Cargando…

DNAshapeR: an R/Bioconductor package for DNA shape prediction and feature encoding

Summary: DNAshapeR predicts DNA shape features in an ultra-fast, high-throughput manner from genomic sequencing data. The package takes either nucleotide sequence or genomic coordinates as input and generates various graphical representations for visualization and further analysis. DNAshapeR further...

Descripción completa

Detalles Bibliográficos
Autores principales:	Chiu, Tsu-Pei, Comoglio, Federico, Zhou, Tianyin, Yang, Lin, Paro, Renato, Rohs, Remo
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Oxford University Press 2016
Materias:	Applications Notes
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4824130/ https://www.ncbi.nlm.nih.gov/pubmed/26668005 http://dx.doi.org/10.1093/bioinformatics/btv735

Ejemplares similares

rGREAT: an R/bioconductor package for functional enrichment on genomic regions
por: Gu, Zuguang, et al.
Publicado: (2022)

twoddpcr: an R/Bioconductor package and Shiny app for Droplet Digital PCR analysis
por: Chiu, Anthony, et al.
Publicado: (2017)

tRanslatome: an R/Bioconductor package to portray translational control
por: Tebaldi, Toma, et al.
Publicado: (2014)

PAA: an R/bioconductor package for biomarker discovery with protein microarrays
por: Turewicz, Michael, et al.
Publicado: (2016)

MWASTools: an R/bioconductor package for metabolome-wide association studies
por: Rodriguez-Martinez, Andrea, et al.
Publicado: (2018)

monaLisa: an R/Bioconductor package for identifying regulatory motifs
por: Machlab, Dania, et al.
Publicado: (2022)

syntenet: an R/Bioconductor package for the inference and analysis of synteny networks
por: Almeida-Silva, Fabricio, et al.
Publicado: (2022)

HTSanalyzeR: an R/Bioconductor package for integrated network analysis of high-throughput screens
por: Wang, Xin, et al.
Publicado: (2011)

karyoploteR: an R/Bioconductor package to plot customizable genomes displaying arbitrary data
por: Gel, Bernat, et al.
Publicado: (2017)

psygenet2r: a R/Bioconductor package for the analysis of psychiatric disease genes
por: Gutiérrez-Sacristán, Alba, et al.
Publicado: (2017)

Pathview: an R/Bioconductor package for pathway-based data integration and visualization
por: Luo, Weijun, et al.
Publicado: (2013)

TFBSTools: an R/bioconductor package for transcription factor binding site analysis
por: Tan, Ge, et al.
Publicado: (2016)

cytomapper: an R/Bioconductor package for visualization of highly multiplexed imaging data
por: Eling, Nils, et al.
Publicado: (2020)

motifbreakR: an R/Bioconductor package for predicting variant effects at transcription factor binding sites
por: Coetzee, Simon G., et al.
Publicado: (2015)

regioneR: an R/Bioconductor package for the association analysis of genomic regions based on permutation tests
por: Gel, Bernat, et al.
Publicado: (2016)

CTCF: an R/bioconductor data package of human and mouse CTCF binding sites
por: Dozmorov, Mikhail G, et al.
Publicado: (2022)

girafe – an R/Bioconductor package for functional exploration of aligned next-generation sequencing reads
por: Toedling, Joern, et al.
Publicado: (2010)

mbQTL: an R/Bioconductor package for microbial quantitative trait loci (QTL) estimation
por: Movassagh, Mercedeh, et al.
Publicado: (2023)

DNAshape: a method for the high-throughput prediction of DNA structural features on a genomic scale
por: Zhou, Tianyin, et al.
Publicado: (2013)

CNVfilteR: an R/Bioconductor package to identify false positives produced by germline NGS CNV detection tools
por: Moreno-Cabrera, José Marcos, et al.
Publicado: (2021)

Top-Down Crawl: a method for the ultra-rapid and motif-free alignment of sequences with associated binding metrics
por: Cooper, Brendon H, et al.
Publicado: (2022)

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data
por: Robinson, Mark D., et al.
Publicado: (2010)

Seq2pathway: an R/Bioconductor package for pathway analysis of next-generation sequencing data
por: Wang, Bin, et al.
Publicado: (2015)

Importing ArrayExpress datasets into R/Bioconductor
por: Kauffmann, Audrey, et al.
Publicado: (2009)

NewWave: a scalable R/Bioconductor package for the dimensionality reduction and batch effect removal of single-cell RNA-seq data
por: Agostinis, Federico, et al.
Publicado: (2022)

Sincell: an R/Bioconductor package for statistical assessment of cell-state hierarchies from single-cell RNA-seq
por: Juliá, Miguel, et al.
Publicado: (2015)

ELMER v.2: an R/Bioconductor package to reconstruct gene regulatory networks from DNA methylation and transcriptome profiles
por: Silva, Tiago C, et al.
Publicado: (2019)

clustComp, a bioconductor package for the comparison of clustering results
por: Torrente, Aurora, et al.
Publicado: (2017)

BPRMeth: a flexible Bioconductor package for modelling methylation profiles
por: Kapourani, Chantriolnt-Andreas, et al.
Publicado: (2018)

Synaptome.db: a bioconductor package for synaptic proteomics data
por: Sorokina, Oksana, et al.
Publicado: (2022)

CTDquerier: a bioconductor R package for Comparative Toxicogenomics Database(TM) data extraction, visualization and enrichment of environmental and toxicological studies
por: Hernandez-Ferrer, Carles, et al.
Publicado: (2018)

KEGGgraph: a graph approach to KEGG PATHWAY in R and bioconductor
por: Zhang, Jitao David, et al.
Publicado: (2009)

easyRNASeq: a bioconductor package for processing RNA-Seq data
por: Delhomme, Nicolas, et al.
Publicado: (2012)

arrayQualityMetrics—a bioconductor package for quality assessment of microarray data
por: Kauffmann, Audrey, et al.
Publicado: (2009)

R/Bioconductor software for Illumina's Infinium whole-genome genotyping BeadChips
por: Ritchie, Matthew E., et al.
Publicado: (2009)

LOLA: enrichment analysis for genomic region sets and regulatory elements in R and Bioconductor
por: Sheffield, Nathan C., et al.
Publicado: (2016)

struct: an R/Bioconductor-based framework for standardized metabolomics data analysis and beyond
por: Lloyd, Gavin Rhys, et al.
Publicado: (2020)

SpatialExperiment: infrastructure for spatially-resolved transcriptomics data in R using Bioconductor
por: Righelli, Dario, et al.
Publicado: (2022)

HPiP: an R/Bioconductor package for predicting host–pathogen protein–protein interactions from protein sequences using ensemble machine learning approach
por: Rahmatbakhsh, Matineh, et al.
Publicado: (2022)

RankProd 2.0: a refactored bioconductor package for detecting differentially expressed features in molecular profiling datasets
por: Del Carratore, Francesco, et al.
Publicado: (2017)

Cannot write session to /tmp/vufind_sessions/sess_fh20k8jmgs5pcubb1rqs984l54