The purpose of this project is to improve the accuracy of statistical software by providing reference datasets with certified computational results that enable the objective evaluation of statistical software. Currently datasets and certified values are provided for assessing the accuracy of software for univariate statistics, linear regression, nonlinear regression, and analysis of variance. The collection includes both generated and 'real-world' data of varying levels of difficulty. Generated datasets are designed to challenge specific computations. These include the classic Wampler datasets for testing linear regression algorithms and the Simon & Lesage datasets for testing analysis of variance algorithms. Real-world data include challenging datasets such as the Longley data for linear regression, and more benign datasets such as the Daniel & Wood data for nonlinear regression. Certified values are 'best-available' solutions. The certification procedure is described in the web pages for each statistical method. Datasets are ordered by level of difficulty (lower, average, and higher). Strictly speaking the level of difficulty of a dataset depends on the algorithm. These levels are merely provided as rough guidance for the user. Producing correct results on all datasets of higher difficulty does not imply that your software will pass all datasets of average or even lower difficulty. Similarly, producing correct results for all datasets in this collection does not imply that your software will do the same for your particular dataset. It will, however, provide some degree of assurance, in the sense that your package provides correct results for datasets known to yield incorrect results for some software. The Statistical Reference Datasets is also supported by the Standard Reference Data Program.
Company Datasets for valuable business insights!
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https://brightdata.com/licensehttps://brightdata.com/license
Stay ahead with our comprehensive News Dataset, designed for businesses, analysts, and researchers to track global events, monitor media trends, and extract valuable insights from news sources worldwide.
Dataset Features
News Articles: Access structured news data, including headlines, summaries, full articles, publication dates, and source details. Ideal for media monitoring and sentiment analysis. Publisher & Source Information: Extract details about news publishers, including domain, region, and credibility indicators. Sentiment & Topic Classification: Analyze news sentiment, categorize articles by topic, and track emerging trends in real time. Historical & Real-Time Data: Retrieve historical archives or access continuously updated news feeds for up-to-date insights.
Customizable Subsets for Specific Needs Our News Dataset is fully customizable, allowing you to filter data based on publication date, region, topic, sentiment, or specific news sources. Whether you need broad coverage for trend analysis or focused data for competitive intelligence, we tailor the dataset to your needs.
Popular Use Cases
Media Monitoring & Reputation Management: Track brand mentions, analyze media coverage, and assess public sentiment. Market & Competitive Intelligence: Monitor industry trends, competitor activity, and emerging market opportunities. AI & Machine Learning Training: Use structured news data to train AI models for sentiment analysis, topic classification, and predictive analytics. Financial & Investment Research: Analyze news impact on stock markets, commodities, and economic indicators. Policy & Risk Analysis: Track regulatory changes, geopolitical events, and crisis developments in real time.
Whether you're analyzing market trends, monitoring brand reputation, or training AI models, our News Dataset provides the structured data you need. Get started today and customize your dataset to fit your business objectives.
Attribution 4.0 (CC BY 4.0)https://creativecommons.org/licenses/by/4.0/
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A diverse selection of 1000 empirical time series, along with results of an hctsa feature extraction, using v1.06 of hctsa and Matlab 2019b, computed on a server at The University of Sydney.The results of the computation are in the hctsa file, HCTSA_Empirical1000.mat for use in Matlab using v1.06 of hctsa.The same data is also provided in .csv format for the hctsa_datamatrix.csv (results of feature computation), with information about rows (time series) in hctsa_timeseries-info.csv, information about columns (features) in hctsa_features.csv (and corresponding hctsa code used to compute each feature in hctsa_masterfeatures.csv), and the data of individual time series (each line a time series, for time series described in hctsa_timeseries-info.csv) is in hctsa_timeseries-data.csv. These .csv files were produced by running >>OutputToCSV(HCTSA_Empirical1000.mat,true,true); in hctsa.The input file, INP_Empirical1000.mat, is for use with hctsa, and contains the time-series data and metadata for the 1000 time series. For example, massive feature extraction from these data on the user's machine, using hctsa, can proceed as>> TS_Init('INP_Empirical1000.mat');Some visualizations of the dataset are in CarpetPlot.png (first 1000 samples of all time series as a carpet (color) plot) and 150TS-250samples.png (conventional time-series plots of the first 250 samples of a sample of 150 time series from the dataset). More visualizations can be performed by the user using TS_PlotTimeSeries from the hctsa package.See links in references for more comprehensive documentation for performing methodological comparison using this dataset, and on how to download and use v1.06 of hctsa.
Attribution 4.0 (CC BY 4.0)https://creativecommons.org/licenses/by/4.0/
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This dataset is part of my PhD research on malware detection and classification using Deep Learning. It contains static analysis data: Top-1000 imported functions extracted from the 'pe_imports' elements of Cuckoo Sandbox reports. PE malware examples were downloaded from virusshare.com. PE goodware examples were downloaded from portableapps.com and from Windows 7 x86 directories.
Attribution-NonCommercial 4.0 (CC BY-NC 4.0)https://creativecommons.org/licenses/by-nc/4.0/
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In this study, we introduce the count-based Morgan fingerprint (C-MF) to represent chemical structures of contaminants and develop machine learning (ML)-based predictive models for their activities and properties. Compared with the binary Morgan fingerprint (B-MF), C-MF not only qualifies the presence or absence of an atom group but also quantifies its counts in a molecule. We employ six different ML algorithms (ridge regression, SVM, KNN, RF, XGBoost, and CatBoost) to develop models on 10 contaminant-related data sets based on C-MF and B-MF to compare them in terms of the model’s predictive performance, interpretation, and applicability domain (AD). Our results show that C-MF outperforms B-MF in nine of 10 data sets in terms of model predictive performance. The advantage of C-MF over B-MF is dependent on the ML algorithm, and the performance enhancements are proportional to the difference in the chemical diversity of data sets calculated by B-MF and C-MF. Model interpretation results show that the C-MF-based model can elucidate the effect of atom group counts on the target and have a wider range of SHAP values. AD analysis shows that C-MF-based models have an AD similar to that of B-MF-based ones. Finally, we developed a “ContaminaNET” platform to deploy these C-MF-based models for free use.
The datasets in this zip file are in support of Intelligent Transportation Systems Joint Program Office (ITS JPO) report FHWA-JPO-16-385, "Analysis, Modeling, and Simulation (AMS) Testbed Development and Evaluation to Support Dynamic Mobility Applications (DMA) and Active Transportation and Demand Management (ATDM) Programs — Evaluation Report for ATDM Program," https://rosap.ntl.bts.gov/view/dot/32520 and FHWA-JPO-16-373, "Analysis, modeling, and simulation (AMS) testbed development and evaluation to support dynamic mobility applications (DMA) and active transportation and demand management (ATDM) programs : Dallas testbed analysis plan," https://rosap.ntl.bts.gov/view/dot/32106 The files in this zip file are specifically related to the Dallas Testbed. The compressed zip files total 2.2 GB in size. The files have been uploaded as-is; no further documentation was supplied by NTL. All located .docx files were converted to .pdf document files which are an open, archival format. These pdfs were then added to the zip file alongside the original .docx files. These files can be unzipped using any zip compression/decompression software. This zip file contains files in the following formats: .pdf document files which can be read using any pdf reader; .cvs text files which can be read using any text editor; .txt text files which can be read using any text editor; .docx document files which can be read in Microsoft Word and some other word processing programs; . xlsx spreadsheet files which can be read in Microsoft Excel and some other spreadsheet programs; .dat data files which may be text or multimedia; as well as GIS or mapping files in the fowlling formats: .mxd, .dbf, .prj, .sbn, .shp., .shp.xml; which may be opened in ArcGIS or other GIS software. [software requirements] These files were last accessed in 2017.
Apache License, v2.0https://www.apache.org/licenses/LICENSE-2.0
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Meta Kaggle Code is an extension to our popular Meta Kaggle dataset. This extension contains all the raw source code from hundreds of thousands of public, Apache 2.0 licensed Python and R notebooks versions on Kaggle used to analyze Datasets, make submissions to Competitions, and more. This represents nearly a decade of data spanning a period of tremendous evolution in the ways ML work is done.
By collecting all of this code created by Kaggle’s community in one dataset, we hope to make it easier for the world to research and share insights about trends in our industry. With the growing significance of AI-assisted development, we expect this data can also be used to fine-tune models for ML-specific code generation tasks.
Meta Kaggle for Code is also a continuation of our commitment to open data and research. This new dataset is a companion to Meta Kaggle which we originally released in 2016. On top of Meta Kaggle, our community has shared nearly 1,000 public code examples. Research papers written using Meta Kaggle have examined how data scientists collaboratively solve problems, analyzed overfitting in machine learning competitions, compared discussions between Kaggle and Stack Overflow communities, and more.
The best part is Meta Kaggle enriches Meta Kaggle for Code. By joining the datasets together, you can easily understand which competitions code was run against, the progression tier of the code’s author, how many votes a notebook had, what kinds of comments it received, and much, much more. We hope the new potential for uncovering deep insights into how ML code is written feels just as limitless to you as it does to us!
While we have made an attempt to filter out notebooks containing potentially sensitive information published by Kaggle users, the dataset may still contain such information. Research, publications, applications, etc. relying on this data should only use or report on publicly available, non-sensitive information.
The files contained here are a subset of the KernelVersions
in Meta Kaggle. The file names match the ids in the KernelVersions
csv file. Whereas Meta Kaggle contains data for all interactive and commit sessions, Meta Kaggle Code contains only data for commit sessions.
The files are organized into a two-level directory structure. Each top level folder contains up to 1 million files, e.g. - folder 123 contains all versions from 123,000,000 to 123,999,999. Each sub folder contains up to 1 thousand files, e.g. - 123/456 contains all versions from 123,456,000 to 123,456,999. In practice, each folder will have many fewer than 1 thousand files due to private and interactive sessions.
The ipynb files in this dataset hosted on Kaggle do not contain the output cells. If the outputs are required, the full set of ipynbs with the outputs embedded can be obtained from this public GCS bucket: kaggle-meta-kaggle-code-downloads
. Note that this is a "requester pays" bucket. This means you will need a GCP account with billing enabled to download. Learn more here: https://cloud.google.com/storage/docs/requester-pays
We love feedback! Let us know in the Discussion tab.
Happy Kaggling!
Attribution 4.0 (CC BY 4.0)https://creativecommons.org/licenses/by/4.0/
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This repository was created for my Master's thesis in Computational Intelligence and Internet of Things at the University of Córdoba, Spain. The purpose of this repository is to store the datasets found that were used in some of the studies that served as research material for this Master's thesis. Also, the datasets used in the experimental part of this work are included.
Below are the datasets specified, along with the details of their references, authors, and download sources.
----------- STS-Gold Dataset ----------------
The dataset consists of 2026 tweets. The file consists of 3 columns: id, polarity, and tweet. The three columns denote the unique id, polarity index of the text and the tweet text respectively.
Reference: Saif, H., Fernandez, M., He, Y., & Alani, H. (2013). Evaluation datasets for Twitter sentiment analysis: a survey and a new dataset, the STS-Gold.
File name: sts_gold_tweet.csv
----------- Amazon Sales Dataset ----------------
This dataset is having the data of 1K+ Amazon Product's Ratings and Reviews as per their details listed on the official website of Amazon. The data was scraped in the month of January 2023 from the Official Website of Amazon.
Owner: Karkavelraja J., Postgraduate student at Puducherry Technological University (Puducherry, Puducherry, India)
Features:
License: CC BY-NC-SA 4.0
File name: amazon.csv
----------- Rotten Tomatoes Reviews Dataset ----------------
This rating inference dataset is a sentiment classification dataset, containing 5,331 positive and 5,331 negative processed sentences from Rotten Tomatoes movie reviews. On average, these reviews consist of 21 words. The first 5331 rows contains only negative samples and the last 5331 rows contain only positive samples, thus the data should be shuffled before usage.
This data is collected from https://www.cs.cornell.edu/people/pabo/movie-review-data/ as a txt file and converted into a csv file. The file consists of 2 columns: reviews and labels (1 for fresh (good) and 0 for rotten (bad)).
Reference: Bo Pang and Lillian Lee. Seeing stars: Exploiting class relationships for sentiment categorization with respect to rating scales. In Proceedings of the 43rd Annual Meeting of the Association for Computational Linguistics (ACL'05), pages 115–124, Ann Arbor, Michigan, June 2005. Association for Computational Linguistics
File name: data_rt.csv
----------- Preprocessed Dataset Sentiment Analysis ----------------
Preprocessed amazon product review data of Gen3EcoDot (Alexa) scrapped entirely from amazon.in
Stemmed and lemmatized using nltk.
Sentiment labels are generated using TextBlob polarity scores.
The file consists of 4 columns: index, review (stemmed and lemmatized review using nltk), polarity (score) and division (categorical label generated using polarity score).
DOI: 10.34740/kaggle/dsv/3877817
Citation: @misc{pradeesh arumadi_2022, title={Preprocessed Dataset Sentiment Analysis}, url={https://www.kaggle.com/dsv/3877817}, DOI={10.34740/KAGGLE/DSV/3877817}, publisher={Kaggle}, author={Pradeesh Arumadi}, year={2022} }
This dataset was used in the experimental phase of my research.
File name: EcoPreprocessed.csv
----------- Amazon Earphones Reviews ----------------
This dataset consists of a 9930 Amazon reviews, star ratings, for 10 latest (as of mid-2019) bluetooth earphone devices for learning how to train Machine for sentiment analysis.
This dataset was employed in the experimental phase of my research. To align it with the objectives of my study, certain reviews were excluded from the original dataset, and an additional column was incorporated into this dataset.
The file consists of 5 columns: ReviewTitle, ReviewBody, ReviewStar, Product and division (manually added - categorical label generated using ReviewStar score)
License: U.S. Government Works
Source: www.amazon.in
File name (original): AllProductReviews.csv (contains 14337 reviews)
File name (edited - used for my research) : AllProductReviews2.csv (contains 9930 reviews)
----------- Amazon Musical Instruments Reviews ----------------
This dataset contains 7137 comments/reviews of different musical instruments coming from Amazon.
This dataset was employed in the experimental phase of my research. To align it with the objectives of my study, certain reviews were excluded from the original dataset, and an additional column was incorporated into this dataset.
The file consists of 10 columns: reviewerID, asin (ID of the product), reviewerName, helpful (helpfulness rating of the review), reviewText, overall (rating of the product), summary (summary of the review), unixReviewTime (time of the review - unix time), reviewTime (time of the review (raw) and division (manually added - categorical label generated using overall score).
Source: http://jmcauley.ucsd.edu/data/amazon/
File name (original): Musical_instruments_reviews.csv (contains 10261 reviews)
File name (edited - used for my research) : Musical_instruments_reviews2.csv (contains 7137 reviews)
Each R script replicates all of the example code from one chapter from the book. All required data for each script are also uploaded, as are all data used in the practice problems at the end of each chapter. The data are drawn from a wide array of sources, so please cite the original work if you ever use any of these data sets for research purposes.
These datasets contain reviews from the Goodreads book review website, and a variety of attributes describing the items. Critically, these datasets have multiple levels of user interaction, raging from adding to a shelf, rating, and reading.
Metadata includes
reviews
add-to-shelf, read, review actions
book attributes: title, isbn
graph of similar books
Basic Statistics:
Items: 1,561,465
Users: 808,749
Interactions: 225,394,930
https://creativecommons.org/publicdomain/zero/1.0/https://creativecommons.org/publicdomain/zero/1.0/
Context
The data presented here was obtained in a Kali Machine from University of Cincinnati,Cincinnati,OHIO by carrying out packet captures for 1 hour during the evening on Oct 9th,2023 using Wireshark.This dataset consists of 394137 instances were obtained and stored in a CSV (Comma Separated Values) file.This large dataset could be used utilised for different machine learning applications for instance classification of Network traffic,Network performance monitoring,Network Security Management , Network Traffic Management ,network intrusion detection and anomaly detection.
The dataset can be used for a variety of machine learning tasks, such as network intrusion detection, traffic classification, and anomaly detection.
Content :
This network traffic dataset consists of 7 features.Each instance contains the information of source and destination IP addresses, The majority of the properties are numeric in nature, however there are also nominal and date kinds due to the Timestamp.
The network traffic flow statistics (No. Time Source Destination Protocol Length Info) were obtained using Wireshark (https://www.wireshark.org/).
Dataset Columns:
No : Number of Instance. Timestamp : Timestamp of instance of network traffic Source IP: IP address of Source Destination IP: IP address of Destination Portocol: Protocol used by the instance Length: Length of Instance Info: Information of Traffic Instance
Acknowledgements :
I would like thank University of Cincinnati for giving the infrastructure for generation of network traffic data set.
Ravikumar Gattu , Susmitha Choppadandi
Inspiration : This dataset goes beyond the majority of network traffic classification datasets, which only identify the type of application (WWW, DNS, ICMP,ARP,RARP) that an IP flow contains. Instead, it generates machine learning models that can identify specific applications (like Tiktok,Wikipedia,Instagram,Youtube,Websites,Blogs etc.) from IP flow statistics (there are currently 25 applications in total).
**Dataset License: ** CC0: Public Domain
Dataset Usages : This dataset can be used for different machine learning applications in the field of cybersecurity such as classification of Network traffic,Network performance monitoring,Network Security Management , Network Traffic Management ,network intrusion detection and anomaly detection.
ML techniques benefits from this Dataset :
This dataset is highly useful because it consists of 394137 instances of network traffic data obtained by using the 25 applications on a public,private and Enterprise networks.Also,the dataset consists of very important features that can be used for most of the applications of Machine learning in cybersecurity.Here are few of the potential machine learning applications that could be benefited from this dataset are :
Network Performance Monitoring : This large network traffic data set can be utilised for analysing the network traffic to identifying the network patterns in the network .This help in designing the network security algorithms for minimise the network probelms.
Anamoly Detection : Large network traffic dataset can be utilised training the machine learning models for finding the irregularitues in the traffic which could help identify the cyber attacks.
3.Network Intrusion Detection : This large dataset could be utilised for machine algorithms training and designing the models for detection of the traffic issues,Malicious traffic network attacks and DOS attacks as well.
MIT Licensehttps://opensource.org/licenses/MIT
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This database studies the performance inconsistency on the biomass HHV ultimate analysis. The research null hypothesis is the consistency in the rank of a biomass HHV model. Fifteen biomass models are trained and tested in four datasets. In each dataset, the rank invariability of these 15 models indicates the performance consistency.
The database includes the datasets and source codes to analyze the performance consistency of the biomass HHV. These datasets are stored in tabular on an excel workbook. The source codes are the biomass HHV machine learning model through the MATLAB Objected Orient Program (OOP). These machine learning models consist of eight regressions, four supervised learnings, and three neural networks.
An excel workbook, "BiomassDataSetUltimate.xlsx," collects the research datasets in six worksheets. The first worksheet, "Ultimate," contains 908 HHV data from 20 pieces of literature. The names of the worksheet column indicate the elements of the ultimate analysis on a % dry basis. The HHV column refers to the higher heating value in MJ/kg. The following worksheet, "Full Residuals," backups the model testing's residuals based on the 20-fold cross-validations. The article (Kijkarncharoensin & Innet, 2021) verifies the performance consistency through these residuals. The other worksheets present the literature datasets implemented to train and test the model performance in many pieces of literature.
A file named "SourceCodeUltimate.rar" collects the MATLAB machine learning models implemented in the article. The list of the folders in this file is the class structure of the machine learning models. These classes extend the features of the original MATLAB's Statistics and Machine Learning Toolbox to support, e.g., the k-fold cross-validation. The MATLAB script, name "runStudyUltimate.m," is the article's main program to analyze the performance consistency of the biomass HHV model through the ultimate analysis. The script instantly loads the datasets from the excel workbook and automatically fits the biomass model through the OOP classes.
The first section of the MATLAB script generates the most accurate model by optimizing the model's higher parameters. It takes a few hours for the first run to train the machine learning model via the trial and error process. The trained models can be saved in MATLAB .mat file and loaded back to the MATLAB workspace. The remaining script, separated by the script section break, performs the residual analysis to inspect the performance consistency. Furthermore, the figure of the biomass data in the 3D scatter plot, and the box plots of the prediction residuals are exhibited. Finally, the interpretations of these results are examined in the author's article.
Reference : Kijkarncharoensin, A., & Innet, S. (2022). Performance inconsistency of the Biomass Higher Heating Value (HHV) Models derived from Ultimate Analysis [Manuscript in preparation]. University of the Thai Chamber of Commerce.
Attribution 4.0 (CC BY 4.0)https://creativecommons.org/licenses/by/4.0/
License information was derived automatically
This book is written for statisticians, data analysts, programmers, researchers, teachers, students, professionals, and general consumers on how to perform different types of statistical data analysis for research purposes using the R programming language. R is an open-source software and object-oriented programming language with a development environment (IDE) called RStudio for computing statistics and graphical displays through data manipulation, modelling, and calculation. R packages and supported libraries provides a wide range of functions for programming and analyzing of data. Unlike many of the existing statistical softwares, R has the added benefit of allowing the users to write more efficient codes by using command-line scripting and vectors. It has several built-in functions and libraries that are extensible and allows the users to define their own (customized) functions on how they expect the program to behave while handling the data, which can also be stored in the simple object system.For all intents and purposes, this book serves as both textbook and manual for R statistics particularly in academic research, data analytics, and computer programming targeted to help inform and guide the work of the R users or statisticians. It provides information about different types of statistical data analysis and methods, and the best scenarios for use of each case in R. It gives a hands-on step-by-step practical guide on how to identify and conduct the different parametric and non-parametric procedures. This includes a description of the different conditions or assumptions that are necessary for performing the various statistical methods or tests, and how to understand the results of the methods. The book also covers the different data formats and sources, and how to test for reliability and validity of the available datasets. Different research experiments, case scenarios and examples are explained in this book. It is the first book to provide a comprehensive description and step-by-step practical hands-on guide to carrying out the different types of statistical analysis in R particularly for research purposes with examples. Ranging from how to import and store datasets in R as Objects, how to code and call the methods or functions for manipulating the datasets or objects, factorization, and vectorization, to better reasoning, interpretation, and storage of the results for future use, and graphical visualizations and representations. Thus, congruence of Statistics and Computer programming for Research.
Market basket analysis with Apriori algorithm
The retailer wants to target customers with suggestions on itemset that a customer is most likely to purchase .I was given dataset contains data of a retailer; the transaction data provides data around all the transactions that have happened over a period of time. Retailer will use result to grove in his industry and provide for customer suggestions on itemset, we be able increase customer engagement and improve customer experience and identify customer behavior. I will solve this problem with use Association Rules type of unsupervised learning technique that checks for the dependency of one data item on another data item.
Association Rule is most used when you are planning to build association in different objects in a set. It works when you are planning to find frequent patterns in a transaction database. It can tell you what items do customers frequently buy together and it allows retailer to identify relationships between the items.
Assume there are 100 customers, 10 of them bought Computer Mouth, 9 bought Mat for Mouse and 8 bought both of them. - bought Computer Mouth => bought Mat for Mouse - support = P(Mouth & Mat) = 8/100 = 0.08 - confidence = support/P(Mat for Mouse) = 0.08/0.09 = 0.89 - lift = confidence/P(Computer Mouth) = 0.89/0.10 = 8.9 This just simple example. In practice, a rule needs the support of several hundred transactions, before it can be considered statistically significant, and datasets often contain thousands or millions of transactions.
Number of Attributes: 7
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First, we need to load required libraries. Shortly I describe all libraries.
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Next, we need to upload Assignment-1_Data. xlsx to R to read the dataset.Now we can see our data in R.
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After we will clear our data frame, will remove missing values.
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To apply Association Rule mining, we need to convert dataframe into transaction data to make all items that are bought together in one invoice will be in ...
https://spdx.org/licenses/CC0-1.0.htmlhttps://spdx.org/licenses/CC0-1.0.html
Pathogen diversity resulting in quasispecies can enable persistence and adaptation to host defenses and therapies. However, accurate quasispecies characterization can be impeded by errors introduced during sample handling and sequencing which can require extensive optimizations to overcome. We present complete laboratory and bioinformatics workflows to overcome many of these hurdles. The Pacific Biosciences single molecule real-time platform was used to sequence PCR amplicons derived from cDNA templates tagged with universal molecular identifiers (SMRT-UMI). Optimized laboratory protocols were developed through extensive testing of different sample preparation conditions to minimize between-template recombination during PCR and the use of UMI allowed accurate template quantitation as well as removal of point mutations introduced during PCR and sequencing to produce a highly accurate consensus sequence from each template. Handling of the large datasets produced from SMRT-UMI sequencing was facilitated by a novel bioinformatic pipeline, Probabilistic Offspring Resolver for Primer IDs (PORPIDpipeline), that automatically filters and parses reads by sample, identifies and discards reads with UMIs likely created from PCR and sequencing errors, generates consensus sequences, checks for contamination within the dataset, and removes any sequence with evidence of PCR recombination or early cycle PCR errors, resulting in highly accurate sequence datasets. The optimized SMRT-UMI sequencing method presented here represents a highly adaptable and established starting point for accurate sequencing of diverse pathogens. These methods are illustrated through characterization of human immunodeficiency virus (HIV) quasispecies.
Methods
This serves as an overview of the analysis performed on PacBio sequence data that is summarized in Analysis Flowchart.pdf and was used as primary data for the paper by Westfall et al. "Optimized SMRT-UMI protocol produces highly accurate sequence datasets from diverse populations – application to HIV-1 quasispecies"
Five different PacBio sequencing datasets were used for this analysis: M027, M2199, M1567, M004, and M005
For the datasets which were indexed (M027, M2199), CCS reads from PacBio sequencing files and the chunked_demux_config files were used as input for the chunked_demux pipeline. Each config file lists the different Index primers added during PCR to each sample. The pipeline produces one fastq file for each Index primer combination in the config. For example, in dataset M027 there were 3–4 samples using each Index combination. The fastq files from each demultiplexed read set were moved to the sUMI_dUMI_comparison pipeline fastq folder for further demultiplexing by sample and consensus generation with that pipeline. More information about the chunked_demux pipeline can be found in the README.md file on GitHub.
The demultiplexed read collections from the chunked_demux pipeline or CCS read files from datasets which were not indexed (M1567, M004, M005) were each used as input for the sUMI_dUMI_comparison pipeline along with each dataset's config file. Each config file contains the primer sequences for each sample (including the sample ID block in the cDNA primer) and further demultiplexes the reads to prepare data tables summarizing all of the UMI sequences and counts for each family (tagged.tar.gz) as well as consensus sequences from each sUMI and rank 1 dUMI family (consensus.tar.gz). More information about the sUMI_dUMI_comparison pipeline can be found in the paper and the README.md file on GitHub.
The consensus.tar.gz and tagged.tar.gz files were moved from sUMI_dUMI_comparison pipeline directory on the server to the Pipeline_Outputs folder in this analysis directory for each dataset and appended with the dataset name (e.g. consensus_M027.tar.gz). Also in this analysis directory is a Sample_Info_Table.csv containing information about how each of the samples was prepared, such as purification methods and number of PCRs. There are also three other folders: Sequence_Analysis, Indentifying_Recombinant_Reads, and Figures. Each has an .Rmd
file with the same name inside which is used to collect, summarize, and analyze the data. All of these collections of code were written and executed in RStudio to track notes and summarize results.
Sequence_Analysis.Rmd
has instructions to decompress all of the consensus.tar.gz files, combine them, and create two fasta files, one with all sUMI and one with all dUMI sequences. Using these as input, two data tables were created, that summarize all sequences and read counts for each sample that pass various criteria. These are used to help create Table 2 and as input for Indentifying_Recombinant_Reads.Rmd
and Figures.Rmd
. Next, 2 fasta files containing all of the rank 1 dUMI sequences and the matching sUMI sequences were created. These were used as input for the python script compare_seqs.py which identifies any matched sequences that are different between sUMI and dUMI read collections. This information was also used to help create Table 2. Finally, to populate the table with the number of sequences and bases in each sequence subset of interest, different sequence collections were saved and viewed in the Geneious program.
To investigate the cause of sequences where the sUMI and dUMI sequences do not match, tagged.tar.gz was decompressed and for each family with discordant sUMI and dUMI sequences the reads from the UMI1_keeping directory were aligned using geneious. Reads from dUMI families failing the 0.7 filter were also aligned in Genious. The uncompressed tagged folder was then removed to save space. These read collections contain all of the reads in a UMI1 family and still include the UMI2 sequence. By examining the alignment and specifically the UMI2 sequences, the site of the discordance and its case were identified for each family as described in the paper. These alignments were saved as "Sequence Alignments.geneious". The counts of how many families were the result of PCR recombination were used in the body of the paper.
Using Identifying_Recombinant_Reads.Rmd
, the dUMI_ranked.csv file from each sample was extracted from all of the tagged.tar.gz files, combined and used as input to create a single dataset containing all UMI information from all samples. This file dUMI_df.csv was used as input for Figures.Rmd.
Figures.Rmd
used dUMI_df.csv, sequence_counts.csv, and read_counts.csv as input to create draft figures and then individual datasets for eachFigure. These were copied into Prism software to create the final figures for the paper.
Attribution 4.0 (CC BY 4.0)https://creativecommons.org/licenses/by/4.0/
License information was derived automatically
These four labeled data sets are targeted at ordinal quantification. The goal of quantification is not to predict the label of each individual instance, but the distribution of labels in unlabeled sets of data.
With the scripts provided, you can extract CSV files from the UCI machine learning repository and from OpenML. The ordinal class labels stem from a binning of a continuous regression label.
We complement this data set with the indices of data items that appear in each sample of our evaluation. Hence, you can precisely replicate our samples by drawing the specified data items. The indices stem from two evaluation protocols that are well suited for ordinal quantification. To this end, each row in the files app_val_indices.csv, app_tst_indices.csv, app-oq_val_indices.csv, and app-oq_tst_indices.csv represents one sample.
Our first protocol is the artificial prevalence protocol (APP), where all possible distributions of labels are drawn with an equal probability. The second protocol, APP-OQ, is a variant thereof, where only the smoothest 20% of all APP samples are considered. This variant is targeted at ordinal quantification tasks, where classes are ordered and a similarity of neighboring classes can be assumed.
Usage
You can extract four CSV files through the provided script extract-oq.jl, which is conveniently wrapped in a Makefile. The Project.toml and Manifest.toml specify the Julia package dependencies, similar to a requirements file in Python.
Preliminaries: You have to have a working Julia installation. We have used Julia v1.6.5 in our experiments.
Data Extraction: In your terminal, you can call either
make
(recommended), or
julia --project="." --eval "using Pkg; Pkg.instantiate()"
julia --project="." extract-oq.jl
Outcome: The first row in each CSV file is the header. The first column, named "class_label", is the ordinal class.
Further Reading
Implementation of our experiments: https://github.com/mirkobunse/regularized-oq
https://brightdata.com/licensehttps://brightdata.com/license
Use our YouTube profiles dataset to extract both business and non-business information from public channels and filter by channel name, views, creation date, or subscribers. Datapoints include URL, handle, banner image, profile image, name, subscribers, description, video count, create date, views, details, and more. You may purchase the entire dataset or a customized subset, depending on your needs. Popular use cases for this dataset include sentiment analysis, brand monitoring, influencer marketing, and more.
https://creativecommons.org/publicdomain/zero/1.0/https://creativecommons.org/publicdomain/zero/1.0/
The Google Merchandise Store sells Google branded merchandise. The data is typical of what you would see for an ecommerce website.
The sample dataset contains Google Analytics 360 data from the Google Merchandise Store, a real ecommerce store. The Google Merchandise Store sells Google branded merchandise. The data is typical of what you would see for an ecommerce website. It includes the following kinds of information:
Traffic source data: information about where website visitors originate. This includes data about organic traffic, paid search traffic, display traffic, etc. Content data: information about the behavior of users on the site. This includes the URLs of pages that visitors look at, how they interact with content, etc. Transactional data: information about the transactions that occur on the Google Merchandise Store website.
Fork this kernel to get started.
Banner Photo by Edho Pratama from Unsplash.
What is the total number of transactions generated per device browser in July 2017?
The real bounce rate is defined as the percentage of visits with a single pageview. What was the real bounce rate per traffic source?
What was the average number of product pageviews for users who made a purchase in July 2017?
What was the average number of product pageviews for users who did not make a purchase in July 2017?
What was the average total transactions per user that made a purchase in July 2017?
What is the average amount of money spent per session in July 2017?
What is the sequence of pages viewed?
Apache License, v2.0https://www.apache.org/licenses/LICENSE-2.0
License information was derived automatically
Homininos_DataSet(1).csv is the original///////// Homininos_DataSet.csv It already has the categorical values encoded
Exploring Human Evolution Through a Comprehensive Dataset
Introduction:
In this dataset, we delve into the fascinating story of human evolution. With 720 rows and 28 columns, this dataset covers a wide range of characteristics of different hominids, from the earliest consensual ancestors to modern Homo sapiens. This comprehensive compilation aims to facilitate the search for relationships between various key variables, thereby providing a more complete and detailed understanding of human evolution.
Objectives:
The main objective of this dataset is to facilitate the exploration and understanding of human evolution from a broader and more detailed perspective. Some specific objectives include:
Seeking relationships between important columns of the dataset. Understanding human evolution considering the collected data. Investigating the possible linearity of evolution over time. Analyzing potential relationships between brain size, developed technologies, diet, and physiological modifications over time. Significance:
This dataset is crucial for advancing our understanding of human evolution and history. It provides a solid foundation for research in various fields, from anthropology and evolutionary biology to archaeology and genetics. By allowing us to examine relationships and patterns among different variables, this dataset helps us trace the course of human evolution and gain a better understanding of our place in the tree of life.
Conclusions:
In summary, this comprehensive dataset provides us with a valuable tool for exploring human evolution in depth. With its numerous rows and columns, it allows us to delve into the complexity and diversity of our evolutionary history. By analyzing and understanding the collected data, we can gain new insights into how we have come to be what we are today and how our species has evolved over time.
This dataset not only expands our knowledge of human evolution but also inspires us to continue researching and discovering more about our shared past as a species.
I studied Biological Anthropology for 4 years at the National University of La Palta, and I had the opportunity to compile these data from classes and books such as Carbonell's "Homínidos: las primeras ocupaciones de los continentes," published in 2005.
INFO About Columns: Genus & Species: (categorical) This column contains the genus and specific name of the species. It provides taxonomic information about each hominid included in the dataset, allowing for precise identification
Time : (categorical) This column indicates the time period during which each hominid species lived. It helps to establish chronological context and understand the temporal distribution of different hominid groups.
Location: (categorical) This column records the continent location where each hominid species lived.
Zone: (categorical) Describes either east, west, south or north of the continent
Current Country: (categorical) Records the modern-day country associated with the location where each hominid species lived, facilitating geographical comparisons.
Habitat: (categorical) This column describes the typical habitat or environment inhabited by each hominid species. It provides information about the ecological niche and adaptation strategies of different hominids throughout history.
Cranial Capacity: (numeric) This column provides data on the cranial capacity of each hominid species. Cranial capacity is a key indicator of brain size and can offer insights into cognitive abilities and evolutionary trends.
Height: (numeric) Describes the average height or stature of each hominid species
Incisor Size: (categorical) Indicates the size of the incisors in each hominid species
Jaw Shape: (categorical) Describes the shape or morphology of the jaw in each hominid species
Torus Supraorbital: (categorical) Specifies the shape or morphology of a supraorbital torus in each hominid species
Prognathism: (categorical) Indicates the degree of facial prognathism or protrusion in each hominid species
Foramen Mágnum Position: (categorical) Describes the position of the foramen magnum in each hominid species
Canine Size: (categorical) Indicates the size of the canines in each hominid species
Canines Shape: (categorical) Describes the shape of the canines in each hominid species, providing information about their dietary adaptations and social behavior.
Tooth Enamel: (categorical) Specifies the characteristics of tooth enamel in each hominid species, which may indicate aspects of dietary ecology and dental health.
Tecno: (categorical) Records the presence or absence of technological advancements
Tecno Type: (categorical) Describes the specific type or style of technology associated with each hom...
The purpose of this project is to improve the accuracy of statistical software by providing reference datasets with certified computational results that enable the objective evaluation of statistical software. Currently datasets and certified values are provided for assessing the accuracy of software for univariate statistics, linear regression, nonlinear regression, and analysis of variance. The collection includes both generated and 'real-world' data of varying levels of difficulty. Generated datasets are designed to challenge specific computations. These include the classic Wampler datasets for testing linear regression algorithms and the Simon & Lesage datasets for testing analysis of variance algorithms. Real-world data include challenging datasets such as the Longley data for linear regression, and more benign datasets such as the Daniel & Wood data for nonlinear regression. Certified values are 'best-available' solutions. The certification procedure is described in the web pages for each statistical method. Datasets are ordered by level of difficulty (lower, average, and higher). Strictly speaking the level of difficulty of a dataset depends on the algorithm. These levels are merely provided as rough guidance for the user. Producing correct results on all datasets of higher difficulty does not imply that your software will pass all datasets of average or even lower difficulty. Similarly, producing correct results for all datasets in this collection does not imply that your software will do the same for your particular dataset. It will, however, provide some degree of assurance, in the sense that your package provides correct results for datasets known to yield incorrect results for some software. The Statistical Reference Datasets is also supported by the Standard Reference Data Program.