Cargando…

HiCUP: pipeline for mapping and processing Hi-C data

HiCUP is a pipeline for processing sequence data generated by Hi-C and Capture Hi-C (CHi-C) experiments, which are techniques used to investigate three-dimensional genomic organisation. The pipeline maps data to a specified reference genome and removes artefacts that would otherwise hinder subsequen...

Descripción completa

Detalles Bibliográficos
Autores principales:	Wingett, Steven, Ewels, Philip, Furlan-Magaril, Mayra, Nagano, Takashi, Schoenfelder, Stefan, Fraser, Peter, Andrews, Simon
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	F1000Research 2015
Materias:	Software Tool Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4706059/ https://www.ncbi.nlm.nih.gov/pubmed/26835000 http://dx.doi.org/10.12688/f1000research.7334.1

Ejemplares similares

Promoter Capture Hi-C: High-resolution, Genome-wide Profiling of Promoter Interactions
por: Schoenfelder, Stefan, et al.
Publicado: (2018)

HiC-Pro: an optimized and flexible pipeline for Hi-C data processing
por: Servant, Nicolas, et al.
Publicado: (2015)

Comparison of Hi-C results using in-solution versus in-nucleus ligation
por: Nagano, Takashi, et al.
Publicado: (2015)

HiCmapTools: a tool to access HiC contact maps
por: Chang, Jia-Ming, et al.
Publicado: (2022)

Global Reorganization of the Nuclear Landscape in Senescent Cells
por: Chandra, Tamir, et al.
Publicado: (2015)

FastQ Screen: A tool for multi-genome mapping and quality control
por: Wingett, Steven W., et al.
Publicado: (2018)

HiCdat: a fast and easy-to-use Hi-C data analysis tool
por: Schmid, Marc W., et al.
Publicado: (2015)

HiCcompare: an R-package for joint normalization and comparison of HI-C datasets
por: Stansfield, John C., et al.
Publicado: (2018)

HiCHap: a package to correct and analyze the diploid Hi-C data
por: Luo, Han, et al.
Publicado: (2020)

Infrastructure for genomic interactions: Bioconductor classes for Hi-C, ChIA-PET and related experiments
por: Lun, Aaron T. L., et al.
Publicado: (2016)

HiFiAdapterFilt, a memory efficient read processing pipeline, prevents occurrence of adapter sequence in PacBio HiFi reads and their negative impacts on genome assembly
por: Sim, Sheina B., et al.
Publicado: (2022)

HiChIP: a high-throughput pipeline for integrative analysis of ChIP-Seq data
por: Yan, Huihuang, et al.
Publicado: (2014)

HiC-bench: comprehensive and reproducible Hi-C data analysis designed for parameter exploration and benchmarking
por: Lazaris, Charalampos, et al.
Publicado: (2017)

HiFive: a tool suite for easy and efficient HiC and 5C data analysis
por: Sauria, Michael EG, et al.
Publicado: (2015)

Qudi-HiM: an open-source acquisition software package for highly multiplexed sequential and combinatorial optical imaging
por: Barho, Franziska, et al.
Publicado: (2022)

Cluster Flow: A user-friendly bioinformatics workflow tool
por: Ewels, Philip, et al.
Publicado: (2017)

HiGlass: web-based visual exploration and analysis of genome interaction maps
por: Kerpedjiev, Peter, et al.
Publicado: (2018)

Hi-C as a tool for precise detection and characterisation of chromosomal rearrangements and copy number variation in human tumours
por: Harewood, Louise, et al.
Publicado: (2017)

MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads
por: Uliano-Silva, Marcela, et al.
Publicado: (2023)

Unbiased analysis of potential targets of breast cancer susceptibility loci by Capture Hi-C
por: Dryden, Nicola H., et al.
Publicado: (2014)

EndHiC: assemble large contigs into chromosome-level scaffolds using the Hi-C links from contig ends
por: Wang, Sen, et al.
Publicado: (2022)

HiCPlotter integrates genomic data with interaction matrices
por: Akdemir, Kadir Caner, et al.
Publicado: (2015)

CHiCAGO: robust detection of DNA looping interactions in Capture Hi-C data
por: Cairns, Jonathan, et al.
Publicado: (2016)

GOPHER: Generator Of Probes for capture Hi-C Experiments at high Resolution
por: Hansen, Peter, et al.
Publicado: (2019)

Single cell Hi-C reveals cell-to-cell variability in chromosome structure
por: Nagano, Takashi, et al.
Publicado: (2013)

Efficient iterative Hi-C scaffolder based on N-best neighbors
por: Guan, Dengfeng, et al.
Publicado: (2021)

HiCognition: a visual exploration and hypothesis testing tool for 3D genomics
por: Langer, Christoph C. H., et al.
Publicado: (2023)

Comparison of Capture Hi-C Analytical Pipelines
por: Aljogol, Dina, et al.
Publicado: (2022)

diffHic: a Bioconductor package to detect differential genomic interactions in Hi-C data
por: Lun, Aaron T.L., et al.
Publicado: (2015)

PUblications Metadata Augmentation (PUMA) pipeline
por: Butters, Oliver W., et al.
Publicado: (2021)

GRAPE: genomic relatedness detection pipeline
por: Medvedev, Alexander, et al.
Publicado: (2023)

SNP HiTLink: a high-throughput linkage analysis system employing dense SNP data
por: Fukuda, Yoko, et al.
Publicado: (2009)

ChromContact: A web tool for analyzing spatial contact of chromosomes from Hi-C data
por: Sato, Tetsuya, et al.
Publicado: (2015)

bin3C: exploiting Hi-C sequencing data to accurately resolve metagenome-assembled genomes
por: DeMaere, Matthew Z., et al.
Publicado: (2019)

MHiC, an integrated user-friendly tool for the identification and visualization of significant interactions in Hi-C data
por: Khakmardan, Saman, et al.
Publicado: (2020)

Pentad: a tool for distance-dependent analysis of Hi-C interactions within and between chromatin compartments
por: Magnitov, Mikhail D., et al.
Publicado: (2022)

snHiC: a complete and simplified snakemake pipeline for grouped Hi-C data analysis
por: Gregoricchio, Sebastian, et al.
Publicado: (2023)

BridgeDb app: unifying identifier mapping services for Cytoscape
por: Gao, Jianjiong, et al.
Publicado: (2014)

Pgltools: a genomic arithmetic tool suite for manipulation of Hi-C peak and other chromatin interaction data
por: Greenwald, William W., et al.
Publicado: (2017)

Geniac: Automatic Configuration GENerator and Installer for nextflow pipelines
por: Allain, Fabrice, et al.
Publicado: (2022)

Cannot write session to /tmp/vufind_sessions/sess_0pqbhrumgistm0rq5u7msqm2dr