Search Results for "data file"
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Showing 12 open source projects for "data file"
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data.table
Extends base R’s data for high-performance data manipulation
data.table is an R package that extends base R’s data.frame for high-performance data manipulation. It offers concise syntax, blazing speed, and memory-efficient operations. It supports fast file reading/writing, joins, grouping, reshaping, and updates by reference. It is heavily used in large data workflows, big data in R, production pipelines, etc. Extremely efficient grouping/aggregation/summarization; can handle very large datasets (hundreds of millions to billions of rows) in memory (if available). ... -
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targets
Function-oriented Make-like declarative workflows for R
The targets package is a pipeline / workflow management tool in R, designed to coordinate multi‐step computational workflows in data science / statistics. It tracks dependencies between “targets” (computational steps), skips steps whose upstream data or code hasn’t changed, supports parallel computation, branching (dynamic generation of sub‐targets), file format abstractions, and encourages reproducible and efficient analyses. It’s something like GNU Make for R, but more integrated. ... -
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gt R
Easily generate information-rich, publication-quality tables from R
...The gt philosophy: we can construct a wide variety of useful tables with a cohesive set of table parts. These include the table header, the stub, the column labels and spanner column labels, the table body, and the table footer. It all begins with table data (be it a tibble or a data frame). You then decide how to compose your gt table with the elements and formatting you need for the task at hand. Finally, the table is rendered by printing it at the console, including it in an R Markdown document, or exporting it to a file using gtsave(). Currently, gt supports the HTML, LaTeX, and RTF output formats. -
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workflowr
Organize your project into a research website
workflowr is an R package that helps researchers organize, version, and share their data science projects in a reproducible and transparent manner. It combines R Markdown, Git, and a structured file system to create a research website that tracks analysis, results, and code changes over time. It’s ideal for academic and collaborative research workflows. -
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Amplicon_Sequencing_Worfklow
Analyzing amplicon data from sequences to stats
This is a collection of scripts and instructions on how to analyzing amplicon sequence data (i.e., 16S, ITS2, & other marker genes). I created this workflow to create a consistent set of methods for analyzing amplicon sequence data, from when you first receive the sequence data to statistical analyses & data visualization. All you need is to have the latest version of R installed, some experience with the command line & shell, and enough memory to run all of the programs. ... -
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activAnalyzer is a Shiny app that has been developed to analyze daily physical behavior data recorded at the hip in adults using an ActiGraph accelerometer (.agd file from a GT3X, GT3X+, wGT3X+ or wGT3X-BT device). Once analysis is completed, the app allows exporting results to .csv files and generating a report of the measurement (in either an .html format or a .pdf format). All the configured inputs relevant for interpreting the results are recorded in the report.
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MitoSAlt
Identification of mitochondrial structural alterations
MitoSAlt is a pipeline to identify large deletions and duplications in human and mouse mitochondrial genomes from next generation whole genome/exome sequencing data. The pipeline is capable of analyzing any circular genome in principle, as long as a proper configuration file is provided. -
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Harmony Data Integration
Fast, sensitive and accurate integration of single-cell data
Harmony is a general-purpose R package with an efficient algorithm for integrating multiple data sets. It is especially useful for large single-cell datasets such as single-cell RNA-seq. Harmony has been tested on R versions =4. Please consult the DESCRIPTION file for more details on required R packages. Harmony has been tested on Linux, OS X, and Windows platforms. -
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Open Intro Statistics
An open-source textbook written at the college level
OpenIntro Statistics is a dynamic take on the traditional curriculum, being successfully used at Community Colleges to the Ivy League. Each chapter's content is in one of the eight chapter folders that start with "ch_". Within each folder, there is a "figures" folder and a "TeX" folder. The TeX folder contains the text files that are used to typeset the chapters in the textbook. In many cases, R code is supplied with figures to regenerate the figure. It will often be necessary to install the... -
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sf (Simple Features)
Simple Features for R
...Reading and writing spatial vector data via many file formats/drivers through GDAL, and spatial databases (PostGIS etc.) Supports all standard simple feature geometry types (points, linestrings, polygons, multi-geometries etc.) in various dimensions (XY, XYZ, XYM, XYZM). -
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DataScienceR
a curated list of R tutorials for Data Science, NLP
...The repository also shows examples of linking R with external resources — APIs, databases, and file formats — and integrating into larger pipelines. It acts as a learning scaffold for students or beginners transitioning to more advanced data science work in R, offering a hands-on, example-driven approach. The structure encourages modularity, readability, and reproducible practices, making it a useful reference repository for learners and educators alike. -
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RNAseq Tutorial
Informatics for RNA-seq: A web resource for analysis on the cloud
rnaseq_tutorial is a tutorial and educational resource created by the Griffith Lab that guides users through the steps of RNA-seq data analysis. It includes working pipelines for alignment, differential expression, alternative splicing, visualization, and interpretation. It is designed to run in the cloud or local environments, providing introductory material on file formats, reference genomes / annotation, QC, mapping, quantifying expression, visualizing results, etc. ...
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