, Bo W., et al.
Publicado: (2015)

NeoFuse: predicting fusion neoantigens from RNA sequencing data
por: Fotakis, Georgios, et al.
Publicado: (2020)

DEUS: an R package for accurate small RNA profiling based on differential expression of unique sequences
por: Jeske, Tim, et al.
Publicado: (2019)

SPsimSeq: semi-parametric simulation of bulk and single-cell RNA-sequencing data
por: Assefa, Alemu Takele, et al.
Publicado: (2020)

RNA interaction format: a general data format for RNA interactions
por: Schäfer, Richard A, et al.
Publicado: (2023)

cellCounts: an R function for quantifying 10x Chromium single-cell RNA sequencing data
por: Liao, Yang, et al.
Publicado: (2023)

RNA-eXpress annotates novel transcript features in RNA-seq data
por: Forster, Samuel C., et al.
Publicado: (2013)

Integration of accessibility data from structure probing into RNA–RNA interaction prediction
por: Miladi, Milad, et al.
Publicado: (2019)

TRAPR: R Package for Statistical Analysis and Visualization of RNA-Seq Data
por: Lim, Jae Hyun, et al.
Publicado: (2017)

ProkSeq for complete analysis of RNA-Seq data from prokaryotes
por: Mahmud, A K M Firoj, et al.
Publicado: (2020)

iS-CellR: a user-friendly tool for analyzing and visualizing single-cell RNA sequencing data
por: Patel, Mitulkumar V
Publicado: (2018)

Identification and removal of ribosomal RNA sequences from metatranscriptomes
por: Schmieder, Robert, et al.
Publicado: (2012)

CORNA: testing gene lists for regulation by microRNAs
por: Wu, X., et al.
Publicado: (2009)

MIRPIPE: quantification of microRNAs in niche model organisms
por: Kuenne, Carsten, et al.
Publicado: (2014)

PsRNA: A Computing Engine for the Comparative Identification of Putative Small RNA Locations within Intergenic Regions
por: Sridhar, Jayavel, et al.
Publicado: (2010)

Scdrake: a reproducible and scalable pipeline for scRNA-seq data analysis
por: Kubovčiak, Jan, et al.
Publicado: (2023)

MAPseq: highly efficient k-mer search with confidence estimates, for rRNA sequence analysis
por: Matias Rodrigues, João F, et al.
Publicado: (2017)

Seqpac: a framework for sRNA-seq analysis in R using sequence-based counts
por: Skog, Signe, et al.
Publicado: (2023)

Modeling RNA loops using sequence homology and geometric constraints
por: Schudoma, Christian, et al.
Publicado: (2010)

VIRTUS: a pipeline for comprehensive virus analysis from conventional RNA-seq data
por: Yasumizu, Yoshiaki, et al.
Publicado: (2020)

DetectIS: a pipeline to rapidly detect exogenous DNA integration sites using DNA or RNA paired-end sequencing data
por: Grassi, Luigi, et al.
Publicado: (2021)

Cerebro: interactive visualization of scRNA-seq data
por: Hillje, Roman, et al.
Publicado: (2020)

Large-scale analysis of microRNA evolution
por: Guerra-Assunção, José Afonso, et al.
Publicado: (2012)

RNA-Rocket: an RNA-Seq analysis resource for infectious disease research
por: Warren, Andrew S., et al.
Publicado: (2015)

Cannot write session to /tmp/vufind_sessions/sess_i8mvpqp8m1gnjtcp7kv00vgsjk