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Showing 138 open source projects for "hash-linux"
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Covidex
Ultra fast and accurate subtyping tool of viral genomes.
Viral subtypes or clades represent clusters among isolates from the global population of a defined species. Subtypification is relevant for studies on virus epidemiology, evolution and pathogenesis. In this sense, Covidex was developed as an open source alignment-free machine learning subtyping tool. It is a shiny app that allows fast and accurate classification of viral genomes in pre-defined clusters. If more than 1000 sequences are loaded the tool will run in multithread mode. Capable of... -
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rethinking
Statistical Rethinking course and book package
This R package accompanies Richard McElreath’s Statistical Rethinking (2nd edition), offering utilities to fit and compare Bayesian models using both MAP estimation (quap) and Hamiltonian Monte Carlo via RStan (ulam). It supports specifying models via explicit distributional assumptions, providing flexibility for advanced statistical workflows. -
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Statistics for Data Scientists
"Statistics for Data Scientists: 50 Essential Concepts"
The “statistics-for-data-scientists” repository is a pedagogical resource designed to bridge rigorous statistics theory and practical data science workflows. The code and materials are intended to help data scientists and analysts grasp statistical principles (e.g. inference, regressions, hypothesis testing, probability, confidence intervals) in contexts relevant to real data analysis tasks. The repository includes Jupyter notebooks, R scripts, worked examples, and possibly problem sets that... -
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KidneyExplorer
Kidney proteomics data explorer enables you to investigate diseases
KidneyExplorer enables you to interactively survey kidney proteomics datasets from different kidney disease models. Here you can download the corresponding SQL database dumps. The original website for the shiny app is: https://kidneyapp.shinyapps.io/kidneyorganoids/ -
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stat-cookbook
The probability and statistics cookbook
A compact “Probability and Statistics Cookbook” offering concise mathematical recipes for key statistical concepts—expectation, variance, distributions and inequalities—packaged as LaTeX and R-based executable documents. -
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QuantifyPoly(A)
Quantification of poly(A) sites from 3' end sequencing data
QuantifyPoly(A) - a tool for quantification of poly(A) sites from 3' end sequencing data. [1] QuantifyPoly(A) user manual Please visit the Wiki page of this website. [2] QuantifyPoly(A) Q&A For Q&A, please visit the Blog page of this website. [3] QuantifyPoly(A) bug report You can report a bug as a Ticket request, or start a topic session in the Discussion webpage of this website. -
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covid19model
Code for modelling estimated deaths and cases for COVID19
Code for modeling estimated deaths and infections for COVID-19 from "Estimating the effects of non-pharmaceutical interventions on COVID-19 in Europe", Flaxman, Mishra, Gandy et al, Nature, 2020, the published version of our original Report 13. This is the release related to our Tiers paper, where we use the latent factor model to estimate the effectiveness of tiers systems in England. Peer-reviewed version is to be out soon. All other code is still the same for previous releases. The code... -
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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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R4DS (R for Data Science)
R for data science: a book
“R for Data Science” (r4ds) is the source material (book + examples) by Hadley Wickham et al., intended to teach data science using R and the tidyverse. It covers the workflow from importing data, tidying, transforming, visualizing, modelling, communicating results, and programming in R. The repository contains the source files (Quarto / RMarkdown), example datasets, visualizations, exercises, and all content needed to build the book. Includes many example datasets, diagrams, code samples,... -
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Reproducible-research
A Reproducible Data Analysis Workflow with R Markdown, Git, Make, etc.
In this tutorial, we describe a workflow to ensure long-term reproducibility of R-based data analyses. The workflow leverages established tools and practices from software engineering. It combines the benefits of various open-source software tools including R Markdown, Git, Make, and Docker, whose interplay ensures seamless integration of version management, dynamic report generation conforming to various journal styles, and full cross-platform and long-term computational reproducibility.... -
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Pain2D are programs which were developed for the automated pain drawing collection and classification of diseases on the basis of pain drawings in pen-and-paper and digital form for research purposes. Pain2D is currently not a diagnostic tool, but is aimed at scientists, physicians and anyone interested in the automated analysis of pain drawings.
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R Markdown Cookbook
R Markdown Cookbook
R Markdown Cookbook. A range of tips and tricks to make better use of R Markdown. R Markdown is a powerful tool for combining analysis and reporting into the same document. Since the birth of the rmarkdown package (Allaire, Xie, Dervieux, McPherson, et al. 2023) in early 2014, R Markdown has grown substantially from a package that supports a few output formats, to an extensive and diverse ecosystem that supports the creation of books, blogs, scientific articles, websites, and even resumes. -
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palmerpenguins
A great intro dataset for data exploration & visualization
palmerpenguins is an R package offering real-world ecological data from the Palmer Archipelago penguin species—Adélie, Chinstrap, and Gentoo. Designed as a more engaging alternative to the classical iris dataset, it provides size measurements, clutch information, and blood isotope data for teaching, visualization, and analytics practice. -
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hrbrthemes
Opinionated, typographic-centric ggplot2 themes and theme components
hrbrthemes is a focused ggplot2 theme package with an emphasis on typography, layout precision, and visual polish. It includes themes like theme_ipsum and Font scales tailored for clean, high‑quality production graphics. -
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Harmony Data Integration
Fast, sensitive and accurate integration of single-cell data
...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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swirl
Learn R, in R
swirl is an R package that allows interactive, in-R learning of statistics, data science, R programming etc. The idea is that you load swirl in R, and it presents you with lessons (within R’s console or RStudio) that ask you to type commands, check results, and progress through tutorial material—without leaving the R environment. It is used for teaching R, especially for beginners, as well as for self-paced learning of packages, data manipulation, visualization, etc. Lessons and content are... -
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posterdown
Use RMarkdown to generate PDF Conference Posters via HTML
Welcome to Posterdown! This is my attempt to provide a semi-smooth workflow for those who wish to take their RMarkdown skills to the conference world. Many creature comforts from RMarkdown are available in this package such as Markdown section notation, figure captioning, and even citations like this one (Allaire, Xie, McPherson, et al. 2018). The rest of this example poster will show how you can insert typical conference poster features into your own document. Posterdown was created as a... -
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benchm-ml
A benchmark of commonly used open source implementations
This repository is designed to provide a minimal benchmark framework comparing commonly used machine learning libraries in terms of scalability, speed, and classification accuracy. The focus is on binary classification tasks without missing data, where inputs can be numeric or categorical (after one-hot encoding). It targets large scale settings by varying the number of observations (n) up to millions and the number of features (after expansion) to about a thousand, to stress test different... -
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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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adv-r
Advanced R: a book
Source repository for Advanced R, the authoritative guide by Hadley Wickham, built with bookdown (R Markdown) and designed to deepen R users’ understanding of language internals, functional programming, object systems, and metaprogramming. -
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bbplot
R package that helps create and export ggplot2 charts
bbplot is an R package developed by the BBC visual journalism team aimed at helping data journalists and analysts produce chart styles consistent with BBC aesthetics. It provides functions and themes that make it easier to adopt BBC’s visual style (fonts, colors, annotations, layout) in ggplot2 plots. The package includes helper functions for axis labels, captions, legends, branding (e.g. BBC red lines or accents), and common chart types styled for editorial presentation. It offers templates... -
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ComplexHeatmap
Make Complex Heatmaps
ComplexHeatmap is an R/Bioconductor package by Zuguang Gu et al. designed to create highly flexible, complex, richly annotated heatmaps and related visualizations. It allows arranging multiple heatmaps, adding annotations, combining heatmaps, customizing colors, layouts, and integrating other plots. Often used in genomics/bioinformatics to show expression, methylation, etc., with sidebars, annotations, clustering, etc. Highly customizable layout: combining different heatmaps, arranging and... -
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bookdownplus
Use R package bookdown for writing varied types of books and documents
The package bookdownplus (Zhao 2017a) is an extension of R bookdown (Xie 2016). It is a collection of multiple templates on the basis of LaTeX, which is tailored so that I can work happily under the umbrella of bookdown. bookdownplus helps you write academic journal articles, guitar books, chemical equations, mails, calendars, and diaries. bookdown features the collaboration of many fantastic tools. However, an R beginner might be confused or depressed in struggling in the flood of LaTeX,... -
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sf (Simple Features)
Simple Features for R
sf is an R package that implements “simple features” (standardized vector spatial data) for R. It allows spatial vector data (points, lines, polygons etc.) to be represented as records in data frames (or tibbles) with geometry list columns, and performs spatial operations (geometry operations, coordinate reference system transformations, reading/writing spatial data, integration with spatial databases etc.). It interfaces to GDAL, GEOS, PROJ libraries for robust operations. Reading and... -
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mathpix
Query the mathpix API to convert math images to LaTeX
Query the mathpix API to convert math images to LaTeX.
