Cargando…

excluderanges: exclusion sets for T2T-CHM13, GRCm39, and other genome assemblies

SUMMARY: Exclusion regions are sections of reference genomes with abnormal pileups of short sequencing reads. Removing reads overlapping them improves biological signal, and these benefits are most pronounced in differential analysis settings. Several labs created exclusion region sets, available pr...

Descripción completa

Detalles Bibliográficos
Autores principales:	Ogata, Jonathan D, Mu, Wancen, Davis, Eric S, Xue, Bingjie, Harrell, J Chuck, Sheffield, Nathan C, Phanstiel, Douglas H, Love, Michael I, Dozmorov, Mikhail G
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Oxford University Press 2023
Materias:	Applications Note
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10126321/ https://www.ncbi.nlm.nih.gov/pubmed/37067481 http://dx.doi.org/10.1093/bioinformatics/btad198

Ejemplares similares

bootRanges: flexible generation of null sets of genomic ranges for hypothesis testing
por: Mu, Wancen, et al.
Publicado: (2023)

matchRanges: generating null hypothesis genomic ranges via covariate-matched sampling
por: Davis, Eric S, et al.
Publicado: (2023)

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

FANTOM5 CAGE profiles of human and mouse reprocessed for GRCh38 and GRCm38 genome assemblies
por: Abugessaisa, Imad, et al.
Publicado: (2017)

Are Michigan State University medical school (MSU-CHM) alumni more likely to practice in the region of their graduate medical education primary care program compared to non-MSU-CHM alumni?
por: Switzer, Richard, et al.
Publicado: (2018)

Novel CHM mutations identified in Chinese families with Choroideremia
por: Cai, Xue-Bi, et al.
Publicado: (2016)

The Spectrum of CHM Gene Mutations in Choroideremia and Their Relationship to Clinical Phenotype
por: Simunovic, Matthew P., et al.
Publicado: (2016)

Synonymous Variant in the CHM Gene Causes Aberrant Splicing in Choroideremia
por: da Palma, Mariana Matioli, et al.
Publicado: (2020)

Sushi.R: flexible, quantitative and integrative genomic visualizations for publication-quality multi-panel figures
por: Phanstiel, Douglas H., et al.
Publicado: (2014)

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

Inexpensive throughfall exclusion experiment for single large trees
por: Cranston, Benjamin M., et al.
Publicado: (2020)

In silico data analyses of the hotspot mutations of CHM gene in choroideremia disease
por: Imani, Saber, et al.
Publicado: (2018)

Identification of Pathogenic Variants in the CHM Gene in Two Korean Patients With Choroideremia
por: Bae, Kunho, et al.
Publicado: (2017)

GEOfetch: a command-line tool for downloading data and standardized metadata from GEO and SRA
por: Khoroshevskyi, Oleksandr, et al.
Publicado: (2023)

Gene Augmentation of CHM Using Non-Viral Episomal Vectors in Models of Choroideremia
por: Toualbi, Lyes, et al.
Publicado: (2023)

MIRA: an R package for DNA methylation-based inference of regulatory activity
por: Lawson, John T, et al.
Publicado: (2018)

Novel CHM mutations in Polish patients with choroideremia – an orphan disease with close perspective of treatment
por: Skorczyk-Werner, Anna, et al.
Publicado: (2018)

Expanding the genetic spectrum of choroideremia in an Australian cohort: report of five novel CHM variants
por: McLaren, Terri L., et al.
Publicado: (2020)

Molecular Characterization of Choroideremia-Associated Deletions Reveals an Unexpected Regulation of CHM Gene Transcription
por: Fioretti, Tiziana, et al.
Publicado: (2021)

Author Response to Letter to the Editor from CHM van den Ende et al
por: Álvarez, et al.
Publicado: (2020)

Rac1 Is Required for Pathogenicity and Chm1-Dependent Conidiogenesis in Rice Fungal Pathogen Magnaporthe grisea
por: Chen, Jisheng, et al.
Publicado: (2008)

Molecular Alterations in Epidermal Growth Factor Receptors as Potential Predictors of Invasion in Complete Hydatidiform Moles (CHM)
por: Jacob, Jemima, et al.
Publicado: (2012)

Genetic defects of CHM and visual acuity outcome in 24 choroideremia patients from 16 Japanese families
por: Hayashi, Takaaki, et al.
Publicado: (2020)

A putative frameshift variant in the CHM gene is associated with an unexpected splicing alteration in a choroideremia patient
por: Fioretti, Tiziana, et al.
Publicado: (2020)

Direct binding of ESCRT protein Chm7 to phosphatidic acid–rich membranes at nuclear envelope herniations
por: Thaller, David J., et al.
Publicado: (2021)

ViTroVo: in vitro assembly search for in vivo adaptive operator guidance: An artificial intelligence framework for highly customised manufacturing
por: Grappiolo, Corrado, et al.
Publicado: (2021)

Refget: standardized access to reference sequences
por: Yates, Andrew D, et al.
Publicado: (2021)

The endochondral bone protein CHM1 sustains an undifferentiated, invasive phenotype, promoting lung metastasis in Ewing sarcoma
por: von Heyking, Kristina, et al.
Publicado: (2017)

Evaluation and recommendations for effective data visualization for seizure forecasting algorithms
por: Chiang, Sharon, et al.
Publicado: (2021)

Designing and testing a blockchain application for patient identity management in healthcare
por: Khurshid, Anjum, et al.
Publicado: (2021)

Identification of nuclear export inhibitor-based combination therapies in preclinical models of triple-negative breast cancer
por: Rashid, Narmeen S., et al.
Publicado: (2021)

Chm-1 gene-modified bone marrow mesenchymal stem cells maintain the chondrogenic phenotype of tissue-engineered cartilage
por: Chen, Zhuoyue, et al.
Publicado: (2016)

Evaluation of amplification refractory mutation system (ARMS) technique for quick and accurate prenatal gene diagnosis of CHM variant in choroideremia
por: Yang, Lisha, et al.
Publicado: (2017)

Reporting Quality of Randomized Controlled Trials for the Treatment of Eczema with Chinese Patent Medicine Based on the CONSORT-CHM Formulas 2017
por: Li, Ming, et al.
Publicado: (2020)

Airpart: interpretable statistical models for analyzing allelic imbalance in single-cell datasets
por: Mu, Wancen, et al.
Publicado: (2022)

Tandem NBPF 3mer HORs (Olduvai triplets) in Neanderthal and two novel HOR tandem arrays in human chromosome 1 T2T-CHM13 assembly
por: Glunčić, Matko, et al.
Publicado: (2023)

Utilization of electronic health records and associated factors among nurses in a faith-based teaching hospital, Ilishan, Nigeria
por: Ayamolowo, Love B, et al.
Publicado: (2023)

Whole-exome sequencing reveals a novel CHM gene mutation in a family with choroideremia initially diagnosed as retinitis pigmentosa
por: Guo, Hui, et al.
Publicado: (2015)

Genome and transcriptome of Papaver somniferum Chinese landrace CHM indicates that massive genome expansion contributes to high benzylisoquinoline alkaloid biosynthesis
por: Pei, Li, et al.
Publicado: (2021)

KofamKOALA: KEGG Ortholog assignment based on profile HMM and adaptive score threshold
por: Aramaki, Takuya, et al.
Publicado: (2020)

Cannot write session to /tmp/vufind_sessions/sess_sqjhcl0b54f03acto3167grf5o