Analysing high-throughput sequencing data in Python with HTSeq 2.0

Article Properties
  • Language
    English
  • Publication Date
    2022/03/21
  • Journal
  • Indian UGC (journal)
  • Refrences
    10
  • Citations
    252
  • Givanna H Putri School of Clinical Medicine, University of New South Wales , Sydney, NSW 2033, AustraliaAdult Cancer Program, Lowy Cancer Research Centre, University of New South Wales , Sydney, NSW 2033, Australia ORCID (unauthenticated)
  • Simon Anders Bioquant Center, University of Heidelberg , 69120 Heidelberg, Germany ORCID (unauthenticated)
  • Paul Theodor Pyl Division of Surgery, Oncology and Pathology, Department of Clinical Sciences Lund, Faculty of Medicine, Lund University , Lund, Sweden ORCID (unauthenticated)
  • John E Pimanda School of Clinical Medicine, University of New South Wales , Sydney, NSW 2033, AustraliaAdult Cancer Program, Lowy Cancer Research Centre, University of New South Wales , Sydney, NSW 2033, AustraliaDepartment of Pathology, School of Medical Sciences, University of New South Wales , Sydney, NSW 2052, AustraliaDepartment of Haematology, The Prince of Wales Hospital , Sydney, NSW 2031, Australia ORCID (unauthenticated)
  • Fabio Zanini School of Clinical Medicine, University of New South Wales , Sydney, NSW 2033, AustraliaAdult Cancer Program, Lowy Cancer Research Centre, University of New South Wales , Sydney, NSW 2033, AustraliaCellular Genomics Futures Institute, University of New South Wales , Sydney, NSW 2033, Australia ORCID (unauthenticated)
Abstract
Cite
Putri, Givanna H, et al. “Analysing High-Throughput Sequencing Data in Python With HTSeq 2.0”. Bioinformatics, vol. 38, no. 10, 2022, pp. 2943-5, https://doi.org/10.1093/bioinformatics/btac166.
Putri, G. H., Anders, S., Pyl, P. T., Pimanda, J. E., & Zanini, F. (2022). Analysing high-throughput sequencing data in Python with HTSeq 2.0. Bioinformatics, 38(10), 2943-2945. https://doi.org/10.1093/bioinformatics/btac166
Putri, Givanna H, Simon Anders, Paul Theodor Pyl, John E Pimanda, and Fabio Zanini. “Analysing High-Throughput Sequencing Data in Python With HTSeq 2.0”. Bioinformatics 38, no. 10 (2022): 2943-45. https://doi.org/10.1093/bioinformatics/btac166.
Putri GH, Anders S, Pyl PT, Pimanda JE, Zanini F. Analysing high-throughput sequencing data in Python with HTSeq 2.0. Bioinformatics. 2022;38(10):2943-5.
Journal Categories
Medicine
Medicine (General)
Computer applications to medicine
Medical informatics
Science
Biology (General)
Science
Chemistry
Organic chemistry
Biochemistry
Science
Mathematics
Instruments and machines
Electronic computers
Computer science
Technology
Chemical technology
Biotechnology
Refrences
Title Journal Journal Categories Citations Publication Date
HTSlib: C library for reading/writing high-throughput sequencing data

GigaScience
  • Medicine: Medicine (General): Computer applications to medicine. Medical informatics
  • Science: Science (General)
  • Agriculture: Plant culture
  • Science: Biology (General)
128 2021
Array programming with NumPy

Nature
  • Science: Science (General)
8,651 2020
SciPy 1.0: fundamental algorithms for scientific computing in Python

Nature Methods
  • Science: Chemistry: Organic chemistry: Biochemistry
  • Science: Chemistry: Analytical chemistry
  • Science: Biology (General)
  • Science: Chemistry: Organic chemistry: Biochemistry
14,589 2020
SCANPY: large-scale single-cell gene expression data analysis Genome Biology
  • Science: Biology (General): Genetics
  • Technology: Chemical technology: Biotechnology
  • Science: Biology (General): Genetics
  • Science: Biology (General): Genetics
2,486 2018
Single-cell transcriptional dynamics of flavivirus infection 2018
Refrences Analysis
The category Science: Biology (General) 6 is the most frequently represented among the references in this article. It primarily includes studies from Nature Methods and Bioinformatics. The chart below illustrates the number of referenced publications per year.
Refrences used by this article by year
Citations
Title Journal Journal Categories Citations Publication Date
Intersection of coral molecular responses to a localized mortality event and ex situ deoxygenation

Ecology and Evolution
  • Science: Biology (General): Ecology
  • Science: Biology (General): Ecology
  • Science: Biology (General): Evolution
  • Technology: Environmental technology. Sanitary engineering
  • Science: Biology (General): Ecology
2024
Analysis of extracellular vesicle microRNA profiles reveals distinct blood and lymphatic endothelial cell origins

Journal of Extracellular Biology
  • Science: Biology (General): Cytology
2024
A core of cell wall proteins functions in wall integrity responses in Arabidopsis thaliana

Plant Direct
  • Science: Botany
  • Agriculture: Plant culture
  • Agriculture: Animal culture
  • Science: Botany: Plant ecology
2024
Elucidating the role of monoacetylphlorogulcinol in the pathogenicity of Pseudomonas ‘gingeri’ against Agaricus bisporus

Pest Management Science
  • Science: Zoology
  • Agriculture: Plant culture
  • Science: Zoology
  • Agriculture
  • Agriculture: Agriculture (General)
2024
Tumor characteristics of dissociated response to immune checkpoint inhibition in advanced melanoma

Cancer Immunology, Immunotherapy
  • Medicine: Internal medicine: Neoplasms. Tumors. Oncology. Including cancer and carcinogens
  • Medicine: Internal medicine: Neoplasms. Tumors. Oncology. Including cancer and carcinogens
  • Medicine: Internal medicine: Neoplasms. Tumors. Oncology. Including cancer and carcinogens
  • Medicine: Internal medicine: Specialties of internal medicine: Immunologic diseases. Allergy
2024
Citations Analysis
Category Category Repetition
Science: Biology (General)73
Science: Biology (General): Genetics70
Science: Biology (General): Cytology35
Agriculture: Plant culture34
Science: Chemistry: Organic chemistry: Biochemistry33
Agriculture: Animal culture29
Medicine: Medicine (General)27
Science: Botany: Plant ecology27
Science: Science (General)25
Science: Microbiology21
Science19
Science: Chemistry18
Medicine17
Technology: Chemical technology: Biotechnology16
Science: Botany15
Science: Chemistry: General. Including alchemy15
Medicine: Internal medicine: Neoplasms. Tumors. Oncology. Including cancer and carcinogens15
Medicine: Internal medicine: Specialties of internal medicine: Immunologic diseases. Allergy14
Agriculture12
Agriculture: Agriculture (General)12
Science: Zoology10
Medicine: Public aspects of medicine: Toxicology. Poisons9
Technology: Environmental technology. Sanitary engineering7
Science: Biology (General): Ecology7
Medicine: Internal medicine: Neurosciences. Biological psychiatry. Neuropsychiatry6
Geography. Anthropology. Recreation: Environmental sciences5
Medicine: Therapeutics. Pharmacology5
Technology: Chemical technology5
Science: Biology (General): Evolution5
Medicine: Medicine (General): Medical technology4
Medicine: Internal medicine4
Agriculture: Animal culture: Veterinary medicine4
Technology: Chemical technology: Food processing and manufacture4
Agriculture: Aquaculture. Fisheries. Angling4
Technology: Engineering (General). Civil engineering (General): Environmental engineering3
Medicine: Medicine (General): Computer applications to medicine. Medical informatics3
Technology: Chemical technology: Chemical engineering3
Science: Physiology3
Geography. Anthropology. Recreation: Oceanography3
Medicine: Internal medicine: Infectious and parasitic diseases3
Medicine: Internal medicine: Specialties of internal medicine: Diseases of the endocrine glands. Clinical endocrinology3
Technology: Engineering (General). Civil engineering (General)2
Technology: Environmental technology. Sanitary engineering: Environmental pollution2
Technology: Home economics: Nutrition. Foods and food supply2
Medicine: Public aspects of medicine2
Medicine: Internal medicine: Special situations and conditions: Geriatrics2
Medicine: Internal medicine: Special situations and conditions: Arctic medicine. Tropical medicine2
Medicine: Internal medicine: Specialties of internal medicine: Diseases of the blood and blood-forming organs2
Medicine: Other systems of medicine1
Science: Mathematics: Instruments and machines: Electronic computers. Computer science1
Technology: Chemical technology: Polymers and polymer manufacture1
Social Sciences1
Social Sciences: Sociology (General)1
Technology: Mechanical engineering and machinery: Renewable energy sources1
Social Sciences: Industries. Land use. Labor: Special industries and trades: Energy industries. Energy policy. Fuel trade1
Science: Chemistry: Physical and theoretical chemistry1
Technology: Electrical engineering. Electronics. Nuclear engineering: Materials of engineering and construction. Mechanics of materials1
Medicine: Dentistry1
Medicine: Ophthalmology1
Medicine: Nursing1
Science: Chemistry: Analytical chemistry1
Science: Mathematics: Instruments and machines1
Science: Physics1
Science: Microbiology: Microbial ecology1
Medicine: Internal medicine: Specialties of internal medicine: Nutritional diseases. Deficiency diseases1
Agriculture: Animal culture: Cattle: Dairy processing. Dairy products1
Agriculture: Animal culture: Cattle: Dairying1
Medicine: Internal medicine: Specialties of internal medicine: Diseases of the digestive system. Gastroenterology1
Medicine: Internal medicine: Neurosciences. Biological psychiatry. Neuropsychiatry: Neurology. Diseases of the nervous system1
Medicine: Pathology1
Science: Biology (General): Reproduction1
The category Science: Biology (General) 73 is the most commonly referenced area in studies that cite this article. The first research to cite this article was titled Dam–Infant Rhesus Macaque Pairs to Dissect Age-Dependent Responses to SARS-CoV-2 Infection and was published in 2022. The most recent citation comes from a 2024 study titled Unveiling the impact of cryptic plasmids curing on Escherichia coli Nissle 1917: massive increase in Ag43c expression. This article reached its peak citation in 2023, with 139 citations. It has been cited in 153 different journals, 40% of which are open access. Among related journals, the International Journal of Molecular Sciences cited this research the most, with 13 citations. The chart below illustrates the annual citation trends for this article.
Citations used this article by year