Výsledky vyhľadávania - "Bioinformatics Workflows"

Standardized and accessible multi-omics bioinformatics workflows through the NMDC EDGE resource

Autori: Kelliher, Julia M Xu, Yan Flynn, Mark C a ďalší

Zdroj: Computational and Structural Biotechnology Journal. 23

Predmety: 31 Biological Sciences (for-2020), 3102 Bioinformatics and Computational Biology (for-2020), Human Genome (rcdc), Microbiome (rcdc), Networking and Information Technology R&D (NITRD) (rcdc), Data Science (rcdc), Genetics (rcdc), 1.5 Resources and infrastructure (underpinning) (hrcs-rac), Generic health relevance (hrcs-hc), Microbiome, Multi-omics, Bioinformatics workflows, Standardization, Software, Open-source, Bioinformatics workflows, Microbiome, Multi-omics, Open-source, Software, Standardization, 0103 Numerical and Computational Mathematics (for), 0802 Computation Theory and Mathematics (for), 3101 Biochemistry and cell biology (for-2020), 4601 Applied computing (for-2020)

Popis súboru: application/pdf

Prístupová URL adresa: https://escholarship.org/uc/item/0xc9h3fn
https://escholarship.org/content/qt0xc9h3fn/qt0xc9h3fn.pdf

Building flexible and robust analysis frameworks for molecular subtyping of cancers

Autori: Christina Bligaard Pedersen Benito Campos Lasse Rene a ďalší

Zdroj: Mol Oncol
Molecular Oncology, Vol 18, Iss 3, Pp 606-619 (2024)
Pedersen, C B, Campos, B, Rene, L, Wegener, H S, Krishnan, N M, Panda, B, Vitting-Seerup, K, Rossing, M, Bagger, F O & Olsen, L R 2024, ' Building flexible and robust analysis frameworks for molecular subtyping of cancers ', Molecular Oncology, vol. 18, no. 3, pp. 606-619 . https://doi.org/10.1002/1878-0261.13580

Predmety: 0301 basic medicine, 0303 health sciences, Gene Expression Profiling, Sample classification, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, Computational Biology, sample classification, Breast Neoplasms, bioinformatics workflows, Clinical bioinformatics, 3. Good health, Gene Expression Regulation, Neoplastic, molecular subtyping, 03 medical and health sciences, Bioinformatics workflows, Humans, RNA, Female, name=SDG 3 - Good Health and Well-being, Molecular subtyping, clinical bioinformatics, RC254-282, Research Articles

Popis súboru: application/pdf

Prístupová URL adresa: https://pubmed.ncbi.nlm.nih.gov/38158740
https://doaj.org/article/91af8075ca0347618bf363e33adca13d
https://orbit.dtu.dk/en/publications/26c5857a-2c8c-46d1-aec5-bd093285566b

Extracting Information in a Low-Resource Setting: Case Study on Bioinformatics Workflows

Autori: Sebe, Clémence Cohen-Boulakia, Sarah Ferret, Olivier a ďalší

Prispievatelia: Sebe, Clémence Cohen-Boulakia, Sarah Ferret, Olivier a ďalší

Zdroj: Lecture Notes in Computer Science ISBN: 9783031913976

Predmety: [INFO.INFO-AI] Computer Science [cs]/Artificial Intelligence [cs.AI], FOS: Computer and information sciences, Computer Science - Computation and Language, Bioinformatics Workflows, [INFO] Computer Science [cs], Information Extraction, Computation and Language (cs.CL), Natural Language Processing, [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM]

Popis súboru: application/pdf

Prístupová URL adresa: http://arxiv.org/abs/2411.19295
https://hal.science/hal-05244222v1
https://doi.org/10.1007/978-3-031-91398-3_21
https://hal.science/hal-05244222v1/document

Sequence Read Archive (SRA) Data Technical User Manual

Autori: Stine, Adam Caetano-Anollés, Derek Durbrow, Kenneth a ďalší

Predmety: FOS: Computer and information sciences, Read Filtering, Bioinformatics, Cloud Data Delivery, SRA Normalized Format, Data Storage Optimization, Bioinformatics Workflows, Data Compression, NCBI SRA Toolkit, Virtual Database (VDB), High-Throughput Sequencing, Sequencing Data Accessibility, SRA Lite, Sequence Read Archive (SRA), Base Quality Scores

Causal Network Analysis of Omics Data Using Prior Knowledge Databases

Autori: Svinin, Gleb GLAAB, Enrico Luxembourg Centre for Systems Biomedicine (LCSB): Biomedical Data Science (Glaab Group)

Prispievatelia: Svinin, Gleb GLAAB, Enrico Luxembourg Centre for Systems Biomedicine (LCSB): Biomedical Data Science (Glaab Group)

Zdroj: Briefings in Bioinformatics, in press (2025)

Predmety: causal analysis, causal reasoning, molecular networks, prior knowledge, systems biology, bioinformatics workflows, Life sciences, Biotechnology, Human health sciences, Sciences du vivant, Biotechnologie, Sciences de la santé humaine

Relation: info:eu-repo/grantAgreement/EC/H2020/825575; FNR17999421 - AD-PLCG2 - Towards Druggable Targets In Alzheimer’S Disease Through Characterization Of Plcg2-related Pathways In Neurons And Microglia, 2023 (01/07/2024-30/06/2027) - Enrico Glaab; urn:issn:1467-5463; urn:issn:1477-4054; https://orbilu.uni.lu/handle/10993/66380; info:hdl:10993/66380

Dostupnosť: https://orbilu.uni.lu/handle/10993/66380

RNA sequencing analysis pipeline using STAR, Salmon, RSEM with gene counts and quality control

Autori: nf-core (9523169) Alexander Peltzer (9563737)

Predmety: Bioinformatics, Bioinformatics Software, RNA sequencing, Bioinformatics Workflows, Open Science, nf-core, Nextflow, FAIR

Relation: https://figshare.com/articles/presentation/RNA_sequencing_analysis_pipeline_using_STAR_Salmon_RSEM_with_gene_counts_and_quality_control/13142534

Dostupnosť: https://doi.org/10.6084/m9.figshare.13142534.v1

2020-04-03-nf-core-general.pdf

Autori: nf-core (9523169) Alexander Peltzer (9563737)

Predmety: Computational Biology, nf-core, FAIR, Nextflow, Community-driven Bioinformatics Workflows

Relation: https://figshare.com/articles/presentation/2020-04-03-nf-core-general_pdf/13142672

Dostupnosť: https://doi.org/10.6084/m9.figshare.13142672.v1

nf-core: Scalable and reproducible bioinformatics workflows using Nextflow and nf-core

Autori: nf-core (9523169) Alexander Peltzer (3499007)

Predmety: Bioinformatics, Nextflow, nf-core, Open Science, FAIR, Community-driven Bioinformatics Workflows, NGS

Relation: https://figshare.com/articles/presentation/nf-core_Scalable_and_reproducible_bioinformatics_workflows_using_Nextflow_and_nf-core/13142561

Dostupnosť: https://doi.org/10.6084/m9.figshare.13142561.v1

Evaluation of false positive fusion calls and relevance to OncoKB cancer gene list.

Autori: Cu Nguyen Trinh Nguyen Gloria Trivitt a ďalší

Predmety: Genetics, Molecular Biology, Evolutionary Biology, Developmental Biology, Cancer, Virology, Biological Sciences not elsewhere classified, national cancer institute, improve cancer immunotherapy, confidence biomarker detection, cancer immune monitoring, evolving bioinformatics standards, google cloud platform, cidc &# 8217, based bioinformatics pipelines, bioinformatics workflows, based technologies, %22">xlink ">, work establishes, variant calling, transcript quantification, source tools, scalable framework, omic analyses, network aims, nci ), leveraging open, gcp ), efficient deployment

Relation: https://figshare.com/articles/figure/Evaluation_of_false_positive_fusion_calls_and_relevance_to_OncoKB_cancer_gene_list_/29990829

Dostupnosť: https://doi.org/10.1371/journal.pone.0330827.g005
https://figshare.com/articles/figure/Evaluation_of_false_positive_fusion_calls_and_relevance_to_OncoKB_cancer_gene_list_/29990829

Goals and objectives for pipeline enhancements.

Autori: Cu Nguyen Trinh Nguyen Gloria Trivitt a ďalší

Predmety: Genetics, Molecular Biology, Evolutionary Biology, Developmental Biology, Cancer, Virology, Biological Sciences not elsewhere classified, national cancer institute, improve cancer immunotherapy, confidence biomarker detection, cancer immune monitoring, evolving bioinformatics standards, google cloud platform, cidc &# 8217, based bioinformatics pipelines, bioinformatics workflows, based technologies, %22">xlink ">, work establishes, variant calling, transcript quantification, source tools, scalable framework, omic analyses, network aims, nci ), leveraging open, gcp ), efficient deployment

Relation: https://figshare.com/articles/dataset/Goals_and_objectives_for_pipeline_enhancements_/29990832

Dostupnosť: https://doi.org/10.1371/journal.pone.0330827.t001
https://figshare.com/articles/dataset/Goals_and_objectives_for_pipeline_enhancements_/29990832

Comparison of the analytical performance of the extant and enhanced pipelines.

Autori: Cu Nguyen Trinh Nguyen Gloria Trivitt a ďalší

Predmety: Genetics, Molecular Biology, Evolutionary Biology, Developmental Biology, Cancer, Virology, Biological Sciences not elsewhere classified, national cancer institute, improve cancer immunotherapy, confidence biomarker detection, cancer immune monitoring, evolving bioinformatics standards, google cloud platform, cidc &# 8217, based bioinformatics pipelines, bioinformatics workflows, based technologies, %22">xlink ">, work establishes, variant calling, transcript quantification, source tools, scalable framework, omic analyses, network aims, nci ), leveraging open, gcp ), efficient deployment

Relation: https://figshare.com/articles/figure/Comparison_of_the_analytical_performance_of_the_extant_and_enhanced_pipelines_/29990826

Dostupnosť: https://doi.org/10.1371/journal.pone.0330827.g004
https://figshare.com/articles/figure/Comparison_of_the_analytical_performance_of_the_extant_and_enhanced_pipelines_/29990826

Validation of enhanced RNA-Seq pipeline for transcript quantification and fusion calling.

Autori: Cu Nguyen Trinh Nguyen Gloria Trivitt a ďalší

Predmety: Genetics, Molecular Biology, Evolutionary Biology, Developmental Biology, Cancer, Virology, Biological Sciences not elsewhere classified, national cancer institute, improve cancer immunotherapy, confidence biomarker detection, cancer immune monitoring, evolving bioinformatics standards, google cloud platform, cidc &# 8217, based bioinformatics pipelines, bioinformatics workflows, based technologies, %22">xlink ">, work establishes, variant calling, transcript quantification, source tools, scalable framework, omic analyses, network aims, nci ), leveraging open, gcp ), efficient deployment

Dostupnosť: https://doi.org/10.1371/journal.pone.0330827.g003
https://figshare.com/articles/figure/Validation_of_enhanced_RNA-Seq_pipeline_for_transcript_quantification_and_fusion_calling_/29990823

Validation of enhanced WES pipeline for variant calling and CNV detection.

Autori: Cu Nguyen Trinh Nguyen Gloria Trivitt a ďalší

Predmety: Genetics, Molecular Biology, Evolutionary Biology, Developmental Biology, Cancer, Virology, Biological Sciences not elsewhere classified, national cancer institute, improve cancer immunotherapy, confidence biomarker detection, cancer immune monitoring, evolving bioinformatics standards, google cloud platform, cidc &# 8217, based bioinformatics pipelines, bioinformatics workflows, based technologies, %22">xlink ">, work establishes, variant calling, transcript quantification, source tools, scalable framework, omic analyses, network aims, nci ), leveraging open, gcp ), efficient deployment

Relation: https://figshare.com/articles/figure/Validation_of_enhanced_WES_pipeline_for_variant_calling_and_CNV_detection_/29990820

Dostupnosť: https://doi.org/10.1371/journal.pone.0330827.g002
https://figshare.com/articles/figure/Validation_of_enhanced_WES_pipeline_for_variant_calling_and_CNV_detection_/29990820

Reference file information for CIDC enhanced WES and RNA-Seq pipelines.

Autori: Cu Nguyen Trinh Nguyen Gloria Trivitt a ďalší

Predmety: Genetics, Molecular Biology, Evolutionary Biology, Developmental Biology, Cancer, Virology, Biological Sciences not elsewhere classified, national cancer institute, improve cancer immunotherapy, confidence biomarker detection, cancer immune monitoring, evolving bioinformatics standards, google cloud platform, cidc &# 8217, based bioinformatics pipelines, bioinformatics workflows, based technologies, %22">xlink ">, work establishes, variant calling, transcript quantification, source tools, scalable framework, omic analyses, network aims, nci ), leveraging open, gcp ), efficient deployment

Dostupnosť: https://doi.org/10.1371/journal.pone.0330827.s008
https://figshare.com/articles/dataset/Reference_file_information_for_CIDC_enhanced_WES_and_RNA-Seq_pipelines_/29990814

Snakemake workflow template for enhanced WES and RNA-Seq pipelines.

Autori: Cu Nguyen Trinh Nguyen Gloria Trivitt a ďalší

Predmety: Genetics, Molecular Biology, Evolutionary Biology, Developmental Biology, Cancer, Virology, Biological Sciences not elsewhere classified, national cancer institute, improve cancer immunotherapy, confidence biomarker detection, cancer immune monitoring, evolving bioinformatics standards, google cloud platform, cidc &# 8217, based bioinformatics pipelines, bioinformatics workflows, based technologies, %22">xlink ">, work establishes, variant calling, transcript quantification, source tools, scalable framework, omic analyses, network aims, nci ), leveraging open, gcp ), efficient deployment

Dostupnosť: https://doi.org/10.1371/journal.pone.0330827.g001
https://figshare.com/articles/figure/Snakemake_workflow_template_for_enhanced_WES_and_RNA-Seq_pipelines_/29990817

Description and source of data and truth sets used in evaluation of the RNA-Seq pipeline.

Autori: Cu Nguyen Trinh Nguyen Gloria Trivitt a ďalší

Predmety: Genetics, Molecular Biology, Evolutionary Biology, Developmental Biology, Cancer, Virology, Biological Sciences not elsewhere classified, national cancer institute, improve cancer immunotherapy, confidence biomarker detection, cancer immune monitoring, evolving bioinformatics standards, google cloud platform, cidc &# 8217, based bioinformatics pipelines, bioinformatics workflows, based technologies, %22">xlink ">, work establishes, variant calling, transcript quantification, source tools, scalable framework, omic analyses, network aims, nci ), leveraging open, gcp ), efficient deployment

Dostupnosť: https://doi.org/10.1371/journal.pone.0330827.s007
https://figshare.com/articles/dataset/Description_and_source_of_data_and_truth_sets_used_in_evaluation_of_the_RNA-Seq_pipeline_/29990811

False positive gene partners with 3 or more sources on OncoKB’s Cancer Gene List uniquely identified in the fusion calls of the original pipeline (i.e., FP original-only ).

Autori: Cu Nguyen Trinh Nguyen Gloria Trivitt a ďalší

Predmety: Genetics, Molecular Biology, Evolutionary Biology, Developmental Biology, Cancer, Virology, Biological Sciences not elsewhere classified, national cancer institute, improve cancer immunotherapy, confidence biomarker detection, cancer immune monitoring, evolving bioinformatics standards, google cloud platform, cidc &# 8217, based bioinformatics pipelines, bioinformatics workflows, based technologies, %22">xlink ">, work establishes, variant calling, transcript quantification, source tools, scalable framework, omic analyses, network aims, nci ), leveraging open, gcp ), efficient deployment

Dostupnosť: https://doi.org/10.1371/journal.pone.0330827.s005
https://figshare.com/articles/dataset/False_positive_gene_partners_with_3_or_more_sources_on_OncoKB_s_Cancer_Gene_List_uniquely_identified_in_the_fusion_calls_of_the_original_pipeline_i_e_FP_sub_original-only_sub_/29990805

Description and source of data and truth sets used in evaluation of the WES pipeline.

Autori: Cu Nguyen Trinh Nguyen Gloria Trivitt a ďalší

Predmety: Genetics, Molecular Biology, Evolutionary Biology, Developmental Biology, Cancer, Virology, Biological Sciences not elsewhere classified, national cancer institute, improve cancer immunotherapy, confidence biomarker detection, cancer immune monitoring, evolving bioinformatics standards, google cloud platform, cidc &# 8217, based bioinformatics pipelines, bioinformatics workflows, based technologies, %22">xlink ">, work establishes, variant calling, transcript quantification, source tools, scalable framework, omic analyses, network aims, nci ), leveraging open, gcp ), efficient deployment

Relation: https://figshare.com/articles/dataset/Description_and_source_of_data_and_truth_sets_used_in_evaluation_of_the_WES_pipeline_/29990808

Dostupnosť: https://doi.org/10.1371/journal.pone.0330827.s006
https://figshare.com/articles/dataset/Description_and_source_of_data_and_truth_sets_used_in_evaluation_of_the_WES_pipeline_/29990808

Schematic of CIDC RNA-Seq pipeline.

Autori: Cu Nguyen Trinh Nguyen Gloria Trivitt a ďalší

Predmety: Genetics, Molecular Biology, Evolutionary Biology, Developmental Biology, Cancer, Virology, Biological Sciences not elsewhere classified, national cancer institute, improve cancer immunotherapy, confidence biomarker detection, cancer immune monitoring, evolving bioinformatics standards, google cloud platform, cidc &# 8217, based bioinformatics pipelines, bioinformatics workflows, based technologies, %22">xlink ">, work establishes, variant calling, transcript quantification, source tools, scalable framework, omic analyses, network aims, nci ), leveraging open, gcp ), efficient deployment

Dostupnosť: https://doi.org/10.1371/journal.pone.0330827.s002
https://figshare.com/articles/figure/Schematic_of_CIDC_RNA-Seq_pipeline_/29990796

Comparison of the analytical performance of the original and enhanced RNA-Seq pipelines.

Autori: Cu Nguyen Trinh Nguyen Gloria Trivitt a ďalší

Predmety: Genetics, Molecular Biology, Evolutionary Biology, Developmental Biology, Cancer, Virology, Biological Sciences not elsewhere classified, national cancer institute, improve cancer immunotherapy, confidence biomarker detection, cancer immune monitoring, evolving bioinformatics standards, google cloud platform, cidc &# 8217, based bioinformatics pipelines, bioinformatics workflows, based technologies, %22">xlink ">, work establishes, variant calling, transcript quantification, source tools, scalable framework, omic analyses, network aims, nci ), leveraging open, gcp ), efficient deployment

Dostupnosť: https://doi.org/10.1371/journal.pone.0330827.s004
https://figshare.com/articles/figure/Comparison_of_the_analytical_performance_of_the_original_and_enhanced_RNA-Seq_pipelines_/29990802