A csv file containing the tidal frequencies used for statistical analyses in the paper "Estimating Freshwater Flows From Tidally-Affected Hydrographic Data" by Dan Pagendam and Don Percival.

A sample rainfall dataset containing 100 records (in CSV file format), which includes some missing values, has been created to practice fundamental data cleaning operations and to extract basic statistical information from the provided CSV file.

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:

• product_id - Product ID
• product_name - Name of the Product
• category - Category of the Product
• discounted_price - Discounted Price of the Product
• actual_price - Actual Price of the Product
• discount_percentage - Percentage of Discount for the Product
• rating - Rating of the Product
• rating_count - Number of people who voted for the Amazon rating
• about_product - Description about the Product
• user_id - ID of the user who wrote review for the Product
• user_name - Name of the user who wrote review for the Product
• review_id - ID of the user review
• review_title - Short review
• review_content - Long review
• img_link - Image Link of the Product
• product_link - Official Website Link of the Product

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)

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.

Ransomware is considered as a significant threat for most enterprises since past few years. In scenarios wherein users can access all files on a shared server, one infected host is capable of locking the access to all shared files. In the article related to this repository, we detect ransomware infection based on file-sharing traffic analysis, even in the case of encrypted traffic. We compare three machine learning models and choose the best for validation. We train and test the detection model using more than 70 ransomware binaries from 26 different families and more than 2500 h of ‘not infected’ traffic from real users. The results reveal that the proposed tool can detect all ransomware binaries, including those not used in the training phase (zero-days). This paper provides a validation of the algorithm by studying the false positive rate and the amount of information from user files that the ransomware could encrypt before being detected.

This dataset directory contains the 'infected' and 'not infected' samples and the models used for each T configuration, each one in a separated folder.

The folders are named NxSy where x is the number of 1-second interval per sample and y the sliding step in seconds.

Each folder (for example N10S10/) contains: - tree.py -> Python script with the Tree model. - ensemble.json -> JSON file with the information about the Ensemble model. - NN_XhiddenLayer.json -> JSON file with the information about the NN model with X hidden layers (1, 2 or 3). - N10S10.csv -> All samples used for training each model in this folder. It is in csv format for using in bigML application. - zeroDays.csv -> All zero-day samples used for testing each model in this folder. It is in csv format for using in bigML application. - userSamples_test -> All samples used for validating each model in this folder. It is in csv format for using in bigML application. - userSamples_train -> User samples used for training the models. - ransomware_train -> Ransomware samples used for training the models - scaler.scaler -> Standard Scaler from python library used for scale the samples. - zeroDays_notFiltered -> Folder with the zeroDay samples.

In the case of N30S30 folder, there is an additional folder (SMBv2SMBv3NFS) with the samples extracted from the SMBv2, SMBv3 and NFS traffic traces. There are more binaries than the ones presented in the article, but it is because some of them are not "unseen" binaries (the families are present in the training set).

The files containing samples (NxSy.csv, zeroDays.csv and userSamples_test.csv) are structured as follows: - Each line is one sample. - Each sample has 3*T features and the label (1 if it is 'infected' sample and 0 if it is not). - The features are separated by ',' because it is a csv file. - The last column is the label of the sample.

Additionally we have placed two pcap files in root directory. There are the traces used for compare both versions of SMB.

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

This dataset titled Human Resources.csv contains anonymized employee data collected for internal HR analysis and research purposes. It includes fields such as employee ID, department, gender, age, job role, and employment status. The data can be used for workforce trend analysis, HR benchmarking, diversity studies, and training models in human resource analytics.The file is provided in CSV format (3.05 MB) and adheres to general data privacy standards, with no personally identifiable information (PII).Last updated: April 11, 2025. Uploaded by Anurag Pardiash.

Demonstrates my ability to use Python basics to analyze data stored in a CSV file. This dataset is synthesized data so it should not be used in an official capacity. Only basic modules for python are utilized within the scripts so it should be usable to anyone with basic access to Python 3.

Adventure Works 2022 dataset

How this Dataset is created?

On the official website the dataset is available over SQL server (localhost) and CSVs to be used via Power BI Desktop running on Virtual Lab (Virtaul Machine). As per first two steps of Importing data are executed in the virtual lab and then resultant Power BI tables are copied in CSVs. Added records till year 2022 as required.

How this Dataset may help you?

this dataset will be helpful in case you want to work offline with Adventure Works data in Power BI desktop in order to carry lab instructions as per training material on official website. The dataset is useful in case you want to work on Power BI desktop Sales Analysis example from Microsoft website PL 300 learning.

How to use this Dataset?

Download the CSV file(s) and import in Power BI desktop as tables. The CSVs are named as tables created after first two steps of importing data as mentioned in the PL-300 Microsoft Power BI Data Analyst exam lab.

Dataset

This dataset was created by Satish Gunjal

Released under Other (specified in description)

Contents

N.B. This is not real data. Only here for an example for project templates.

Project Title: Add title here

Project Team: Add contact information for research project team members

Summary: Provide a descriptive summary of the nature of your research project and its aims/focal research questions.

Relevant publications/outputs: When available, add links to the related publications/outputs from this data.

Data availability statement: If your data is not linked on figshare directly, provide links to where it is being hosted here (i.e., Open Science Framework, Github, etc.). If your data is not going to be made publicly available, please provide details here as to the conditions under which interested individuals could gain access to the data and how to go about doing so.

Data collection details: 1. When was your data collected? 2. How were your participants sampled/recruited?

Sample information: How many and who are your participants? Demographic summaries are helpful additions to this section.

Research Project Materials: What materials are necessary to fully reproduce your the contents of your dataset? Include a list of all relevant materials (e.g., surveys, interview questions) with a brief description of what is included in each file that should be uploaded alongside your datasets.

List of relevant datafile(s): If your project produces data that cannot be contained in a single file, list the names of each of the files here with a brief description of what parts of your research project each file is related to.

Data codebook: What is in each column of your dataset? Provide variable names as they are encoded in your data files, verbatim question associated with each response, response options, details of any post-collection coding that has been done on the raw-response (and whether that's encoded in a separate column).

Examples available at: https://www.thearda.com/data-archive?fid=PEWMU17 https://www.thearda.com/data-archive?fid=RELLAND14

Complete dataset of “Film Circulation on the International Film Festival Network and the Impact on Global Film Culture”

A peer-reviewed data paper for this dataset is in review to be published in NECSUS_European Journal of Media Studies - an open access journal aiming at enhancing data transparency and reusability, and will be available from https://necsus-ejms.org/ and https://mediarep.org

Please cite this when using the dataset.

Detailed description of the dataset:

1 Film Dataset: Festival Programs

The Film Dataset consists a data scheme image file, a codebook and two dataset tables in csv format.

The codebook (csv file “1_codebook_film-dataset_festival-program”) offers a detailed description of all variables within the Film Dataset. Along with the definition of variables it lists explanations for the units of measurement, data sources, coding and information on missing data.

The csv file “1_film-dataset_festival-program_long” comprises a dataset of all films and the festivals, festival sections, and the year of the festival edition that they were sampled from. The dataset is structured in the long format, i.e. the same film can appear in several rows when it appeared in more than one sample festival. However, films are identifiable via their unique ID.

The csv file “1_film-dataset_festival-program_wide” consists of the dataset listing only unique films (n=9,348). The dataset is in the wide format, i.e. each row corresponds to a unique film, identifiable via its unique ID. For easy analysis, and since the overlap is only six percent, in this dataset the variable sample festival (fest) corresponds to the first sample festival where the film appeared. For instance, if a film was first shown at Berlinale (in February) and then at Frameline (in June of the same year), the sample festival will list “Berlinale”. This file includes information on unique and IMDb IDs, the film title, production year, length, categorization in length, production countries, regional attribution, director names, genre attribution, the festival, festival section and festival edition the film was sampled from, and information whether there is festival run information available through the IMDb data.

2 Survey Dataset

The Survey Dataset consists of a data scheme image file, a codebook and two dataset tables in csv format.

The codebook “2_codebook_survey-dataset” includes coding information for both survey datasets. It lists the definition of the variables or survey questions (corresponding to Samoilova/Loist 2019), units of measurement, data source, variable type, range and coding, and information on missing data.

The csv file “2_survey-dataset_long-festivals_shared-consent” consists of a subset (n=161) of the original survey dataset (n=454), where respondents provided festival run data for films (n=206) and gave consent to share their data for research purposes. This dataset consists of the festival data in a long format, so that each row corresponds to the festival appearance of a film.

The csv file “2_survey-dataset_wide-no-festivals_shared-consent” consists of a subset (n=372) of the original dataset (n=454) of survey responses corresponding to sample films. It includes data only for those films for which respondents provided consent to share their data for research purposes. This dataset is shown in wide format of the survey data, i.e. information for each response corresponding to a film is listed in one row. This includes data on film IDs, film title, survey questions regarding completeness and availability of provided information, information on number of festival screenings, screening fees, budgets, marketing costs, market screenings, and distribution. As the file name suggests, no data on festival screenings is included in the wide format dataset.

3 IMDb & Scripts

The IMDb dataset consists of a data scheme image file, one codebook and eight datasets, all in csv format. It also includes the R scripts that we used for scraping and matching.

The codebook “3_codebook_imdb-dataset” includes information for all IMDb datasets. This includes ID information and their data source, coding and value ranges, and information on missing data.

The csv file “3_imdb-dataset_aka-titles_long” contains film title data in different languages scraped from IMDb in a long format, i.e. each row corresponds to a title in a given language.

The csv file “3_imdb-dataset_awards_long” contains film award data in a long format, i.e. each row corresponds to an award of a given film.

The csv file “3_imdb-dataset_companies_long” contains data on production and distribution companies of films. The dataset is in a long format, so that each row corresponds to a particular company of a particular film.

The csv file “3_imdb-dataset_crew_long” contains data on names and roles of crew members in a long format, i.e. each row corresponds to each crew member. The file also contains binary gender assigned to directors based on their first names using the GenderizeR application.

The csv file “3_imdb-dataset_festival-runs_long” contains festival run data scraped from IMDb in a long format, i.e. each row corresponds to the festival appearance of a given film. The dataset does not include each film screening, but the first screening of a film at a festival within a given year. The data includes festival runs up to 2019.

The csv file “3_imdb-dataset_general-info_wide” contains general information about films such as genre as defined by IMDb, languages in which a film was shown, ratings, and budget. The dataset is in wide format, so that each row corresponds to a unique film.

The csv file “3_imdb-dataset_release-info_long” contains data about non-festival release (e.g., theatrical, digital, tv, dvd/blueray). The dataset is in a long format, so that each row corresponds to a particular release of a particular film.

The csv file “3_imdb-dataset_websites_long” contains data on available websites (official websites, miscellaneous, photos, video clips). The dataset is in a long format, so that each row corresponds to a website of a particular film.

The dataset includes 8 text files containing the script for webscraping. They were written using the R-3.6.3 version for Windows.

The R script “r_1_unite_data” demonstrates the structure of the dataset, that we use in the following steps to identify, scrape, and match the film data.

The R script “r_2_scrape_matches” reads in the dataset with the film characteristics described in the “r_1_unite_data” and uses various R packages to create a search URL for each film from the core dataset on the IMDb website. The script attempts to match each film from the core dataset to IMDb records by first conducting an advanced search based on the movie title and year, and then potentially using an alternative title and a basic search if no matches are found in the advanced search. The script scrapes the title, release year, directors, running time, genre, and IMDb film URL from the first page of the suggested records from the IMDb website. The script then defines a loop that matches (including matching scores) each film in the core dataset with suggested films on the IMDb search page. Matching was done using data on directors, production year (+/- one year), and title, a fuzzy matching approach with two methods: “cosine” and “osa.” where the cosine similarity is used to match titles with a high degree of similarity, and the OSA algorithm is used to match titles that may have typos or minor variations.

The script “r_3_matching” creates a dataset with the matches for a manual check. Each pair of films (original film from the core dataset and the suggested match from the IMDb website was categorized in the following five categories: a) 100% match: perfect match on title, year, and director; b) likely good match; c) maybe match; d) unlikely match; and e) no match). The script also checks for possible doubles in the dataset and identifies them for a manual check.

The script “r_4_scraping_functions” creates a function for scraping the data from the identified matches (based on the scripts described above and manually checked). These functions are used for scraping the data in the next script.

The script “r_5a_extracting_info_sample” uses the function defined in the “r_4_scraping_functions”, in order to scrape the IMDb data for the identified matches. This script does that for the first 100 films, to check, if everything works. Scraping for the entire dataset took a few hours. Therefore, a test with a subsample of 100 films is advisable.

The script “r_5b_extracting_info_all” extracts the data for the entire dataset of the identified matches.

The script “r_5c_extracting_info_skipped” checks the films with missing data (where data was not scraped) and tried to extract data one more time to make sure that the errors were not caused by disruptions in the internet connection or other technical issues.

The script “r_check_logs” is used for troubleshooting and tracking the progress of all of the R scripts used. It gives information on the amount of missing values and errors.

4 Festival Library Dataset

The Festival Library Dataset consists of a data scheme image file, one codebook and one dataset, all in csv format.

The codebook (csv file “4_codebook_festival-library_dataset”) offers a detailed description of all variables within the Library Dataset. It lists the definition of variables, such as location and festival name, and festival categories,

Sample data for exercises in Further Adventures in Data Cleaning.

This replication package contains datasets and scripts related to the paper: "*How do Hugging Face Models Document Datasets, Bias, and Licenses? An Empirical Study*"

## Root directory

- `statistics.r`: R script used to compute the correlation between usage and downloads, and the RQ1/RQ2 inter-rater agreements

- `modelsInfo.zip`: zip file containing all the downloaded model cards (in JSON format)

- `script`: directory containing all the scripts used to collect and process data. For further details, see README file inside the script directory.

## Dataset

- `Dataset/Dataset_HF-models-list.csv`: list of HF models analyzed

- `Dataset/Dataset_github-prj-list.txt`: list of GitHub projects using the *transformers* library

- `Dataset/Dataset_github-Prj_model-Used.csv`: contains usage pairs: project, model

- `Dataset/Dataset_prj-num-models-reused.csv`: number of models used by each GitHub project

- `Dataset/Dataset_model-download_num-prj_correlation.csv` contains, for each model used by GitHub projects: the name, the task, the number of reusing projects, and the number of downloads

## RQ1

- `RQ1/RQ1_dataset-list.txt`: list of HF datasets

- `RQ1/RQ1_datasetSample.csv`: sample set of models used for the manual analysis of datasets

- `RQ1/RQ1_analyzeDatasetTags.py`: Python script to analyze model tags for the presence of datasets. it requires to unzip the `modelsInfo.zip` in a directory with the same name (`modelsInfo`) at the root of the replication package folder. Produces the output to stdout. To redirect in a file fo be analyzed by the `RQ2/countDataset.py` script

- `RQ1/RQ1_countDataset.py`: given the output of `RQ2/analyzeDatasetTags.py` (passed as argument) produces, for each model, a list of Booleans indicating whether (i) the model only declares HF datasets, (ii) the model only declares external datasets, (iii) the model declares both, and (iv) the model is part of the sample for the manual analysis

- `RQ1/RQ1_datasetTags.csv`: output of `RQ2/analyzeDatasetTags.py`

- `RQ1/RQ1_dataset_usage_count.csv`: output of `RQ2/countDataset.py`

## RQ2

- `RQ2/tableBias.pdf`: table detailing the number of occurrences of different types of bias by model Task

- `RQ2/RQ2_bias_classification_sheet.csv`: results of the manual labeling

- `RQ2/RQ2_isBiased.csv`: file to compute the inter-rater agreement of whether or not a model documents Bias

- `RQ2/RQ2_biasAgrLabels.csv`: file to compute the inter-rater agreement related to bias categories

- `RQ2/RQ2_final_bias_categories_with_levels.csv`: for each model in the sample, this file lists (i) the bias leaf category, (ii) the first-level category, and (iii) the intermediate category

## RQ3

- `RQ3/RQ3_LicenseValidation.csv`: manual validation of a sample of licenses

- `RQ3/RQ3_{NETWORK-RESTRICTIVE|RESTRICTIVE|WEAK-RESTRICTIVE|PERMISSIVE}-license-list.txt`: lists of licenses with different permissiveness

- `RQ3/RQ3_prjs_license.csv`: for each project linked to models, among other fields it indicates the license tag and name

- `RQ3/RQ3_models_license.csv`: for each model, indicates among other pieces of info, whether the model has a license, and if yes what kind of license

- `RQ3/RQ3_model-prj-license_contingency_table.csv`: usage contingency table between projects' licenses (columns) and models' licenses (rows)

- `RQ3/RQ3_models_prjs_licenses_with_type.csv`: pairs project-model, with their respective licenses and permissiveness level

## scripts

Contains the scripts used to mine Hugging Face and GitHub. Details are in the enclosed README

The present study updates and extends the meta-analysis by Haus et al. (2013) who applied the theory of planned behavior (TPB) to analyze gender differences in the motivation to start a business. We extend this meta-analysis by investigating the moderating role of the societal context in which the motivation to start a business emerges and proceeds. The results, based on 119 studies analyzing 129 samples with 266,958 individuals from 36 countries, show smaller gender differences than the original study and reveal little differences across cultural regions in the effects of the tested model. A meta-regression analyzing the role of specific cultural dimensions and economic factors on gender-related correlations reveals significant effects only of gender egalitarianism and in the opposite direction as expected. In summary, the study contributes to the discussion on gender differences, the importance of study replications and updates of meta-analyses, and the generalizability of theories across cultural contexts. Dataset for: Steinmetz, H., Isidor, R., & Bauer, C. (2021). Gender Differences in the Intention to Start a Business. Zeitschrift Für Psychologie, 229(1), 70–84. https://doi.org/10.1027/2151-2604/a000435: Electronic supplementary material D - Data file

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.

Dataset

This dataset was created by Shiva Vashishtha

Contents

This data package contains mean values for dissolved organic carbon (DOC) and dissolved inorganic carbon (DIC) for water samples taken from the East River Watershed in Colorado. The East River is part of the Watershed Function Scientific Focus Area (WFSFA) located in the Upper Colorado River Basin, United States. DOC and DIC concentrations in water samples were determined using a TOC-VCPH analyzer (Shimadzu Corporation, Japan). DOC was analyzed as non-purgeable organic carbon (NPOC) by purging HCl acidified samples with carbon-free air to remove DIC prior to measurement. After the acidified sample has been sparged, it is injected into a combustion tube filled with oxidation catalyst heated to 680 degrees C. The DOC in samples is combusted to CO2 and measured by a non-dispersive infrared (NDIR) detector. The peak area of the analog signal produced by the NDIR detector is proportional to the DOC concentration of the sample. DIC was determined by acidifying the samples with HCl first, and then purge with carbon-free air to release CO2 for analysis by NDIR detector. All files are labeled by location and variable, and data reported are the mean values upon minimum three replicate measurements with a relative standard deviation < 3%. All samples were analyzed under a rigorous quality assurance and quality control (QA/QC) process as detailed in the methods. This data package contains (1) a zip file (dic_npoc_data_2014-2023.zip) containing a total of 319 files: 318 data files of DIC and NPOC data from across the Lawrence Berkeley National Laboratory (LBNL) Watershed Function Scientific Focus Area (SFA) which is reported in .csv files per location and a locations.csv (1 file) with latitude and longitude for each location; (2) a file-level metadata (v3_20230808_flmd.csv) file that lists each file contained in the dataset with associated metadata; (3) a data dictionary (v3_20230808_dd.csv) file that contains terms/column_headers used throughout the files along with a definition, units, and data type; and (4) PDF and docx files for the determination of Method Detection Limits (MDLs) for DIC and NPOC data. There are a total of 106 locations containing DIC/NPOC data. Update on 2020-10-07: Updated the data files to remove times from the timestamps, so that only dates remain. The data values have not changed. Update on 2021-04-11: Added Determination of Method Detection Limits (MDLs) for DIC, NPOC and TDN Analyses document, which can be accessed as a PDF or with Microsoft Word. Update on 2022-06-10: versioned updates to this dataset was made along with these changes: (1) updated dissolved inorganic carbon and dissolved organic carbon data for all locations up to 2021-12-31, (2) removal of units from column headers in datafiles, (3) added row underneath headers to contain units of variables, (4) restructure of units to comply with CSV reporting format requirements, (5) added -9999 for empty numerical cells, and (6) the addition of the file-level metadata (flmd.csv) and data dictionary (dd.csv) were added to comply with the File-Level Metadata Reporting Format. Update on 2022-09-09: Updates were made to reporting format specific files (file-level metadata and data dictionary) to correct swapped file names, add additional details on metadata descriptions on both files, add a header_row column to enable parsing, and add version number and date to file names (v2_20220909_flmd.csv and v2_20220909_dd.csv). Update on 2023-08-08: Updates were made to both the data files and reporting format specific files. New available anion data was added, up until 2023-01-05. The file level metadata and data dictionary files were updated to reflect the additional data added.

This data release provides data in support of an assessment of water quality and discharge in the Herring River at the Chequessett Neck Road dike in Wellfleet, Massachusetts, from November 2015 to September 2017. The assessment was a cooperative project among the U.S. Geological Survey, National Park Service, Cape Cod National Seashore, and the Friends of Herring River to characterize environmental conditions prior to a future removal of the dike. It is described in U.S. Geological Survey (USGS) Scientific Investigations Report "Assessment of Water Quality and Discharge in the Herring River, Wellfleet, Massachusetts, November 2015 – September 2017." This data release is structured as a set of comma-separated values (CSV) files, each of which contains information on data source (or laboratory used for analysis), USGS site identification (ID) number, beginning date of time of observation or sampling, ending date and time of observation or sampling and data such as flow rate and analytical results. The CSV files include calculated tidal daily flows (Flood_Tide_Tidal_Day.csv and Ebb_Tide_Tidal_Day.csv) that were used in Huntington and others (2020) for estimation of nutrient loads. Tidal daily flows are the estimated mean daily discharges for two consecutive flood and ebb tide cycles (average duration: 24 hours, 48 minutes). The associated date is the day on which most of the flow occurred. CSV files contain quality assurance data for water-quality samples including blanks (Blanks.csv), replicates (Replicates.csv), standard reference materials (Standard_Reference_Material.csv), and atmospheric ammonium contamination (NH4_Atmospheric_Contamination.csv). One CSV file (EWI_vs_ISCO.csv) contains data comparing composite samples collected by an automatic sampler (ISCO) at a fixed point with depth-integrated samples collected at equal width increments (EWI). One CSV file (Cross_Section_Field_Parameters.csv) contains field parameter data (specific conductance, temperature, pH, and dissolved oxygen) collected at a fixed location and data collected along the cross sections at variable water depths and horizontal distances across the openings of the culverts at the Chequessett Neck Road dike. One CSV file (LOADEST_Bias_Statistics.csv) contains data that include estimated natural log of load, model residuals, Z-scores, and seasonal model residuals for winter (December, January, and February); spring (March, April and May); summer (June, July and August); and fall (September, October, and November). The data release also includes a data dictionary (Data_Dictionary.csv) that provides detailed descriptions of each field in each CSV file, including: data filename; laboratory or data source; U.S. Geological Survey site ID numbers; data types; constituent (analyte) U.S. Geological Survey parameter codes; descriptions of parameters; units; methods; minimum reporting limits; limits of quantitation, if appropriate; method reference citations; and minimum, maximum, median, and average values for each analyte. The data release also includes an abbreviations file (Abbreviations.pdf) that defines all the abbreviations in the data dictionary and CSV files. Note that the USGS site ID includes a leading zero (011058798) and some of the parameter codes contain leading zeros, so care must be taken in opening and subsequently saving these files in other formats where leading zeros may be dropped.

These are .csv files for statistical analysis in MetaboAnalyst.