Cargando…

pycoMeth: a toolbox for differential methylation testing from Nanopore methylation calls

We present pycoMeth, a toolbox to store, manage and analyze DNA methylation calls from long-read sequencing data obtained using the Oxford Nanopore Technologies sequencing platform. Building on a novel, rapid-access, read-level and reference-anchored methylation storage format MetH5, we propose effi...

Descripción completa

Detalles Bibliográficos
Autores principales:	Snajder, Rene, Leger, Adrien, Stegle, Oliver, Bonder, Marc Jan
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	BioMed Central 2023
Materias:	Software
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10120131/ https://www.ncbi.nlm.nih.gov/pubmed/37081487 http://dx.doi.org/10.1186/s13059-023-02917-w

Ejemplares similares

Megabase-scale methylation phasing using nanopore long reads and NanoMethPhase
por: Akbari, Vahid, et al.
Publicado: (2021)

MethMarker: user-friendly design and optimization of gene-specific DNA methylation assays
por: Schüffler, Peter, et al.
Publicado: (2009)

MethHaplo: combining allele-specific DNA methylation and SNPs for haplotype region identification
por: Zhou, Qiangwei, et al.
Publicado: (2020)

MethPat: a tool for the analysis and visualisation of complex methylation patterns obtained by massively parallel sequencing
por: Wong, Nicholas C., et al.
Publicado: (2016)

MethGET: web-based bioinformatics software for correlating genome-wide DNA methylation and gene expression
por: Teng, Chin-Sheng, et al.
Publicado: (2020)

Duet: SNP-assisted structural variant calling and phasing using Oxford nanopore sequencing
por: Zhou, Yekai, et al.
Publicado: (2022)

DMRfinder: efficiently identifying differentially methylated regions from MethylC-seq data
por: Gaspar, John M., et al.
Publicado: (2017)

MethFinder - A software package for prediction of human tissue-specific methylation status of CpG islands
por: James, Priyanka, et al.
Publicado: (2013)

EpiMethEx: a tool for large-scale integrated analysis in methylation hotspots linked to genetic regulation
por: Candido, Saverio, et al.
Publicado: (2019)

ampliMethProfiler: a pipeline for the analysis of CpG methylation profiles of targeted deep bisulfite sequenced amplicons
por: Scala, Giovanni, et al.
Publicado: (2016)

DMRforPairs: identifying Differentially Methylated Regions between unique samples using array based methylation profiles
por: Rijlaarsdam, Martin A, et al.
Publicado: (2014)

Bump time-frequency toolbox: a toolbox for time-frequency oscillatory bursts extraction in electrophysiological signals
por: Vialatte, François B, et al.
Publicado: (2009)

Open Babel: An open chemical toolbox
por: O'Boyle, Noel M, et al.
Publicado: (2011)

The MULTICOM toolbox for protein structure prediction
por: Cheng, Jianlin, et al.
Publicado: (2012)

TOGGLE: toolbox for generic NGS analyses
por: Monat, Cécile, et al.
Publicado: (2015)

QPCR: Application for real-time PCR data management and analysis
por: Pabinger, Stephan, et al.
Publicado: (2009)

Multi-tissue DNA methylation age predictor in mouse
por: Stubbs, Thomas M., et al.
Publicado: (2017)

SNA – a toolbox for the stoichiometric analysis of metabolic networks
por: Urbanczik, Robert
Publicado: (2006)

DeltaProt: a software toolbox for comparative genomics
por: Thorvaldsen, Steinar, et al.
Publicado: (2010)

RepBox: a toolbox for the identification of repetitive elements
por: Burkes-Patton, Shelvasha, et al.
Publicado: (2023)

MUON: multimodal omics analysis framework
por: Bredikhin, Danila, et al.
Publicado: (2022)

MT-Toolbox: improved amplicon sequencing using molecule tags
por: Yourstone, Scott M, et al.
Publicado: (2014)

ΔΔPT: a comprehensive toolbox for the analysis of protein motion
por: Rodgers, Thomas L, et al.
Publicado: (2013)

ConEVA: a toolbox for comprehensive assessment of protein contacts
por: Adhikari, Badri, et al.
Publicado: (2016)

ACES: a machine learning toolbox for clustering analysis and visualization
por: Gao, Jiangning, et al.
Publicado: (2018)

PFA toolbox: a MATLAB tool for Metabolic Flux Analysis
por: Morales, Yeimy, et al.
Publicado: (2016)

methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles
por: Akalin, Altuna, et al.
Publicado: (2012)

DOTcvpSB, a software toolbox for dynamic optimization in systems biology
por: Hirmajer, Tomáš, et al.
Publicado: (2009)

IRProfiler – a software toolbox for high throughput immune receptor profiling
por: Maramis, Christos, et al.
Publicado: (2018)

The ChemicalToolbox: reproducible, user-friendly cheminformatics analysis on the Galaxy platform
por: Bray, Simon A., et al.
Publicado: (2020)

FastMM: an efficient toolbox for personalized constraint-based metabolic modeling
por: Li, Gong-Hua, et al.
Publicado: (2020)

BoardION: real-time monitoring of Oxford Nanopore sequencing instruments
por: Bruno, Aimeric, et al.
Publicado: (2021)

MBEToolbox: a Matlab toolbox for sequence data analysis in molecular biology and evolution
por: Cai, James J, et al.
Publicado: (2005)

The R0 package: a toolbox to estimate reproduction numbers for epidemic outbreaks
por: Obadia, Thomas, et al.
Publicado: (2012)

VREX: an open-source toolbox for creating 3D virtual reality experiments
por: Vasser, Madis, et al.
Publicado: (2017)

Matisse: a MATLAB-based analysis toolbox for in situ sequencing expression maps
por: Marco Salas, Sergio, et al.
Publicado: (2021)

CaPTure: Calcium PeakToolbox for analysis of in vitro calcium imaging data
por: Tippani, Madhavi, et al.
Publicado: (2022)

RGT: a toolbox for the integrative analysis of high throughput regulatory genomics data
por: Li, Zhijian, et al.
Publicado: (2023)

DMRscaler: a scale-aware method to identify regions of differential DNA methylation spanning basepair to multi-megabase features
por: Bondhus, Leroy, et al.
Publicado: (2022)

GEDI: a user-friendly toolbox for analysis of large-scale gene expression data
por: Fujita, André, et al.
Publicado: (2007)

Cannot write session to /tmp/vufind_sessions/sess_ptk7efj4l33lgcnnp1niqhf8ag