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检索条件"主题词=Bioinformatics workflow"
22 条 记 录,以下是1-10 订阅
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UTAP2: an enhanced user-friendly transcriptome and epigenome analysis pipeline
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BMC bioinformatics 2025年 第1期26卷 1-12页
作者: Lindner, Jordana Dassa, Bareket Wigoda, Noa Stelzer, Gil Feldmesser, Ester Prilusky, Jaime Leshkowitz, Dena Weizmann Inst Sci Dept Life Sci Core Facil Bioinformat Unit IL-76100 Rehovot Israel
BackgroundThe emergence of next-generation sequencing (NGS) marked a revolution in biological research, enabling comprehensive characterization of the transcriptome and detailed analysis of the epigenome landscape. Th... 详细信息
来源: 评论
Closha 2.0: a bio-workflow design system for massive genome data analysis on high performance cluster infrastructure
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BMC bioinformatics 2024年 第1期25卷 353页
作者: Ko, Gunhwan Kim, Pan-Gyu Yoon, Byung-Ha Kim, JaeHee Song, Wangho Byeon, IkSu Yoon, JongCheol Lee, Byungwook Kim, Young-Kuk KRIBB Korean Bioinformat Ctr KOBIC 125 Gwahangno Daejeon 34141 South Korea Chungnam Natl Univ Dept Bio AI Convergence Daejeon 34134 South Korea
BackgroundThe explosive growth of next-generation sequencing data has resulted in ultra-large-scale datasets and significant computational challenges. As the cost of next-generation sequencing (NGS) has decreased, the... 详细信息
来源: 评论
MAGqual: a stand-alone pipeline to assess the quality of metagenome-assembled genomes
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MICROBIOME 2024年 第1期12卷 226页
作者: Cansdale, Annabel Chong, James P. J. Univ York Ctr Excellence Anaerob Digest Dept Biol Wentworth Way York YO10 5DD England
BackgroundMetagenomics, the whole genome sequencing of microbial communities, has provided insight into complex ecosystems. It has facilitated the discovery of novel microorganisms, explained community interactions an... 详细信息
来源: 评论
Exploring S-RNase diversity in the Andean black cherry (Prunus serotina) using MinION sequencing: a cost-effective approach with increased genotyping resolution
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EUPHYTICA 2023年 第10期219卷 1-15页
作者: Becerra-Wong, Monica Gordillo-Romero, Milton Baus, Lisa C. Teran-Velastegui, Martin Torres, Maria de Lourdes Torres, Andres F. Univ San Francisco Quito Lab Biotecnol Vegetal COCIBA Quito Ecuador Ludwig Maximilians Univ Munchen Fac Biol Genet D-82152 Martinsried Germany
The Andean black cherry (P. serotina) is an underutilized fruit species that could contribute to the development of sustainable food systems in the Andean region. The species displays gametophytic self-incompatibility... 详细信息
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Optimizing the Illumina COVIDSeq laboratorial and bioinformatics pipeline on thousands of samples for SARS-CoV-2 Variants of Concern tracking
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COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL 2022年 20卷 2558-2563页
作者: Donzelli, Sara Ciuffreda, Ludovica Pontone, Martina Betti, Martina Massacci, Alice Mottini, Carla De Nicola, Francesca Orlandi, Giulia Goeman, Frauke Giuliani, Eugenia Sperandio, Eleonora Piaggio, Giulia Morrone, Aldo Ciliberto, Gennaro Fanciulli, Maurizio Blandino, Giovanni Pimpinelli, Fulvia Pallocca, Matteo IRCCS Regina Elena Natl Canc Inst Oncogen & Epigenet Rome Italy IRCCS Regina Elena Natl Canc Inst SAFU Unit Rome Italy IRCCS San Gallicano Dermatol Inst Microbiol & Virol Unit Rome Italy IRCCS Regina Elena Natl Canc Inst Biostat Bioinformat & Clin Trial Ctr Rome Italy IRCCS San Gallicano Dermatol Inst Sci Direct Rome Italy IRCCS Regina Elena Natl Canc Inst Sci Direct Rome Italy
The SARS-CoV-2 Variants of Concern tracking via Whole Genome Sequencing represents a pillar of public health measures for the containment of the pandemic. The ability to track down the lineage distribution on a local ... 详细信息
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Cancer Predisposition Sequencing Reporter (CPSR): A flexible variant report engine for high-throughput germline screening in cancer
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INTERNATIONAL JOURNAL OF CANCER 2021年 第11期149卷 1955-1960页
作者: Nakken, Sigve Saveliev, Vladislav Hofmann, Oliver Moller, Pal Myklebost, Ola Hovig, Eivind Oslo Univ Hosp Inst Canc Res Dept Tumor Biol Oslo Norway Univ Oslo Fac Med Ctr Canc Cell Reprogramming Inst Clin Med Oslo Norway Univ Melbourne Ctr Canc Res Melbourne Vic Australia Univ Bergen Dept Clin Sci Bergen Norway Haukeland Hosp Western Norway Familial Canc Ctr Bergen Norway Univ Oslo Ctr Bioinformat Dept Informat Oslo Norway
The value of high-throughput germline genetic testing is increasingly recognized in clinical cancer care. Disease-associated germline variants in cancer patients are important for risk management and surveillance, sur... 详细信息
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CellHeap: A workflow for Optimizing COVID-19 Single-Cell RNA-Seq Data Processing in the Santos Dumont Supercomputer  14th
CellHeap: A Workflow for Optimizing COVID-19 Single-Cell RNA...
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14th Brazilian Symposium on bioinformatics (BSB)
作者: Silva, Vanessa S. Costa, Maiana O. C. Castro, Maria Clicia S. Silva, Helena S. Walter, Maria Emilia M. T. Melo, Alba C. M. A. Ocana, Kary A. C. dos Santos, Marcelo T. Nicolas, Marisa F. Carvalho, Anna Cristina C. Henriques-Pons, Andrea Silva, Fabricio A. B. Fundacao Oswaldo Cruz Rio De Janeiro Brazil Natl Lab Sci Comp Petropolis RJ Brazil Univ Brasilia Brasilia DF Brazil Univ Estado Rio De Janeiro Rio De Janeiro Brazil
Currently, several hundreds of Terabytes of COVID-19 single-cell RNA-seq (scRNA-seq) data are available in public repositories. This data refers to multiple tissues, comorbidities, and conditions. We expect this trend... 详细信息
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A detailed workflow to develop QIIME2-formatted reference databases for taxonomic analysis of DNA metabarcoding data
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BMC GENOMIC DATA 2022年 第1期23卷 53-53页
作者: Dubois, Benjamin Debode, Frederic Hautier, Louis Hulin, Julie San Martin, Gilles Delvaux, Alain Janssen, Eric Mingeot, Dominique Walloon Agr Res Ctr Bioengn Unit Life Sci Dept Chaussee Charleroi 234 B-5030 Gembloux Belgium Walloon Agr Res Ctr Plant & Forest Hlth Unit Life Sci Dept Rue Liroux 2 B-5030 Gembloux Belgium Walloon Agr Res Ctr Knowledge & Valorizat Agr Prod Dept Qual & Authenticat Unit Chaussee Namur 24 B-5030 Gembloux Belgium Walloon Agr Res Ctr Protect Control Prod & Residues Unit Knowledge & Valorizat Agr Prod Dept Rue Bordia 11 B-5030 Gembloux Belgium
Background The DNA metabarcoding approach has become one of the most used techniques to study the taxa composition of various sample types. To deal with the high amount of data generated by the high-throughput sequenc... 详细信息
来源: 评论
aTAP: automated transcriptome analysis platform for processing RNA-seq data by de novo assembly
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HELIYON 2022年 第8期8卷 e10255页
作者: Surachat, Komwit Taylor, Todd Duane Wattanamatiphot, Wanicbut Sukpisit, Sukgamon Jeenkeawpiam, Kongpop Prince Songkla Univ Fac Med Dept Biomed Sci & Biomed Engn Hat Yai 90110 Songkhla Thailand Prince Songkla Univ Fac Med Translat Med Res Ctr Hat Yai 90110 Songkhla Thailand Prince Songkla Univ Fac Sci Mol Evolut & Computat Biol Res Unit Hat Yai 90110 Songkhla Thailand RIKEN Ctr Integrat Med Sci Yokohama Kanagawa 2300045 Japan Prince Songkla Univ Fac Sci Div Computat Sci Hat Yai 90110 Songkhla Thailand
RNA-seq is a sequencing technique that uses next-generation sequencing (NGS) to explore and study the entire transcriptome of a biological sample. NGS-based analyses are mostly performed via command-line interfaces, w... 详细信息
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workflow for Rapidly Extracting Biological Insights from Complex, Multicondition Proteomics Experiments with WGCNA and PloGO2
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JOURNAL OF PROTEOME RESEARCH 2020年 第7期19卷 2898-2906页
作者: Wu, Jemma X. Pascovici, Dana Wu, Yunqi Walker, Adam K. Mirzaei, Mehdi Macquarie Univ Australian Proteome Anal Facil Sydney NSW 2109 Australia Univ Queensland Queensland Brain Inst Neurodegenerat Pathobiol Lab St Lucia Qld 4072 Australia Macquarie Univ Fac Med & Hlth Sci Ctr Motor Neuron Dis Res Dept Biomed Sci Sydney NSW 2109 Australia Macquarie Univ Dept Clin Sci Sydney NSW 2109 Australia
We describe a useful workflow for characterizing proteomics experiments incorporating many conditions and abundance data using the popular weighted gene correlation network analysis (WGCNA) approach and functional ann... 详细信息
来源: 评论