100+ datasets found
  1. f

    SW#db: GPU-Accelerated Exact Sequence Similarity Database Search

    • plos.figshare.com
    docx
    Updated May 31, 2023
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    Matija Korpar; Martin Šošić; Dino Blažeka; Mile Šikić (2023). SW#db: GPU-Accelerated Exact Sequence Similarity Database Search [Dataset]. http://doi.org/10.1371/journal.pone.0145857
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    docxAvailable download formats
    Dataset updated
    May 31, 2023
    Dataset provided by
    PLOS ONE
    Authors
    Matija Korpar; Martin Šošić; Dino Blažeka; Mile Šikić
    License

    Attribution 4.0 (CC BY 4.0)https://creativecommons.org/licenses/by/4.0/
    License information was derived automatically

    Description

    In recent years we have witnessed a growth in sequencing yield, the number of samples sequenced, and as a result–the growth of publicly maintained sequence databases. The increase of data present all around has put high requirements on protein similarity search algorithms with two ever-opposite goals: how to keep the running times acceptable while maintaining a high-enough level of sensitivity. The most time consuming step of similarity search are the local alignments between query and database sequences. This step is usually performed using exact local alignment algorithms such as Smith-Waterman. Due to its quadratic time complexity, alignments of a query to the whole database are usually too slow. Therefore, the majority of the protein similarity search methods prior to doing the exact local alignment apply heuristics to reduce the number of possible candidate sequences in the database. However, there is still a need for the alignment of a query sequence to a reduced database. In this paper we present the SW#db tool and a library for fast exact similarity search. Although its running times, as a standalone tool, are comparable to the running times of BLAST, it is primarily intended to be used for exact local alignment phase in which the database of sequences has already been reduced. It uses both GPU and CPU parallelization and was 4–5 times faster than SSEARCH, 6–25 times faster than CUDASW++ and more than 20 times faster than SSW at the time of writing, using multiple queries on Swiss-prot and Uniref90 databases

  2. T

    Exact Sciences | EXAS - Debt

    • tradingeconomics.com
    csv, excel, json, xml
    Updated Mar 15, 2025
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    TRADING ECONOMICS (2025). Exact Sciences | EXAS - Debt [Dataset]. https://tradingeconomics.com/exas:us:debt
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    excel, xml, json, csvAvailable download formats
    Dataset updated
    Mar 15, 2025
    Dataset authored and provided by
    TRADING ECONOMICS
    License

    Attribution 4.0 (CC BY 4.0)https://creativecommons.org/licenses/by/4.0/
    License information was derived automatically

    Time period covered
    Jan 1, 2000 - Jul 4, 2025
    Area covered
    United States
    Description

    Exact Sciences reported $2.34B in Debt for its fiscal quarter ending in March of 2025. Data for Exact Sciences | EXAS - Debt including historical, tables and charts were last updated by Trading Economics this last July in 2025.

  3. Global import data of Exact Dahi

    • volza.com
    csv
    Updated Mar 6, 2025
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    Volza FZ LLC (2025). Global import data of Exact Dahi [Dataset]. https://www.volza.com/p/exact-dahi/import/
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    csvAvailable download formats
    Dataset updated
    Mar 6, 2025
    Dataset provided by
    Volza
    Authors
    Volza FZ LLC
    License

    Attribution 4.0 (CC BY 4.0)https://creativecommons.org/licenses/by/4.0/
    License information was derived automatically

    Variables measured
    Count of importers, Sum of import value, 2014-01-01/2021-09-30, Count of import shipments
    Description

    78 Global import shipment records of Exact Dahi with prices, volume & current Buyer's suppliers relationships based on actual Global export trade database.

  4. T

    Exact Sciences | EXAS - Ebitda

    • tradingeconomics.com
    csv, excel, json, xml
    Updated Mar 15, 2025
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    TRADING ECONOMICS (2025). Exact Sciences | EXAS - Ebitda [Dataset]. https://tradingeconomics.com/exas:us:ebitda
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    xml, csv, json, excelAvailable download formats
    Dataset updated
    Mar 15, 2025
    Dataset authored and provided by
    TRADING ECONOMICS
    License

    Attribution 4.0 (CC BY 4.0)https://creativecommons.org/licenses/by/4.0/
    License information was derived automatically

    Time period covered
    Jan 1, 2000 - Jul 5, 2025
    Area covered
    United States
    Description

    Exact Sciences reported $-35658000 in EBITDA for its fiscal quarter ending in March of 2025. Data for Exact Sciences | EXAS - Ebitda including historical, tables and charts were last updated by Trading Economics this last July in 2025.

  5. h

    daily-historical-stock-price-data-for-exact-sciences-corporation-20012025

    • huggingface.co
    Updated Jan 20, 2025
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    Khaled Ben Ali (2025). daily-historical-stock-price-data-for-exact-sciences-corporation-20012025 [Dataset]. https://huggingface.co/datasets/khaledxbenali/daily-historical-stock-price-data-for-exact-sciences-corporation-20012025
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    Dataset updated
    Jan 20, 2025
    Authors
    Khaled Ben Ali
    Description

    📈 Daily Historical Stock Price Data for Exact Sciences Corporation (2001–2025)

    A clean, ready-to-use dataset containing daily stock prices for Exact Sciences Corporation from 2001-02-01 to 2025-05-28. This dataset is ideal for use in financial analysis, algorithmic trading, machine learning, and academic research.

      🗂️ Dataset Overview
    

    Company: Exact Sciences Corporation Ticker Symbol: EXAS Date Range: 2001-02-01 to 2025-05-28 Frequency: Daily Total Records: 6116 rows… See the full description on the dataset page: https://huggingface.co/datasets/khaledxbenali/daily-historical-stock-price-data-for-exact-sciences-corporation-20012025.

  6. Current Population Survey, 1973, and Social Security Records: Exact Match...

    • icpsr.umich.edu
    ascii, sas, spss +1
    Updated Nov 4, 2005
    + more versions
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    Social Security Administration (2005). Current Population Survey, 1973, and Social Security Records: Exact Match Data [Dataset]. http://doi.org/10.3886/ICPSR07616.v1
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    stata, spss, ascii, sasAvailable download formats
    Dataset updated
    Nov 4, 2005
    Dataset provided by
    Inter-university Consortium for Political and Social Researchhttps://www.icpsr.umich.edu/web/pages/
    Authors
    Social Security Administration
    License

    https://www.icpsr.umich.edu/web/ICPSR/studies/7616/termshttps://www.icpsr.umich.edu/web/ICPSR/studies/7616/terms

    Time period covered
    1973
    Area covered
    United States
    Description

    This data collection supplies standard monthly labor force data for the week prior to the survey. Comprehensive information is given on the employment status, occupation, and industry of persons 14 years old and older. Additional data are available concerning weeks worked and hours per week worked, reason not working full-time, total income and income components, and residence. This study matches data taken from CURRENT POPULATION SURVEY: ANNUAL DEMOGRAPHIC FILE, 1973 (ICPSR 7564) with Social Security benefit and earnings records. Also included is a limited set of tax items furnished by the Internal Revenue Service from the 1972 Federal Income Tax Returns. Information on demographic characteristics such as, sex, ages, race, marital status, veteran status, educational attainment, household relationship, and Hispanic origin, is available for each person in the household enumerated.

  7. Global exporters importers-export import data of Exact dahi

    • volza.com
    csv
    Updated Apr 6, 2025
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    Volza FZ LLC (2025). Global exporters importers-export import data of Exact dahi [Dataset]. https://www.volza.com/p/exact-dahi/
    Explore at:
    csvAvailable download formats
    Dataset updated
    Apr 6, 2025
    Dataset provided by
    Volza
    Authors
    Volza FZ LLC
    License

    Attribution 4.0 (CC BY 4.0)https://creativecommons.org/licenses/by/4.0/
    License information was derived automatically

    Variables measured
    Count of exporters, Count of importers, Count of shipments, Sum of export import value
    Description

    18 Global exporters importers export import shipment records of Exact dahi with prices, volume & current Buyer's suppliers relationships based on actual Global export trade database.

  8. Z

    Supplemental Data and Code for "An exact version of Life Table Response...

    • data.niaid.nih.gov
    • zenodo.org
    Updated Feb 1, 2023
    + more versions
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    Hernandez, Christina M. (2023). Supplemental Data and Code for "An exact version of Life Table Response Experiment analysis, and the R package exactLTRE" [Dataset]. https://data.niaid.nih.gov/resources?id=zenodo_6461580
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    Dataset updated
    Feb 1, 2023
    Dataset provided by
    Hernandez, Christina M.
    Ellner, Stephen P.
    Hooker, Giles
    Snyder, Robin E.
    Adler, Peter B.
    Description

    This dataset enables the user to repeat the analyses presented in "An exact version of Life Table Response Experiment analysis, and the R package exactLTRE." It is comprised of two compressed archives: one which contains code, and one which contains data.

  9. T

    Exact Sciences | EXAS - Ebit

    • tradingeconomics.com
    csv, excel, json, xml
    Updated Mar 15, 2025
    + more versions
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    TRADING ECONOMICS (2025). Exact Sciences | EXAS - Ebit [Dataset]. https://tradingeconomics.com/exas:us:ebit
    Explore at:
    xml, excel, json, csvAvailable download formats
    Dataset updated
    Mar 15, 2025
    Dataset authored and provided by
    TRADING ECONOMICS
    License

    Attribution 4.0 (CC BY 4.0)https://creativecommons.org/licenses/by/4.0/
    License information was derived automatically

    Time period covered
    Jan 1, 2000 - Jul 5, 2025
    Area covered
    United States
    Description

    Exact Sciences reported $-96010000 in EBIT for its fiscal quarter ending in March of 2025. Data for Exact Sciences | EXAS - Ebit including historical, tables and charts were last updated by Trading Economics this last July in 2025.

  10. f

    Data from: Combining High-Resolution and Exact Calibration To Boost...

    • figshare.com
    zip
    Updated Jun 4, 2023
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    Andy Lin; J. Jeffry Howbert; William Stafford Noble (2023). Combining High-Resolution and Exact Calibration To Boost Statistical Power: A Well-Calibrated Score Function for High-Resolution MS2 Data [Dataset]. http://doi.org/10.1021/acs.jproteome.8b00206.s007
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    zipAvailable download formats
    Dataset updated
    Jun 4, 2023
    Dataset provided by
    ACS Publications
    Authors
    Andy Lin; J. Jeffry Howbert; William Stafford Noble
    License

    Attribution-NonCommercial 4.0 (CC BY-NC 4.0)https://creativecommons.org/licenses/by-nc/4.0/
    License information was derived automatically

    Description

    To achieve accurate assignment of peptide sequences to observed fragmentation spectra, a shotgun proteomics database search tool must make good use of the very high-resolution information produced by state-of-the-art mass spectrometers. However, making use of this information while also ensuring that the search engine’s scores are well calibrated, that is, that the score assigned to one spectrum can be meaningfully compared to the score assigned to a different spectrum, has proven to be challenging. Here we describe a database search score function, the “residue evidence” (res-ev) score, that achieves both of these goals simultaneously. We also demonstrate how to combine calibrated res-ev scores with calibrated XCorr scores to produce a “combined p value” score function. We provide a benchmark consisting of four mass spectrometry data sets, which we use to compare the combined p value to the score functions used by several existing search engines. Our results suggest that the combined p value achieves state-of-the-art performance, generally outperforming MS Amanda and Morpheus and performing comparably to MS-GF+. The res-ev and combined p-value score functions are freely available as part of the Tide search engine in the Crux mass spectrometry toolkit (http://crux.ms).

  11. The Comprehensive Brazilian Age Database

    • zenodo.org
    Updated Jul 12, 2024
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    Astolfo Gomes de Mello Araujo; Astolfo Gomes de Mello Araujo; Letícia Cristina Correa; Letícia Cristina Correa; Glauco Constantino Perez; Glauco Constantino Perez; Enrico Dalmas Baggio Di Gregorio; Mercedes Okumura; Mercedes Okumura; Enrico Dalmas Baggio Di Gregorio (2024). The Comprehensive Brazilian Age Database [Dataset]. http://doi.org/10.5281/zenodo.7637553
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    Dataset updated
    Jul 12, 2024
    Dataset provided by
    Zenodohttp://zenodo.org/
    Authors
    Astolfo Gomes de Mello Araujo; Astolfo Gomes de Mello Araujo; Letícia Cristina Correa; Letícia Cristina Correa; Glauco Constantino Perez; Glauco Constantino Perez; Enrico Dalmas Baggio Di Gregorio; Mercedes Okumura; Mercedes Okumura; Enrico Dalmas Baggio Di Gregorio
    License

    Attribution 4.0 (CC BY 4.0)https://creativecommons.org/licenses/by/4.0/
    License information was derived automatically

    Description

    The archaeological database is composed mainly of radiocarbon ages, and they were subject to calibration using the CalPal program (Weninger and Jöris 2008), version 2020.11.

    In some portions of Brazil, OSL and TL ages were widely used, and we had to cope with this issue by means of a “reverse calibration”, i.e., entering ages into the CalPal program and running the calibration until a given (fictious) radiocarbon age, once calibrated, matched as closely as possible the luminescence age. The TL/OSL ages are marked in gray, with blue numbers standing for the “fictious” age, and the actual age appearing in the “Cal age” column.

    We also decided to be inclusive in our database, and by this we mean that we are making available all radiocarbon or luminescence ages that were considered bona fide by the researchers who published them, regardless of the fact that other researchers consider these ages inconsistent with their own models or beliefs. The same goes for papers that select ages based on the standard deviations. A large standard deviation means low precision, not necessarily low accuracy. We take for granted that judgements about the appropriateness of the ages can be made individually by the reader, since we provided the full references. We prefer to publish an age with a large associated error than to ignore it. Once again, since we are providing the tables as supplementary material, it is up to the reader to disregard specific ages and run his/her own analysis.

    In terms of the geographic location of the sites/ages, we chose to provide UTM coordinates of the nearest municipality, instead of providing “exact” locations. This decision was made on three grounds: first, in the scale of analysis we are presenting, the location of the nearest municipality is more than sufficient to provide an adequate overview of the spatial distribution of the ages; second, the majority of the sites published before the advent and popularization of handheld GPS devices do not have an accurate location and therefore, to provide an “exact” location would be meaningless; third, when trying to plot sites using available databases, be they compilations of data or first publications of a given site, it is common to observe that the apparently “exact” geographic coordinates were plainly wrong, falling outside a given region or even the state. This is something that plagues large databases, generally compiled by several researchers and their students, so we argue that it is much easier to detect errors and convey the right location of a given site, at least approximately, if the municipality is taken into account. Hence, our database has a redundant location scheme: state, municipality, and UTM coordinates. If by some reason the UTM is wrong, the reader at least knows in which state and municipality it is located. The only exception to this procedure was made in the Amazon region (states of Amazonas, Pará, Maranhão, Rondonia). Municipalities in the region are fairly large, and we chose to plot the location of the site when it was considered to be too far away from the nearest urbanized area.

  12. u

    Data from: Dataset of the paper “Variable selection for linear regression in...

    • investigacion.ubu.es
    Updated 2020
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    Pacheco Bonrostro, Joaquín; Casado Yusta, Silvia; Pacheco Bonrostro, Joaquín; Casado Yusta, Silvia (2020). Dataset of the paper “Variable selection for linear regression in large databases: exact methods” Applied Intelligence, 51(6), 3736-3756 [Dataset]. https://investigacion.ubu.es/documentos/682afba74c44bf76b28811e1
    Explore at:
    Dataset updated
    2020
    Authors
    Pacheco Bonrostro, Joaquín; Casado Yusta, Silvia; Pacheco Bonrostro, Joaquín; Casado Yusta, Silvia
    Description

    The variable selection problem in the context of Linear Regression for large databases is analysed. The problem consists in selecting a small subset of independent variables that can perform the prediction task optimally. This problem has a wide range of applications. One important type of application is the design of composite indicators in various areas (sociology and economics, for example). Other important applications of variable selection in linear regression can be found in fields such as chemometrics, genetics, and climate prediction, among many others. For this problem, we propose a Branch & Bound method. This is an exact method and therefore guarantees optimal solutions. We also provide strategies that enable this method to be applied in very large databases (with hundreds of thousands of cases) in a moderate computation time. A series of computational experiments shows that our method performs well compared with well-known methods in the literature and with commercial software.

  13. T

    Exact Sciences | EXAS - Market Capitalization

    • tradingeconomics.com
    csv, excel, json, xml
    Updated Feb 5, 2018
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    TRADING ECONOMICS (2018). Exact Sciences | EXAS - Market Capitalization [Dataset]. https://tradingeconomics.com/exas:us:market-capitalization
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    xml, excel, json, csvAvailable download formats
    Dataset updated
    Feb 5, 2018
    Dataset authored and provided by
    TRADING ECONOMICS
    License

    Attribution 4.0 (CC BY 4.0)https://creativecommons.org/licenses/by/4.0/
    License information was derived automatically

    Time period covered
    Jan 1, 2000 - Jul 4, 2025
    Area covered
    United States
    Description

    Exact Sciences reported $9.88B in Market Capitalization this July of 2025, considering the latest stock price and the number of outstanding shares.Data for Exact Sciences | EXAS - Market Capitalization including historical, tables and charts were last updated by Trading Economics this last July in 2025.

  14. t

    EXACT COMMERCE USA INC QINGDAO C.O. EXACT COMMERCE ENTERPRISES CO.,LTD|Full...

    • tradeindata.com
    Updated Dec 4, 2019
    + more versions
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    tradeindata (2019). EXACT COMMERCE USA INC QINGDAO C.O. EXACT COMMERCE ENTERPRISES CO.,LTD|Full export Customs Data Records|tradeindata [Dataset]. https://www.tradeindata.com/supplier_detail/?id=43b3428be2c325144a352c8d2d4e1c32
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    Dataset updated
    Dec 4, 2019
    Dataset authored and provided by
    tradeindata
    License

    Attribution 4.0 (CC BY 4.0)https://creativecommons.org/licenses/by/4.0/
    License information was derived automatically

    Area covered
    Qingdao, United States
    Description

    Customs records of are available for EXACT COMMERCE USA INC QINGDAO C.O. EXACT COMMERCE ENTERPRISES CO.,LTD. Learn about its Importer, supply capabilities and the countries to which it supplies goods

  15. J

    Estimating Euler equations with noisy data: two exact GMM estimators...

    • jda-test.zbw.eu
    • journaldata.zbw.eu
    txt
    Updated Nov 4, 2022
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    Sule Alan; Orazio Attanasio; Martin Browning; Sule Alan; Orazio Attanasio; Martin Browning (2022). Estimating Euler equations with noisy data: two exact GMM estimators (replication data) [Dataset]. https://jda-test.zbw.eu/dataset/estimating-euler-equations-with-noisy-data-two-exact-gmm-estimators
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    txt(24483216), txt(4067)Available download formats
    Dataset updated
    Nov 4, 2022
    Dataset provided by
    ZBW - Leibniz Informationszentrum Wirtschaft
    Authors
    Sule Alan; Orazio Attanasio; Martin Browning; Sule Alan; Orazio Attanasio; Martin Browning
    License

    Attribution 4.0 (CC BY 4.0)https://creativecommons.org/licenses/by/4.0/
    License information was derived automatically

    Description

    In this paper we exploit the specific structure of the Euler equation and develop two alternative GMM estimators that deal explicitly with measurement error. The first estimator assumes that the measurement error is log-normally distributed. The second estimator drops the distributional assumption at the cost of less precision. Our Monte Carlo results suggest that both proposed estimators perform much better than conventional alternatives based on the exact Euler equation or its log-linear approximation, especially with short panels. An empirical application to the PSID yields plausible and precise estimates of the coefficient of relative risk aversion and the discount rate.

  16. Data from: Exact and Near-miss Clone Detection in Spreadsheets

    • figshare.com
    pdf
    Updated Jan 11, 2016
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    Felienne Hermans (2016). Exact and Near-miss Clone Detection in Spreadsheets [Dataset]. http://doi.org/10.6084/m9.figshare.94136.v1
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    pdfAvailable download formats
    Dataset updated
    Jan 11, 2016
    Dataset provided by
    Figsharehttp://figshare.com/
    Authors
    Felienne Hermans
    License

    Attribution 4.0 (CC BY 4.0)https://creativecommons.org/licenses/by/4.0/
    License information was derived automatically

    Description

    Spreadsheets are used extensively in business, in many domains. The applicability of software engineering methods to spreadsheets has been a topic of research for several years, but the main focus has been on analyzing the formulas, and not on analyzing the data in the spreadsheets. One of the factors that plays a role in spreadsheet data quality is the occurrence of clones in the spreadsheet data.

    Clones in data are caused by copy-pasting. This is a very common practice in spreadsheet use, however, it can have a negative impact on the spreadsheet's quality, since 1) editing the copied data needs to be done in multiple places increasing maintenance effort and 2) when editing, some copies might be forgotten, leading to errors.

    Clone detection has been proven useful in the realm of source code analysis, in two different forms: exact clones, and clones that differ slightly, called near-miss clones. Because of the success of clone detection and removal in source code, it seems feasible to research the applicability of both techniques on clones in spreadsheet data. Our work shows that this is a promising avenue.}

  17. N

    Nigeria NG: Mortality from CVD, Cancer, Diabetes or CRD between Exact Ages...

    • ceicdata.com
    Updated Dec 15, 2024
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    CEICdata.com (2024). Nigeria NG: Mortality from CVD, Cancer, Diabetes or CRD between Exact Ages 30 and 70 [Dataset]. https://www.ceicdata.com/en/nigeria/health-statistics/ng-mortality-from-cvd-cancer-diabetes-or-crd-between-exact-ages-30-and-70
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    Dataset updated
    Dec 15, 2024
    Dataset provided by
    CEICdata.com
    License

    Attribution 4.0 (CC BY 4.0)https://creativecommons.org/licenses/by/4.0/
    License information was derived automatically

    Time period covered
    Dec 1, 2000 - Dec 1, 2016
    Area covered
    Nigeria
    Description

    Nigeria NG: Mortality from CVD, Cancer, Diabetes or CRD between Exact Ages 30 and 70 data was reported at 22.500 % in 2016. This stayed constant from the previous number of 22.500 % for 2015. Nigeria NG: Mortality from CVD, Cancer, Diabetes or CRD between Exact Ages 30 and 70 data is updated yearly, averaging 22.900 % from Dec 2000 (Median) to 2016, with 5 observations. The data reached an all-time high of 25.500 % in 2000 and a record low of 22.500 % in 2016. Nigeria NG: Mortality from CVD, Cancer, Diabetes or CRD between Exact Ages 30 and 70 data remains active status in CEIC and is reported by World Bank. The data is categorized under Global Database’s Nigeria – Table NG.World Bank: Health Statistics. Mortality from CVD, cancer, diabetes or CRD is the percent of 30-year-old-people who would die before their 70th birthday from any of cardiovascular disease, cancer, diabetes, or chronic respiratory disease, assuming that s/he would experience current mortality rates at every age and s/he would not die from any other cause of death (e.g., injuries or HIV/AIDS).; ; World Health Organization, Global Health Observatory Data Repository (http://apps.who.int/ghodata/).; Weighted Average;

  18. Exact 9371 Import Data India – Buyers & Importers List

    • seair.co.in
    + more versions
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    Seair Exim, Exact 9371 Import Data India – Buyers & Importers List [Dataset]. https://www.seair.co.in
    Explore at:
    .bin, .xml, .csv, .xlsAvailable download formats
    Dataset provided by
    Seair Exim Solutions
    Authors
    Seair Exim
    Area covered
    India
    Description

    Subscribers can find out export and import data of 23 countries by HS code or product’s name. This demo is helpful for market analysis.

  19. n

    DBTSS: Database of Transcriptional Start Sites

    • neuinfo.org
    • scicrunch.org
    • +1more
    Updated Jan 29, 2022
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    (2022). DBTSS: Database of Transcriptional Start Sites [Dataset]. http://identifiers.org/RRID:SCR_002354
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    Dataset updated
    Jan 29, 2022
    Description

    Database of transcriptional start sites (TSSs) representing exact positions in the genome based on a unique experimentally validated TSS sequencing method, TSS Seq. A major part of human adult and embryonic tissues are covered. DBTSS contains 491 million TSS tag sequences collected from a total of 20 tissues and 7 cell cultures. Also integrated is generated RNA-seq data of subcellular- fractionated RNAs and ChIP Seq data of histone modifications, RNA polymerase II and several transcriptional regulatory factors in cultured cell lines. Also included is external epigenomic data, such as chromatin map of the ENCODE project. They associated those TSS information with public and original SNV data, in order to identify single nucleotide variations (SNVs) in the regulatory regions.

  20. f

    EXACT09: PICASSO experiments vs top teams.

    • plos.figshare.com
    xls
    Updated May 31, 2023
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    Debora Gil; Carles Sanchez; Agnes Borras; Marta Diez-Ferrer; Antoni Rosell (2023). EXACT09: PICASSO experiments vs top teams. [Dataset]. http://doi.org/10.1371/journal.pone.0226006.t002
    Explore at:
    xlsAvailable download formats
    Dataset updated
    May 31, 2023
    Dataset provided by
    PLOS ONE
    Authors
    Debora Gil; Carles Sanchez; Agnes Borras; Marta Diez-Ferrer; Antoni Rosell
    License

    Attribution 4.0 (CC BY 4.0)https://creativecommons.org/licenses/by/4.0/
    License information was derived automatically

    Description

    EXACT09: PICASSO experiments vs top teams.

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Matija Korpar; Martin Šošić; Dino Blažeka; Mile Šikić (2023). SW#db: GPU-Accelerated Exact Sequence Similarity Database Search [Dataset]. http://doi.org/10.1371/journal.pone.0145857

SW#db: GPU-Accelerated Exact Sequence Similarity Database Search

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6 scholarly articles cite this dataset (View in Google Scholar)
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Dataset updated
May 31, 2023
Dataset provided by
PLOS ONE
Authors
Matija Korpar; Martin Šošić; Dino Blažeka; Mile Šikić
License

Attribution 4.0 (CC BY 4.0)https://creativecommons.org/licenses/by/4.0/
License information was derived automatically

Description

In recent years we have witnessed a growth in sequencing yield, the number of samples sequenced, and as a result–the growth of publicly maintained sequence databases. The increase of data present all around has put high requirements on protein similarity search algorithms with two ever-opposite goals: how to keep the running times acceptable while maintaining a high-enough level of sensitivity. The most time consuming step of similarity search are the local alignments between query and database sequences. This step is usually performed using exact local alignment algorithms such as Smith-Waterman. Due to its quadratic time complexity, alignments of a query to the whole database are usually too slow. Therefore, the majority of the protein similarity search methods prior to doing the exact local alignment apply heuristics to reduce the number of possible candidate sequences in the database. However, there is still a need for the alignment of a query sequence to a reduced database. In this paper we present the SW#db tool and a library for fast exact similarity search. Although its running times, as a standalone tool, are comparable to the running times of BLAST, it is primarily intended to be used for exact local alignment phase in which the database of sequences has already been reduced. It uses both GPU and CPU parallelization and was 4–5 times faster than SSEARCH, 6–25 times faster than CUDASW++ and more than 20 times faster than SSW at the time of writing, using multiple queries on Swiss-prot and Uniref90 databases

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