Showing 136 of total 136 results (show query)
crsh
papaja:Prepare American Psychological Association Journal Articles with R Markdown
Tools to create dynamic, submission-ready manuscripts, which conform to American Psychological Association manuscript guidelines. We provide R Markdown document formats for manuscripts (PDF and Word) and revision letters (PDF). Helper functions facilitate reporting statistical analyses or create publication-ready tables and plots.
Maintained by Frederik Aust. Last updated 1 months ago.
apaapa-guidelinesjournalmanuscriptpsychologyreproducible-paperreproducible-researchrmarkdown
663 stars 12.00 score 1.7k scripts 2 dependents
rstudio
pagedown:Paginate the HTML Output of R Markdown with CSS for Print
Use the paged media properties in CSS and the JavaScript library 'paged.js' to split the content of an HTML document into discrete pages. Each page can have its page size, page numbers, margin boxes, and running headers, etc. Applications of this package include books, letters, reports, papers, business cards, resumes, and posters.
Maintained by Yihui Xie. Last updated 3 months ago.
csshtmlpaged-mediapdfprintingtypesetting
909 stars 11.73 score 350 scripts 19 dependentsrstudio
blogdown:Create Blogs and Websites with R Markdown
Write blog posts and web pages in R Markdown. This package supports the static site generator 'Hugo' (<https://gohugo.io>) best, and it also supports 'Jekyll' (<https://jekyllrb.com>) and 'Hexo' (<https://hexo.io>).
Maintained by Yihui Xie. Last updated 14 days ago.
blog-engineblogdownhugormarkdownrstudiowebsite-generation
1.8k stars 11.55 score 1.4k scripts 1 dependents
bioc
BiocStyle:Standard styles for vignettes and other Bioconductor documents
Provides standard formatting styles for Bioconductor PDF and HTML documents. Package vignettes illustrate use and functionality.
Maintained by Bioconductor Package Maintainer. Last updated 5 months ago.
softwarebioconductor-packagecore-package
12 stars 11.31 score 1.2k scripts 47 dependents
choonghyunryu
dlookr:Tools for Data Diagnosis, Exploration, Transformation
A collection of tools that support data diagnosis, exploration, and transformation. Data diagnostics provides information and visualization of missing values, outliers, and unique and negative values to help you understand the distribution and quality of your data. Data exploration provides information and visualization of the descriptive statistics of univariate variables, normality tests and outliers, correlation of two variables, and the relationship between the target variable and predictor. Data transformation supports binning for categorizing continuous variables, imputes missing values and outliers, and resolves skewness. And it creates automated reports that support these three tasks.
Maintained by Choonghyun Ryu. Last updated 10 months ago.
212 stars 11.05 score 748 scripts 2 dependents
juba
rmdformats:HTML Output Formats and Templates for 'rmarkdown' Documents
HTML formats and templates for 'rmarkdown' documents, with some extra features such as automatic table of contents, lightboxed figures, dynamic crosstab helper.
Maintained by Julien Barnier. Last updated 1 years ago.
doccohtmlhtml-themematerialrmarkdownrstudio
723 stars 10.22 score 1.4k scripts 5 dependentsrstudio
distill:'R Markdown' Format for Scientific and Technical Writing
Scientific and technical article format for the web. 'Distill' articles feature attractive, reader-friendly typography, flexible layout options for visualizations, and full support for footnotes and citations.
Maintained by Christophe Dervieux. Last updated 1 years ago.
423 stars 9.85 score 402 scripts 6 dependents
rjournal
rjtools:Preparing, Checking, and Submitting Articles to the 'R Journal'
Create an 'R Journal' 'Rmarkdown' template article, that will generate html and pdf versions of your paper. Check that the paper folder has all the required components needed for submission. Examples of 'R Journal' publications can be found at <https://journal.r-project.org>.
Maintained by Di Cook. Last updated 2 months ago.
33 stars 8.81 score 37 scripts 1 dependentsbioc
hypeR:An R Package For Geneset Enrichment Workflows
An R Package for Geneset Enrichment Workflows.
Maintained by Anthony Federico. Last updated 5 months ago.
genesetenrichmentannotationpathwaysbioinformaticscomputational-biologygeneset-enrichment-analysis
76 stars 8.22 score 145 scripts
dstanley4
apaTables:Create American Psychological Association (APA) Style Tables
A common task faced by researchers is the creation of APA style (i.e., American Psychological Association style) tables from statistical output. In R a large number of function calls are often needed to obtain all of the desired information for a single APA style table. As well, the process of manually creating APA style tables in a word processor is prone to transcription errors. This package creates Word files (.doc files) and latex code containing APA style tables for several types of analyses. Using this package minimizes transcription errors and reduces the number commands needed by the user.
Maintained by David Stanley. Last updated 6 months ago.
61 stars 7.86 score 438 scriptsbioc
PhyloProfile:PhyloProfile
PhyloProfile is a tool for exploring complex phylogenetic profiles. Phylogenetic profiles, presence/absence patterns of genes over a set of species, are commonly used to trace the functional and evolutionary history of genes across species and time. With PhyloProfile we can enrich regular phylogenetic profiles with further data like sequence/structure similarity, to make phylogenetic profiling more meaningful. Besides the interactive visualisation powered by R-Shiny, the package offers a set of further analysis features to gain insights like the gene age estimation or core gene identification.
Maintained by Vinh Tran. Last updated 8 days ago.
softwarevisualizationdatarepresentationmultiplecomparisonfunctionalpredictiondimensionreductionbioinformaticsheatmapinteractive-visualizationsorthologsphylogenetic-profileshiny
33 stars 7.79 score 10 scripts
brentthorne
posterdown:Generate PDF Conference Posters Using R Markdown
Use 'rmarkdown' and 'pagedown' to generate HTML and PDF conference posters.
Maintained by Brent Thorne. Last updated 5 years ago.
conference-postercsshtmlpdfpdf-posterposterrmarkdownrstudiotypesetting
859 stars 7.54 score 10 scripts
atlas-aai
ratlas:ATLAS Formatting Functions and Templates
Provides templates, formatting tools, and 'ggplot2' themes tailored for the Accessible Teaching, Learning, and Assessment Systems (ATLAS) organization. These templates facilitate the creation of topic guides and technical reports, while the formatting functions enable users to customize numbers and tables to meet specific requirements. Additionally, the themes ensure a uniform visual style across graphics.
Maintained by W. Jake Thompson. Last updated 5 months ago.
bookdownggplot2ggplot2-themesrmarkdownrmarkdown-template
29 stars 7.28 score 20 scriptsbioc
regionReport:Generate HTML or PDF reports for a set of genomic regions or DESeq2/edgeR results
Generate HTML or PDF reports to explore a set of regions such as the results from annotation-agnostic expression analysis of RNA-seq data at base-pair resolution performed by derfinder. You can also create reports for DESeq2 or edgeR results.
Maintained by Leonardo Collado-Torres. Last updated 2 months ago.
differentialexpressionsequencingrnaseqsoftwarevisualizationtranscriptioncoveragereportwritingdifferentialmethylationdifferentialpeakcallingimmunooncologyqualitycontrolbioconductorderfinderdeseq2edgerregionreportrmarkdown
9 stars 7.22 score 46 scripts
openanalytics
clinDataReview:Clinical Data Review Tool
Creation of interactive tables, listings and figures ('TLFs') and associated report for exploratory analysis of data in a clinical trial, e.g. for clinical oversight activities. Interactive figures include sunburst, treemap, scatterplot, line plot and barplot of counts data. Interactive tables include table of summary statistics (as counts of adverse events, enrollment table) and listings. Possibility to compare data (summary table or listing) across two data batches/sets. A clinical data review report is created via study-specific configuration files and template 'R Markdown' reports contained in the package.
Maintained by Laure Cougnaud. Last updated 10 months ago.
11 stars 7.10 score 36 scripts
yihui
rolldown:R Markdown Output Formats for Storytelling
R Markdown output formats based on JavaScript libraries such as 'Scrollama' (<https://github.com/russellgoldenberg/scrollama>) for storytelling.
Maintained by Yihui Xie. Last updated 5 years ago.
186 stars 6.87 score 1 scripts
raymondbalise
rUM:R Templates from the University of Miami
This holds some r markdown and quarto templates and a template to create a research project in "R Studio".
Maintained by Raymond Balise. Last updated 8 days ago.
9 stars 6.84 score 16 scriptsbioc
chimeraviz:Visualization tools for gene fusions
chimeraviz manages data from fusion gene finders and provides useful visualization tools.
Maintained by Stian Lågstad. Last updated 5 months ago.
37 stars 6.71 score 14 scriptsbioc
COMPASS:Combinatorial Polyfunctionality Analysis of Single Cells
COMPASS is a statistical framework that enables unbiased analysis of antigen-specific T-cell subsets. COMPASS uses a Bayesian hierarchical framework to model all observed cell-subsets and select the most likely to be antigen-specific while regularizing the small cell counts that often arise in multi-parameter space. The model provides a posterior probability of specificity for each cell subset and each sample, which can be used to profile a subject's immune response to external stimuli such as infection or vaccination.
Maintained by Greg Finak. Last updated 5 months ago.
immunooncologyflowcytometrycpp
7 stars 6.51 score 42 scripts
jhudsl
ottrpal:Companion Tools for Open-Source Tools for Training Resources (OTTR)
Tools for converting Open-Source Tools for Training Resources (OTTR) courses into Leanpub or Coursera courses. 'ottrpal' is for use with the OTTR Template repository to create courses.
Maintained by Candace Savonen. Last updated 9 days ago.
3 stars 6.50 score 10 scripts 1 dependents
ericmarcon
memoiR:R Markdown and Bookdown Templates to Publish Documents
Producing high-quality documents suitable for publication directly from R is made possible by the R Markdown ecosystem. 'memoiR' makes it easy. It provides templates to knit memoirs, articles and slideshows with helpers to publish the documents on GitHub Pages and activate continuous integration.
Maintained by Eric Marcon. Last updated 28 days ago.
articlebeamerbookdowngitbooklatextemplatethesis
23 stars 6.48 score
abhi-1u
texor:Converting 'LaTeX' 'R Journal' Articles into 'RJ-web-articles'
Articles in the 'R Journal' were first authored in 'LaTeX', which performs admirably for 'PDF' files but is less than ideal for modern online interfaces. The 'texor' package does all the transitional chores and conversions necessary to move to the online versions.
Maintained by Abhishek Ulayil. Last updated 4 months ago.
7 stars 6.28 score 8 scriptsbioc
SBGNview:"SBGNview: Data Analysis, Integration and Visualization on SBGN Pathways"
SBGNview is a tool set for pathway based data visalization, integration and analysis. SBGNview is similar and complementary to the widely used Pathview, with the following key features: 1. Pathway definition by the widely adopted Systems Biology Graphical Notation (SBGN); 2. Supports multiple major pathway databases beyond KEGG (Reactome, MetaCyc, SMPDB, PANTHER, METACROP) and user defined pathways; 3. Covers 5,200 reference pathways and over 3,000 species by default; 4. Extensive graphics controls, including glyph and edge attributes, graph layout and sub-pathway highlight; 5. SBGN pathway data manipulation, processing, extraction and analysis.
Maintained by Weijun Luo. Last updated 5 months ago.
genetargetpathwaysgraphandnetworkvisualizationgenesetenrichmentdifferentialexpressiongeneexpressionmicroarrayrnaseqgeneticsmetabolomicsproteomicssystemsbiologysequencing
26 stars 6.23 score 22 scriptsbioc
scMET:Bayesian modelling of cell-to-cell DNA methylation heterogeneity
High-throughput single-cell measurements of DNA methylomes can quantify methylation heterogeneity and uncover its role in gene regulation. However, technical limitations and sparse coverage can preclude this task. scMET is a hierarchical Bayesian model which overcomes sparsity, sharing information across cells and genomic features to robustly quantify genuine biological heterogeneity. scMET can identify highly variable features that drive epigenetic heterogeneity, and perform differential methylation and variability analyses. We illustrate how scMET facilitates the characterization of epigenetically distinct cell populations and how it enables the formulation of novel hypotheses on the epigenetic regulation of gene expression.
Maintained by Andreas C. Kapourani. Last updated 5 months ago.
immunooncologydnamethylationdifferentialmethylationdifferentialexpressiongeneexpressiongeneregulationepigeneticsgeneticsclusteringfeatureextractionregressionbayesiansequencingcoveragesinglecellbayesian-inferencegeneralised-linear-modelsheterogeneityhierarchical-modelsmethylation-analysissingle-cellcpp
20 stars 6.23 score 42 scriptsbioc
iNETgrate:Integrates DNA methylation data with gene expression in a single gene network
The iNETgrate package provides functions to build a correlation network in which nodes are genes. DNA methylation and gene expression data are integrated to define the connections between genes. This network is used to identify modules (clusters) of genes. The biological information in each of the resulting modules is represented by an eigengene. These biological signatures can be used as features e.g., for classification of patients into risk categories. The resulting biological signatures are very robust and give a holistic view of the underlying molecular changes.
Maintained by Habil Zare. Last updated 5 months ago.
geneexpressionrnaseqdnamethylationnetworkinferencenetworkgraphandnetworkbiomedicalinformaticssystemsbiologytranscriptomicsclassificationclusteringdimensionreductionprincipalcomponentmrnamicroarraynormalizationgenepredictionkeggsurvivalcore-services
74 stars 6.21 score 1 scripts
iheid-library
iheiddown:For Writing Geneva Graduate Institute Documents
A set of tools for writing documents according to Geneva Graduate Institute conventions and regulations. The most common use is for writing and compiling theses or thesis chapters, as drafts or for examination with correct preamble formatting. However, the package also offers users to create HTML presentation slides with 'xaringan', complete problem sets, format posters, and, for course instructors, prepare a syllabus. The package includes additional functions for institutional color palettes, an institutional 'ggplot' theme, a function for counting manuscript words, and a bibliographical analysis toolkit.
Maintained by James Hollway. Last updated 2 years ago.
11 stars 6.14 score 5 scriptsbioc
gDRstyle:A package with style requirements for the gDR suite
Package fills a helper package role for whole gDR suite. It helps to support good development practices by keeping style requirements and style tests for other packages. It also contains build helpers to make all package requirements met.
Maintained by Arkadiusz Gladki. Last updated 2 months ago.
2 stars 6.10 score 2 scriptsbioc
metaseqR2:An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms
Provides an interface to several normalization and statistical testing packages for RNA-Seq gene expression data. Additionally, it creates several diagnostic plots, performs meta-analysis by combinining the results of several statistical tests and reports the results in an interactive way.
Maintained by Panagiotis Moulos. Last updated 18 days ago.
softwaregeneexpressiondifferentialexpressionworkflowsteppreprocessingqualitycontrolnormalizationreportwritingrnaseqtranscriptionsequencingtranscriptomicsbayesianclusteringcellbiologybiomedicalinformaticsfunctionalgenomicssystemsbiologyimmunooncologyalternativesplicingdifferentialsplicingmultiplecomparisontimecoursedataimportatacseqepigeneticsregressionproprietaryplatformsgenesetenrichmentbatcheffectchipseq
7 stars 6.05 score 3 scripts
thinkr-open
gitdown:Turn Your Git Commit Messages into a HTML Book
Read all commit messages of your local git repository and sort them according to tags or specific text pattern into chapters of a HTML book using 'bookdown'. The git history book presentation helps organisms required to testify for every changes in their source code, in relation to features requests.
Maintained by Sébastien Rochette. Last updated 1 years ago.
34 stars 6.01 score 15 scriptsbioc
Rqc:Quality Control Tool for High-Throughput Sequencing Data
Rqc is an optimised tool designed for quality control and assessment of high-throughput sequencing data. It performs parallel processing of entire files and produces a report which contains a set of high-resolution graphics.
Maintained by Welliton Souza. Last updated 5 months ago.
sequencingqualitycontroldataimportcpp
6.00 score 67 scriptsbioc
PathoStat:PathoStat Statistical Microbiome Analysis Package
The purpose of this package is to perform Statistical Microbiome Analysis on metagenomics results from sequencing data samples. In particular, it supports analyses on the PathoScope generated report files. PathoStat provides various functionalities including Relative Abundance charts, Diversity estimates and plots, tests of Differential Abundance, Time Series visualization, and Core OTU analysis.
Maintained by Solaiappan Manimaran. Last updated 5 months ago.
microbiomemetagenomicsgraphandnetworkmicroarraypatternlogicprincipalcomponentsequencingsoftwarevisualizationrnaseqimmunooncology
8 stars 5.90 score 8 scriptsbioc
DiscoRhythm:Interactive Workflow for Discovering Rhythmicity in Biological Data
Set of functions for estimation of cyclical characteristics, such as period, phase, amplitude, and statistical significance in large temporal datasets. Supporting functions are available for quality control, dimensionality reduction, spectral analysis, and analysis of experimental replicates. Contains a R Shiny web interface to execute all workflow steps.
Maintained by Matthew Carlucci. Last updated 5 months ago.
softwaretimecoursequalitycontrolvisualizationguiprincipalcomponentbioconductordata-visualizationoscillationsrhythm-detectionwebapp
13 stars 5.89 score 9 scripts
fdetsch
Orcs:Omnidirectional R Code Snippets
I tend to repeat the same code chunks over and over again. At first, this was fine for me and I paid little attention to such redundancies. A little later, when I got tired of manually replacing Linux filepaths with the referring Windows versions, and vice versa, I started to stuff some very frequently used work-steps into functions and, even later, into a proper R package. And that's what this package is - a hodgepodge of various R functions meant to simplify (my) everyday-life coding work without, at the same time, being devoted to a particular scope of application.
Maintained by Florian Detsch. Last updated 2 years ago.
5 stars 5.87 score 98 scripts
renzetti
gWQS:Generalized Weighted Quantile Sum Regression
Fits Weighted Quantile Sum (WQS) regression (Carrico et al. (2014) <doi:10.1007/s13253-014-0180-3>), a random subset implementation of WQS (Curtin et al. (2019) <doi:10.1080/03610918.2019.1577971>), a repeated holdout validation WQS (Tanner et al. (2019) <doi:10.1016/j.mex.2019.11.008>) and a WQS with 2 indices (Renzetti et al. (2023) <doi:10.3389/fpubh.2023.1289579>) for continuous, binomial, multinomial, Poisson, quasi-Poisson and negative binomial outcomes.
Maintained by Stefano Renzetti. Last updated 1 years ago.
7 stars 5.84 score 44 scripts 2 dependentsbioc
RPA:RPA: Robust Probabilistic Averaging for probe-level analysis
Probabilistic analysis of probe reliability and differential gene expression on short oligonucleotide arrays.
Maintained by Leo Lahti. Last updated 5 months ago.
geneexpressionmicroarraypreprocessingqualitycontrol
5.78 score 20 scripts 1 dependentsbioc
sangeranalyseR:sangeranalyseR: a suite of functions for the analysis of Sanger sequence data in R
This package builds on sangerseqR to allow users to create contigs from collections of Sanger sequencing reads. It provides a wide range of options for a number of commonly-performed actions including read trimming, detecting secondary peaks, and detecting indels using a reference sequence. All parameters can be adjusted interactively either in R or in the associated Shiny applications. There is extensive online documentation, and the package can outputs detailed HTML reports, including chromatograms.
Maintained by Kuan-Hao Chao. Last updated 27 days ago.
geneticsalignmentsequencingsangerseqpreprocessingqualitycontrolvisualizationgui
5.76 score 46 scriptsbioc
BPRMeth:Model higher-order methylation profiles
The BPRMeth package is a probabilistic method to quantify explicit features of methylation profiles, in a way that would make it easier to formally use such profiles in downstream modelling efforts, such as predicting gene expression levels or clustering genomic regions or cells according to their methylation profiles.
Maintained by Chantriolnt-Andreas Kapourani. Last updated 5 months ago.
immunooncologydnamethylationgeneexpressiongeneregulationepigeneticsgeneticsclusteringfeatureextractionregressionrnaseqbayesiankeggsequencingcoveragesinglecellopenblascpp
5.75 score 94 scripts 1 dependentsbioc
netresponse:Functional Network Analysis
Algorithms for functional network analysis. Includes an implementation of a variational Dirichlet process Gaussian mixture model for nonparametric mixture modeling.
Maintained by Leo Lahti. Last updated 5 months ago.
cellbiologyclusteringgeneexpressiongeneticsnetworkgraphandnetworkdifferentialexpressionmicroarraynetworkinferencetranscription
3 stars 5.64 score 21 scripts
dnme-minturdep
comunicacion:DNMyE - Comunicación
Herramientas para la comunicación de la Dirección Nacional de Mercados y Estadística de la Subsecretaría de Turismo de Argentina.
Maintained by Juan Pablo Ruiz Nicolini. Last updated 8 months ago.
4 stars 5.57 score 124 scripts 1 dependentsbioc
bandle:An R package for the Bayesian analysis of differential subcellular localisation experiments
The Bandle package enables the analysis and visualisation of differential localisation experiments using mass-spectrometry data. Experimental methods supported include dynamic LOPIT-DC, hyperLOPIT, Dynamic Organellar Maps, Dynamic PCP. It provides Bioconductor infrastructure to analyse these data.
Maintained by Oliver M. Crook. Last updated 2 months ago.
bayesianclassificationclusteringimmunooncologyqualitycontroldataimportproteomicsmassspectrometryopenblascppopenmp
4 stars 5.56 score 3 scripts
pheymanss
chronicle:Grammar for Creating R Markdown Reports
A system for creating R Markdown reports with a sequential syntax.
Maintained by Philippe Heymans Smith. Last updated 1 years ago.
29 stars 5.54 score 24 scripts
difm-brain
ofpetrial:Design on-Farm Precision Field Agronomic Trials
A comprehensive system for designing and implementing on-farm precision field agronomic trials. You provide field data, tell 'ofpetrial' how to design a trial, and get readily-usable trial design files and a report checks the validity and reliability of the trial design.
Maintained by Taro Mieno. Last updated 4 months ago.
3 stars 5.49 score 23 scripts
byzheng
rtiddlywiki:R Interface for 'TiddlyWiki'
'TiddlyWiki' is a unique non-linear notebook for capturing, organising and sharing complex information. 'rtiddlywiki' is a R interface of 'TiddlyWiki' <https://tiddlywiki.com> to create new tiddler from Rmarkdown file, and then put into a local 'TiddlyWiki' node.js server if it is available.
Maintained by Bangyou Zheng. Last updated 4 days ago.
3 stars 5.45 score 7 scriptsthinkr-open
lozen:Management tools for missions
Management tools for missions (internal and external). Includes weekly, GL projects, etc.
Maintained by Sébastien Rochette. Last updated 12 months ago.
7 stars 5.42 score 14 scripts
maelstrom-research
madshapR:Support Technical Processes Following 'Maelstrom Research' Standards
Functions to support rigorous processes in data cleaning, evaluation, and documentation across datasets from different studies based on Maelstrom Research guidelines. The package includes the core functions to evaluate and format the main inputs that define the process, diagnose errors, and summarize and evaluate datasets and their associated data dictionaries. The main outputs are clean datasets and associated metadata, and tabular and visual summary reports. As described in Maelstrom Research guidelines for rigorous retrospective data harmonization (Fortier I and al. (2017) <doi:10.1093/ije/dyw075>).
Maintained by Guillaume Fabre. Last updated 11 months ago.
2 stars 5.40 score 28 scripts 3 dependentschoonghyunryu
alookr:Model Classifier for Binary Classification
A collection of tools that support data splitting, predictive modeling, and model evaluation. A typical function is to split a dataset into a training dataset and a test dataset. Then compare the data distribution of the two datasets. Another feature is to support the development of predictive models and to compare the performance of several predictive models, helping to select the best model.
Maintained by Choonghyun Ryu. Last updated 1 years ago.
12 stars 5.38 score 9 scriptsbioc
PLSDAbatch:PLSDA-batch
A novel framework to correct for batch effects prior to any downstream analysis in microbiome data based on Projection to Latent Structures Discriminant Analysis. The main method is named “PLSDA-batch”. It first estimates treatment and batch variation with latent components, then subtracts batch-associated components from the data whilst preserving biological variation of interest. PLSDA-batch is highly suitable for microbiome data as it is non-parametric, multivariate and allows for ordination and data visualisation. Combined with centered log-ratio transformation for addressing uneven library sizes and compositional structure, PLSDA-batch addresses all characteristics of microbiome data that existing correction methods have ignored so far. Two other variants are proposed for 1/ unbalanced batch x treatment designs that are commonly encountered in studies with small sample sizes, and for 2/ selection of discriminative variables amongst treatment groups to avoid overfitting in classification problems. These two variants have widened the scope of applicability of PLSDA-batch to different data settings.
Maintained by Yiwen (Eva) Wang. Last updated 5 months ago.
statisticalmethoddimensionreductionprincipalcomponentclassificationmicrobiomebatcheffectnormalizationvisualization
13 stars 5.37 score 18 scripts
unhcr-dataviz
unhcrdown:UNHCR Branded Templates for R Markdown Documents
Create United Nations High Commissioner for Refugees (UNHCR) branded documents, presentations, and reports using R Markdown templates. This package provides customized formats that align with UNHCR's official brand guidelines for creating professional PDF reports, Word documents, PowerPoint presentations, and HTML outputs.
Maintained by Cédric Vidonne. Last updated 2 months ago.
pagedownrmarkdownrmarkdown-templatexaringan
21 stars 5.32 score 1 scriptsbioc
ASpli:Analysis of Alternative Splicing Using RNA-Seq
Integrative pipeline for the analysis of alternative splicing using RNAseq.
Maintained by Ariel Chernomoretz. Last updated 5 months ago.
immunooncologygeneexpressiontranscriptionalternativesplicingcoveragedifferentialexpressiondifferentialsplicingtimecoursernaseqgenomeannotationsequencingalignment
5.21 score 45 scripts 1 dependents
massimoaria
tall:Text Analysis for All
An R 'shiny' app designed for diverse text analysis tasks, offering a wide range of methodologies tailored to Natural Language Processing (NLP) needs. It is a versatile, general-purpose tool for analyzing textual data. 'tall' features a comprehensive workflow, including data cleaning, preprocessing, statistical analysis, and visualization, all integrated for effective text analysis.
Maintained by Massimo Aria. Last updated 10 days ago.
r-shinytext-analysis-and-sentiment-analysistext-classificationtext-miningtextual-analysiscpp
15 stars 5.15 score
guifabre
fabR:Wrapper Functions Collection Used in Data Pipelines
The goal of this package is to provide wrapper functions in the data cleaning and cleansing processes. These function helps in messages and interaction with the user, keep track of information in pipelines, help in the wrangling, munging, assessment and visualization of data frame-like material.
Maintained by Guillaume Fabre. Last updated 11 months ago.
1 stars 5.14 score 23 scripts 4 dependentsbioc
MSnID:Utilities for Exploration and Assessment of Confidence of LC-MSn Proteomics Identifications
Extracts MS/MS ID data from mzIdentML (leveraging mzID package) or text files. After collating the search results from multiple datasets it assesses their identification quality and optimize filtering criteria to achieve the maximum number of identifications while not exceeding a specified false discovery rate. Also contains a number of utilities to explore the MS/MS results and assess missed and irregular enzymatic cleavages, mass measurement accuracy, etc.
Maintained by Vlad Petyuk. Last updated 5 months ago.
proteomicsmassspectrometryimmunooncology
5.06 score 57 scriptsbioc
broadSeq:broadSeq : for streamlined exploration of RNA-seq data
This package helps user to do easily RNA-seq data analysis with multiple methods (usually which needs many different input formats). Here the user will provid the expression data as a SummarizedExperiment object and will get results from different methods. It will help user to quickly evaluate different methods.
Maintained by Rishi Das Roy. Last updated 5 months ago.
geneexpressiondifferentialexpressionrnaseqtranscriptomicssequencingcoveragegenesetenrichmentgo
4 stars 5.00 score 7 scriptsbioc
Melissa:Bayesian clustering and imputationa of single cell methylomes
Melissa is a Baysian probabilistic model for jointly clustering and imputing single cell methylomes. This is done by taking into account local correlations via a Generalised Linear Model approach and global similarities using a mixture modelling approach.
Maintained by C. A. Kapourani. Last updated 5 months ago.
immunooncologydnamethylationgeneexpressiongeneregulationepigeneticsgeneticsclusteringfeatureextractionregressionrnaseqbayesiankeggsequencingcoveragesinglecell
4.90 score 7 scripts
scholaempirica
reschola:The Schola Empirica Package
A collection of utilies, themes and templates for data analysis at Schola Empirica.
Maintained by Jan Netík. Last updated 6 months ago.
4 stars 4.83 score 14 scripts
jillbo1000
EZtune:Tunes AdaBoost, Elastic Net, Support Vector Machines, and Gradient Boosting Machines
Contains two functions that are intended to make tuning supervised learning methods easy. The eztune function uses a genetic algorithm or Hooke-Jeeves optimizer to find the best set of tuning parameters. The user can choose the optimizer, the learning method, and if optimization will be based on accuracy obtained through validation error, cross validation, or resubstitution. The function eztune_cv will compute a cross validated error rate. The purpose of eztune_cv is to provide a cross validated accuracy or MSE when resubstitution or validation data are used for optimization because error measures from both approaches can be misleading.
Maintained by Jill Lundell. Last updated 3 years ago.
4.76 score 38 scripts 1 dependentsbioc
geyser:Gene Expression displaYer of SummarizedExperiment in R
Lightweight Expression displaYer (plotter / viewer) of SummarizedExperiment object in R. This package provides a quick and easy Shiny-based GUI to empower a user to use a SummarizedExperiment object to view (gene) expression grouped from the sample metadata columns (in the `colData` slot). Feature expression can either be viewed with a box plot or a heatmap.
Maintained by David McGaughey. Last updated 2 months ago.
softwareshinyappsguigeneexpression
4.65 score 18 scriptsbioc
methodical:Discovering genomic regions where methylation is strongly associated with transcriptional activity
DNA methylation is generally considered to be associated with transcriptional silencing. However, comprehensive, genome-wide investigation of this relationship requires the evaluation of potentially millions of correlation values between the methylation of individual genomic loci and expression of associated transcripts in a relatively large numbers of samples. Methodical makes this process quick and easy while keeping a low memory footprint. It also provides a novel method for identifying regions where a number of methylation sites are consistently strongly associated with transcriptional expression. In addition, Methodical enables housing DNA methylation data from diverse sources (e.g. WGBS, RRBS and methylation arrays) with a common framework, lifting over DNA methylation data between different genome builds and creating base-resolution plots of the association between DNA methylation and transcriptional activity at transcriptional start sites.
Maintained by Richard Heery. Last updated 2 months ago.
dnamethylationmethylationarraytranscriptiongenomewideassociationsoftwareopenjdk
4.65 score 14 scriptsbioc
meshr:Tools for conducting enrichment analysis of MeSH
A set of annotation maps describing the entire MeSH assembled using data from MeSH.
Maintained by Koki Tsuyuzaki. Last updated 5 months ago.
annotationdatafunctionalannotationbioinformaticsstatisticsannotationmultiplecomparisonsmeshdb
4.56 score 9 scripts 1 dependentsbioc
Pigengene:Infers biological signatures from gene expression data
Pigengene package provides an efficient way to infer biological signatures from gene expression profiles. The signatures are independent from the underlying platform, e.g., the input can be microarray or RNA Seq data. It can even infer the signatures using data from one platform, and evaluate them on the other. Pigengene identifies the modules (clusters) of highly coexpressed genes using coexpression network analysis, summarizes the biological information of each module in an eigengene, learns a Bayesian network that models the probabilistic dependencies between modules, and builds a decision tree based on the expression of eigengenes.
Maintained by Habil Zare. Last updated 5 months ago.
geneexpressionrnaseqnetworkinferencenetworkgraphandnetworkbiomedicalinformaticssystemsbiologytranscriptomicsclassificationclusteringdecisiontreedimensionreductionprincipalcomponentmicroarraynormalizationimmunooncology
4.56 score 10 scripts 1 dependentsbioc
BioGA:Bioinformatics Genetic Algorithm (BioGA)
Genetic algorithm are a class of optimization algorithms inspired by the process of natural selection and genetics. This package allows users to analyze and optimize high throughput genomic data using genetic algorithms. The functions provided are implemented in C++ for improved speed and efficiency, with an easy-to-use interface for use within R.
Maintained by Dany Mukesha. Last updated 5 months ago.
experimentaldesigntechnologygenetic-algorithmoptimizationcpp
4.54 score 5 scripts
inbo
INBOmd:Markdown Templates for INBO
Several templates to generate reports, presentations and posters.
Maintained by Thierry Onkelinx. Last updated 1 years ago.
12 stars 4.52 score 11 scriptsbioc
HiCool:HiCool
HiCool provides an R interface to process and normalize Hi-C paired-end fastq reads into .(m)cool files. .(m)cool is a compact, indexed HDF5 file format specifically tailored for efficiently storing HiC-based data. On top of processing fastq reads, HiCool provides a convenient reporting function to generate shareable reports summarizing Hi-C experiments and including quality controls.
Maintained by Jacques Serizay. Last updated 11 days ago.
2 stars 4.52 score 11 scripts
bioc
ExpressionAtlas:Download datasets from EMBL-EBI Expression Atlas
This package is for searching for datasets in EMBL-EBI Expression Atlas, and downloading them into R for further analysis. Each Expression Atlas dataset is represented as a SimpleList object with one element per platform. Sequencing data is contained in a SummarizedExperiment object, while microarray data is contained in an ExpressionSet or MAList object.
Maintained by Pedro Madrigal. Last updated 5 months ago.
expressiondataexperimentdatasequencingdatamicroarraydataarrayexpress
4.42 score 19 scriptsthinkr-open
papillon:Build And Highlight Package Documentation With Customized Templates
Helps creating company visual identity. Build your templates for your package vignettes, reports with {bookdown}, package presentation with {pkgdown}. Highlight your documentation in your projects. Allow for code folding.
Maintained by Sébastien Rochette. Last updated 2 years ago.
11 stars 4.34 score 4 scriptsbioc
RegionalST:Investigating regions of interest and performing regional cell type-specific analysis with spatial transcriptomics data
This package analyze spatial transcriptomics data through cross-regional cell type-specific analysis. It selects regions of interest (ROIs) and identifys cross-regional cell type-specific differential signals. The ROIs can be selected using automatic algorithm or through manual selection. It facilitates manual selection of ROIs using a shiny application.
Maintained by Ziyi Li. Last updated 4 months ago.
spatialtranscriptomicsreactomekegg
4.30 score 8 scriptsbioc
cytofQC:Labels normalized cells for CyTOF data and assigns probabilities for each label
cytofQC is a package for initial cleaning of CyTOF data. It uses a semi-supervised approach for labeling cells with their most likely data type (bead, doublet, debris, dead) and the probability that they belong to each label type. This package does not remove data from the dataset, but provides labels and information to aid the data user in cleaning their data. Our algorithm is able to distinguish between doublets and large cells.
Maintained by Jill Lundell. Last updated 5 months ago.
2 stars 4.30 score 3 scriptsbioc
BiocWorkflowTools:Tools to aid the development of Bioconductor Workflow packages
Provides functions to ease the transition between Rmarkdown and LaTeX documents when authoring a Bioconductor Workflow.
Maintained by Mike Smith. Last updated 5 months ago.
4.30 score 10 scriptsbioc
saseR:Scalable Aberrant Splicing and Expression Retrieval
saseR is a highly performant and fast framework for aberrant expression and splicing analyses. The main functions are: \itemize{ \item \code{\link{BamtoAspliCounts}} - Process BAM files to ASpli counts \item \code{\link{convertASpli}} - Get gene, bin or junction counts from ASpli SummarizedExperiment \item \code{\link{calculateOffsets}} - Create an offsets assays for aberrant expression or splicing analysis \item \code{\link{saseRfindEncodingDim}} - Estimate the optimal number of latent factors to include when estimating the mean expression \item \code{\link{saseRfit}} - Parameter estimation of the negative binomial distribution and compute p-values for aberrant expression and splicing } For information upon how to use these functions, check out our vignette at \url{https://github.com/statOmics/saseR/blob/main/vignettes/Vignette.Rmd} and the saseR paper: Segers, A. et al. (2023). Juggling offsets unlocks RNA-seq tools for fast scalable differential usage, aberrant splicing and expression analyses. bioRxiv. \url{https://doi.org/10.1101/2023.06.29.547014}.
Maintained by Alexandre Segers. Last updated 5 months ago.
differentialexpressiondifferentialsplicingregressiongeneexpressionalternativesplicingrnaseqsequencingsoftware
1 stars 4.30 score 1 scripts
conig
revise:Dynamic Revision Letters for 'Rmarkdown' Manuscripts
Extracts tagged text from markdown manuscripts for inclusion in dynamically generated revision letters. Provides an R markdown template based on papaja::revision_letter_pdf() with comment cross-referencing, a system for managing multiple sections of extracted text, and a way to automatically determine the page number of quoted sections from PDF manuscripts.
Maintained by James Conigrave. Last updated 26 days ago.
3 stars 4.26 score
bblodfon
rtemps:R Templates for Reproducible Data Analyses
A collection of R Markdown templates for nicely structured, reproducible data analyses in R. The templates have embedded examples on how to write citations, footnotes, equations and use colored message/info boxes, how to cross-reference different parts/sections in the report, provide a nice table of contents (toc) with a References section and proper R session information as well as examples using DT tables and ggplot2 graphs. The bookdown Lite template theme supports code folding.
Maintained by John Zobolas. Last updated 3 years ago.
r-templatesrmarkdownrmarkdown-templatesrstudio
33 stars 4.22 score 2 scripts
airr-community
ogrdbstats:Analysis of Adaptive Immune Receptor Repertoire Germ Line Statistics
Multiple tools are now available for inferring the personalised germ line set from an adaptive immune receptor repertoire. Output from these tools is converted to a single format and supplemented with rich data such as usage and characterisation of 'novel' germ line alleles. This data can be particularly useful when considering the validity of novel inferences. Use of the analysis provided is described in <doi:10.3389/fimmu.2019.00435>.
Maintained by William Lees. Last updated 1 months ago.
1 stars 4.18 score 8 scriptsbioc
partCNV:Infer locally aneuploid cells using single cell RNA-seq data
This package uses a statistical framework for rapid and accurate detection of aneuploid cells with local copy number deletion or amplification. Our method uses an EM algorithm with mixtures of Poisson distributions while incorporating cytogenetics information (e.g., regional deletion or amplification) to guide the classification (partCNV). When applicable, we further improve the accuracy by integrating a Hidden Markov Model for feature selection (partCNVH).
Maintained by Ziyi Li. Last updated 5 months ago.
softwarecopynumbervariationhiddenmarkovmodelsinglecellclassification
4.18 score 4 scriptsbioc
hdxmsqc:An R package for quality Control for hydrogen deuterium exchange mass spectrometry experiments
The hdxmsqc package enables us to analyse and visualise the quality of HDX-MS experiments. Either as a final quality check before downstream analysis and publication or as part of a interative procedure to determine the quality of the data. The package builds on the QFeatures and Spectra packages to integrate with other mass-spectrometry data.
Maintained by Oliver M. Crook. Last updated 5 months ago.
qualitycontroldataimportproteomicsmassspectrometrymetabolomics
4.18 score 2 scriptsbioc
netboost:Network Analysis Supported by Boosting
Boosting supported network analysis for high-dimensional omics applications. This package comes bundled with the MC-UPGMA clustering package by Yaniv Loewenstein.
Maintained by Pascal Schlosser. Last updated 5 months ago.
softwarestatisticalmethodgraphandnetworknetworkclusteringdimensionreductionbiomedicalinformaticsepigeneticsmetabolomicstranscriptomicscpp
4.18 score 1 scripts
statnmap
pdfreport:A template for pdf report written in Rmarkdown
Create a tex file that defines caracteristics of your PDF report template.
Maintained by Sebastien Rochette. Last updated 4 years ago.
27 stars 4.13 score 4 scriptsinbo
protocolhelper:Helper Functions to Manage Protocols
Helper functions to manage INBO protocols.
Maintained by Hans Van Calster. Last updated 10 days ago.
5 stars 4.09 score 55 scripts
jlaake
marked:Mark-Recapture Analysis for Survival and Abundance Estimation
Functions for fitting various models to capture-recapture data including mixed-effects Cormack-Jolly-Seber(CJS) and multistate models and the multi-variate state model structure for survival estimation and POPAN structured Jolly-Seber models for abundance estimation. There are also Hidden Markov model (HMM) implementations of CJS and multistate models with and without state uncertainty and a simulation capability for HMM models.
Maintained by Jeff Laake. Last updated 1 years ago.
1 stars 4.09 score 85 scripts 1 dependents
rmi-pacta
pacta.portfolio.report:pacta.portfolio.report
For more information visit <https://rmi.org/>.
Maintained by Monika Furdyna. Last updated 2 months ago.
climate-changesustainable-finance
1 stars 4.06 score 2 scripts 1 dependents
pakillo
rmdTemplates:A collection of Rmarkdown templates
A collection of Rmarkdown templates for writing scientific manuscripts, manuscript reviews, Beamer slides (metropolis theme), xaringan slides, and other Rmarkdown documents, with support for cross-references, citations and different bibliography styles.
Maintained by F. Rodriguez-Sanchez. Last updated 3 years ago.
reproducible-researchrmarkdownrmarkdown-templatesrstudio
129 stars 4.04 score 17 scriptsbioc
abseqR:Reporting and data analysis functionalities for Rep-Seq datasets of antibody libraries
AbSeq is a comprehensive bioinformatic pipeline for the analysis of sequencing datasets generated from antibody libraries and abseqR is one of its packages. abseqR empowers the users of abseqPy (https://github.com/malhamdoosh/abseqPy) with plotting and reporting capabilities and allows them to generate interactive HTML reports for the convenience of viewing and sharing with other researchers. Additionally, abseqR extends abseqPy to compare multiple repertoire analyses and perform further downstream analysis on its output.
Maintained by JiaHong Fong. Last updated 5 months ago.
sequencingvisualizationreportwritingqualitycontrolmultiplecomparison
4.00 score 3 scriptsbioc
scTensor:Detection of cell-cell interaction from single-cell RNA-seq dataset by tensor decomposition
The algorithm is based on the non-negative tucker decomposition (NTD2) of nnTensor.
Maintained by Koki Tsuyuzaki. Last updated 5 months ago.
dimensionreductionsinglecellsoftwaregeneexpression
4.00 score 2 scripts
datatrail-jhu
rgoogleclassroom:API Wrapper for Google Classroom and Google Forms
This is a Google Forms and Google Classroom API Wrapper for R for managing Google Classrooms from R. The documentation for these APIs is here <https://developers.google.com/forms/api/guides> .
Maintained by Candace Savonen. Last updated 1 years ago.
2 stars 4.00 score 6 scriptsbioc
scTGIF:Cell type annotation for unannotated single-cell RNA-Seq data
scTGIF connects the cells and the related gene functions without cell type label.
Maintained by Koki Tsuyuzaki. Last updated 5 months ago.
dimensionreductionqualitycontrolsinglecellsoftwaregeneexpression
4.00 score 2 scripts
bioc
EasyCellType:Annotate cell types for scRNA-seq data
We developed EasyCellType which can automatically examine the input marker lists obtained from existing software such as Seurat over the cell markerdatabases. Two quantification approaches to annotate cell types are provided: Gene set enrichment analysis (GSEA) and a modified versio of Fisher's exact test. The function presents annotation recommendations in graphical outcomes: bar plots for each cluster showing candidate cell types, as well as a dot plot summarizing the top 5 significant annotations for each cluster.
Maintained by Ruoxing Li. Last updated 5 months ago.
singlecellsoftwaregeneexpressiongenesetenrichment
4.00 score 6 scriptsbioc
BubbleTree:BubbleTree: an intuitive visualization to elucidate tumoral aneuploidy and clonality in somatic mosaicism using next generation sequencing data
CNV analysis in groups of tumor samples.
Maintained by Todd Creasy. Last updated 5 months ago.
copynumbervariationsoftwaresequencingcoverage
3.95 score 15 scriptsbioc
geneXtendeR:Optimized Functional Annotation Of ChIP-seq Data
geneXtendeR optimizes the functional annotation of ChIP-seq peaks by exploring relative differences in annotating ChIP-seq peak sets to variable-length gene bodies. In contrast to prior techniques, geneXtendeR considers peak annotations beyond just the closest gene, allowing users to see peak summary statistics for the first-closest gene, second-closest gene, ..., n-closest gene whilst ranking the output according to biologically relevant events and iteratively comparing the fidelity of peak-to-gene overlap across a user-defined range of upstream and downstream extensions on the original boundaries of each gene's coordinates. Since different ChIP-seq peak callers produce different differentially enriched peaks with a large variance in peak length distribution and total peak count, annotating peak lists with their nearest genes can often be a noisy process. As such, the goal of geneXtendeR is to robustly link differentially enriched peaks with their respective genes, thereby aiding experimental follow-up and validation in designing primers for a set of prospective gene candidates during qPCR.
Maintained by Bohdan Khomtchouk. Last updated 5 months ago.
chipseqgeneticsannotationgenomeannotationdifferentialpeakcallingcoveragepeakdetectionchiponchiphistonemodificationdataimportnaturallanguageprocessingvisualizationgosoftwarebioconductorbioinformaticscchip-seqcomputational-biologyepigeneticsfunctional-annotation
9 stars 3.95 score 5 scripts
bavodc
CalibrationCurves:Calibration Performance
Plots calibration curves and computes statistics for assessing calibration performance. See De Cock Campo (2023) <doi:10.48550/arXiv.2309.08559> and Van Calster et al. (2016) <doi:10.1016/j.jclinepi.2015.12.005>.
Maintained by De Cock Bavo. Last updated 2 months ago.
3.90 score 53 scripts
paezha
discrtr:A Companion Package for the Book "Discrete Choice Analysis with 'R'"
Templates and data files to support "Discrete Choice Analysis with R", Páez, A. and Boisjoly, G. (2023) <doi:10.1007/978-3-031-20719-8>.
Maintained by Antonio Paez. Last updated 2 years ago.
discrete-choicediscrete-choice-data
3 stars 3.87 score 49 scripts
openvolley
volleyreport:Reports from Volleyball Match Files
Functions for generating reports from volleyball match files.
Maintained by Adrien Ickowicz. Last updated 4 months ago.
3 stars 3.84 score 19 scripts 1 dependentsbioc
RegEnrich:Gene regulator enrichment analysis
This package is a pipeline to identify the key gene regulators in a biological process, for example in cell differentiation and in cell development after stimulation. There are four major steps in this pipeline: (1) differential expression analysis; (2) regulator-target network inference; (3) enrichment analysis; and (4) regulators scoring and ranking.
Maintained by Weiyang Tao. Last updated 5 months ago.
geneexpressiontranscriptomicsrnaseqtwochanneltranscriptiongenetargetnetworkenrichmentdifferentialexpressionnetworknetworkinferencegenesetenrichmentfunctionalprediction
3.82 score 22 scriptsopenvolley
ovscout2:An R Shiny App for Scouting Volleyball Match Files
Functions for scouting volleyball match files.
Maintained by Ben Raymond. Last updated 11 months ago.
6 stars 3.78 score 8 scriptsrmi-pacta
pactaverse:Easily Install and Load the 'PACTA-verse'
The 'pactaverse' is a set of packages that work to help R users implement various functionality related to the PACTA open source project.
Maintained by Jackson Hoffart. Last updated 4 months ago.
6 stars 3.73 score 3 scriptsmaelstrom-research
mlstrOpalr:Support Compatibility Between 'Maelstrom' R Packages and 'Opal' Environment
Functions to support compatibility between 'Maelstrom' R packages and 'Opal' environment. 'Opal' is the 'OBiBa' core database application for biobanks. It is used to build data repositories that integrates data collected from multiple sources. 'Opal Maelstrom' is a specific implementation of this software. This 'Opal' client is specifically designed to interact with 'Opal Maelstrom' distributions to perform operations on the R server side. The user must have adequate credentials. Please see <https://opaldoc.obiba.org/> for complete documentation.
Maintained by Guillaume Fabre. Last updated 11 months ago.
1 stars 3.70 score 3 scriptsbioc
srnadiff:Finding differentially expressed unannotated genomic regions from RNA-seq data
srnadiff is a package that finds differently expressed regions from RNA-seq data at base-resolution level without relying on existing annotation. To do so, the package implements the identify-then-annotate methodology that builds on the idea of combining two pipelines approachs differential expressed regions detection and differential expression quantification. It reads BAM files as input, and outputs a list differentially regions, together with the adjusted p-values.
Maintained by Zytnicki Matthias. Last updated 3 months ago.
immunooncologygeneexpressioncoveragesmallrnaepigeneticsstatisticalmethodpreprocessingdifferentialexpressioncpp
3.70 score 3 scripts
jolars
rmdplugr:Plugins for R Markdown Formats
Formats for R Markdown that undo modifications by 'pandoc' and 'rmarkdown' to original 'latex' templates, such as smaller margins, paragraph spacing, and compact titles. In addition, enhancements such as author blocks with affiliations and headers and footers are introduced. All of this functionality is built around plugins that modify the default 'pandoc' template without relying on custom templates.
Maintained by Johan Larsson. Last updated 5 years ago.
3.70 score 1 scriptsbioc
rebook:Re-using Content in Bioconductor Books
Provides utilities to re-use content across chapters of a Bioconductor book. This is mostly based on functionality developed while writing the OSCA book, but generalized for potential use in other large books with heavy compute. Also contains some functions to assist book deployment.
Maintained by Aaron Lun. Last updated 5 months ago.
softwareinfrastructurereportwriting
3.65 score 223 scripts
litgde
Spectran:Visual and Non-Visual Spectral Analysis of Light
Analyse light spectra for visual and non-visual (often called melanopic) needs, wrapped up in a Shiny App. 'Spectran' allows for the import of spectra in various CSV forms but also provides a wide range of example spectra and even the creation of own spectral power distributions. The goal of the app is to provide easy access and a visual overview of the spectral calculations underlying common parameters used in the field. It is thus ideal for educational purposes or the creation of presentation ready graphs in lighting research and application. 'Spectran' uses equations and action spectra described in CIE S026 (2018) <doi:10.25039/S026.2018>, DIN/TS 5031-100 (2021) <doi:10.31030/3287213>, and ISO/CIE 23539 (2023) <doi:10.25039/IS0.CIE.23539.2023>.
Maintained by Johannes Zauner. Last updated 6 months ago.
2 stars 3.60 score 3 scripts
grimbough
msmbstyle:MSMB Styles for R Markdown Documents
Provides R Markdown output formats to use with Modern Statistics for Modern Biology.
Maintained by Mike Smith. Last updated 3 years ago.
59 stars 3.47 score 4 scripts
foadesmaeili5
RTLknitr:Right to Left Dynamic Documents Using 'knitr'
Provide seamless support for right-to-left (RTL) languages, such as Persian and Arabic, in R Markdown documents and 'LaTeX' output. It includes functions and hooks that enable easy integration of RTL language content, allowing users to create documents that adhere to RTL writing conventions. For in-depth insights into dynamic documents and the 'knitr' package, consider referring to Xie, Y (2014) <ISBN: 978-1-482-20353-0>.
Maintained by Foad Esmaeili. Last updated 2 years ago.
4 stars 3.30 scorebioc
Rmmquant:RNA-Seq multi-mapping Reads Quantification Tool
RNA-Seq is currently used routinely, and it provides accurate information on gene transcription. However, the method cannot accurately estimate duplicated genes expression. Several strategies have been previously used, but all of them provide biased results. With Rmmquant, if a read maps at different positions, the tool detects that the corresponding genes are duplicated; it merges the genes and creates a merged gene. The counts of ambiguous reads is then based on the input genes and the merged genes. Rmmquant is a drop-in replacement of the widely used tools findOverlaps and featureCounts that handles multi-mapping reads in an unabiased way.
Maintained by Zytnicki Matthias. Last updated 5 months ago.
geneexpressiontranscriptionzlibcpp
3.30 score 5 scripts
tjmahr
notestar:Notebooks Using 'Targets' and 'Bookdown'
'Targets' is an R package for dependency and build management in data analysis projects. This package provides a set of targets and project infrastructure to create 'bookdown'-based notebooks using 'targets'.
Maintained by Tristan Mahr. Last updated 2 months ago.
bookdownknitrpandocrmarkdowntargets
30 stars 3.18 score 7 scripts
rbarkerclarke
gtexture:Generalized Application of Co-Occurrence Matrices and Haralick Texture
Generalizes application of gray-level co-occurrence matrix (GLCM) metrics to objects outside of images. The current focus is to apply GLCM metrics to the study of biological networks and fitness landscapes that are used in studying evolutionary medicine and biology, particularly the evolution of cancer resistance. The package was used in our publication, Barker-Clarke et al. (2023) <doi:10.1088/1361-6560/ace305>. A general reference to learn more about mathematical oncology can be found at Rockne et al. (2019) <doi:10.1088/1478-3975/ab1a09>.
Maintained by Rowan Barker-Clarke. Last updated 12 months ago.
3.00 score 1 scripts
carlosyanez
uofgdataanalyticsreport:R Markdown template to create assigment reports for UofG Data Analytics programmes.
Provides an R Markdown template to use in UofG Data Analytics reports.
Maintained by Carlos Yanez Santibanez. Last updated 2 years ago.
indiedown-templatermarkdown-template
2 stars 3.00 score 6 scripts
poissonconsulting
shinywqg:Water Quality Guideline Shiny App
User interface to calculate water quality guidelines.
Maintained by Pearson Ayla. Last updated 2 months ago.
3.00 score 1 scripts
roaldarbol
rpix:R package to manage dependencies with pixi
More about what it does (maybe more than one line) Use four spaces when indenting paragraphs within the Description.
Maintained by Mikkel Roald-Arbøl. Last updated 8 months ago.
6 stars 2.95 score 3 scripts
zkamvar
beaverdown:An updated R Markdown thesis template for Oregon State University using the bookdown package
Using the bookdown package and LaTeX and Word thesis templates from Oregon State University, this package was derived from Chester Ismay's package "thesisdown"
Maintained by Zhian N. Kamvar. Last updated 8 years ago.
17 stars 2.93 score 2 scripts
drmowinckels
uiothemes:Branding themes for the University of Oslo, Norway
Contains templates, themeing files and functions. Made specifically for branding purposes for the University of Oslo.
Maintained by Athanasia Mo Mowinckel. Last updated 4 years ago.
14 stars 2.85 score 2 scripts
capro-uio
uiothemes:Branding themes for the University of Oslo, Norway
Contains templates, themeing files and functions. Made specifically for branding purposes for the University of Oslo.
Maintained by Athanasia Mo Mowinckel. Last updated 4 years ago.
14 stars 2.85 score 2 scripts
paocorrales
mesoda:Mesoscale Data Assimilation - PhD Thesis
En el futuro: mi tesis de doctorado. Por ahora será un compendio de análisis ordenados.
Maintained by Paola Corrales. Last updated 2 years ago.
3 stars 2.73 score 36 scripts
dchiu911
rsf:Report of Statistical Findings in 'bookdown'
A report of statistical findings (RSF) project template is generated using a 'bookdown' format. 'YAML' fields can be further customized. Additional helper functions provide extra features to the RSF.
Maintained by Derek Chiu. Last updated 3 years ago.
2.70 score
ctu-bern
CTUtemplate:Example RStudio Project Templates
Templates and functions for use in CTU Bern.
Maintained by Alan G. Haynes. Last updated 30 days ago.
1 stars 2.70 score 3 scripts
cran
ncappc:NCA Calculations and Population Model Diagnosis
A flexible tool that can perform (i) traditional non-compartmental analysis (NCA) and (ii) Simulation-based posterior predictive checks for population pharmacokinetic (PK) and/or pharmacodynamic (PKPD) models using NCA metrics.
Maintained by Andrew C. Hooker. Last updated 7 years ago.
2.70 score
wenjie2wang
jds.rmd:R Markdown Templates for Journal of Data Science
Customized R Markdown templates for authoring articles for Journal of Data Science.
Maintained by Wenjie Wang. Last updated 10 months ago.
1 stars 2.70 score
ajpelu
famexploreR:Exploration of Threathened Flora field data
A shiny app that explores data from Threathened Flora. It uses customized forms to explore the data and generate several plots, tables.
Maintained by Antonio Jesús Pérez-Luque. Last updated 4 months ago.
2 stars 2.60 score 2 scripts
nenuial
geovizr:Support for Knitr (Quarto/Rmd)
Provide support functions for Quarto and Rmd documents.
Maintained by Pascal Burkhard. Last updated 1 months ago.
2.60 score 3 scripts
cct-datascience
datadrivencv:Templates and helper functions for building a CV with spreadsheets
Separates the CV format from the content using spreadsheets, RMarkdown, and Pagedown. Built to allow easy out-of-the-box behavior, but also to allow you to go beyond the defaults with customization and lack of lock-in to a given format.
Maintained by Nick Strayer. Last updated 1 years ago.
2.59 score 39 scripts
inventionate
TimeSpaceAnalysis:Statistical tools for time-space analysis
Use Geometric Data Analysis approaches (e.g. MCA or MFA), time pattern analysis (see "time sequence clustering") and places chronologies (see "time geography") analysis.
Maintained by Fabian Mundt. Last updated 20 days ago.
2.48 score 2 scriptsopenvolley
ovpaged:Openvolley Pagedown Templates
Pagedown templates for the Openvolley project.
Maintained by Ben Raymond. Last updated 2 years ago.
2.48 score 1 scripts 2 dependentsbioc
prebs:Probe region expression estimation for RNA-seq data for improved microarray comparability
The prebs package aims at making RNA-sequencing (RNA-seq) data more comparable to microarray data. The comparability is achieved by summarizing sequencing-based expressions of probe regions using a modified version of RMA algorithm. The pipeline takes mapped reads in BAM format as an input and produces either gene expressions or original microarray probe set expressions as an output.
Maintained by Karolis Uziela. Last updated 5 months ago.
immunooncologymicroarrayrnaseqsequencinggeneexpressionpreprocessing
2.30 score 1 scripts
sjbonner
RWildbook:Interface for the 'Wildbook' Wildlife Data Management Framework
Provides an interface with the 'Wildbook' mark-recapture ecological database framework. It helps users to pull data from the 'Wildbook' framework and format data for further analysis with mark-recapture applications like 'Program MARK' (which can be accessed via the 'RMark' package in 'R'). Further information on the 'Wildbook' framework is available at: <http://www.wildbook.org/doku.php>.
Maintained by Simon Bonner. Last updated 7 years ago.
1 stars 2.30 score 4 scripts
mattkerlogue
deckhand2:Create slide decks and grid layout paginated HTML reports
An extension to the pagedown package that uses the CSS grid layout module to provide extensive layout control of page based Rmarkdown reports.
Maintained by Matt Kerlogue. Last updated 2 years ago.
3 stars 2.18 score 1 scripts
bayesstats
jarbes:Just a Rather Bayesian Evidence Synthesis
Provides a new class of Bayesian meta-analysis models that incorporates a model for internal and external validity bias. In this way, it is possible to combine studies of diverse quality and different types. For example, we can combine the results of randomized control trials (RCTs) with the results of observational studies (OS).
Maintained by Pablo Emilio Verde. Last updated 1 days ago.
1 stars 2.03 score 27 scriptscran
lwqs:Lagged Weighted Quantile Sum Regression
Wrapper functions for the implementation of lagged weighted quantile sum regression, as per 'Gennings et al' (2020) <doi:10.1016/j.envres.2020.109529>.
Maintained by Paul Curtin. Last updated 4 years ago.
2.00 score
mps9506
bookdowntargets:Targets for bookdown pipeline
Provides a targets pipeline extension for bookdown projects. For the underlying methodology, please refer to the documentation of 'targets' <doi:10.21105/joss.02959>.
Maintained by Michael Schramm. Last updated 9 months ago.
2.00 score 3 scripts
marchionnilab
covid19census:Extracts Covid-19 and other demographic metrics regarding U.S.A and Italy
Package with functions to scrape data regarding COVID-19 epidemic in U.S.A and Italy, as well as datasets with related indexes.
Maintained by claudio_zanettini. Last updated 4 years ago.
2 stars 2.00 score 5 scripts
txwri
twriTemplates:Templates for TWRI reports
Provides word and pdf Rmarkdown templates that meet TWRI branding guidance.
Maintained by Michael Schramm. Last updated 1 years ago.
1.78 score 12 scripts
rekyt
fddimensionality:Test Effect of Traits of FD-Environment Relationship
Companion code for paper XXX <doi:xxx> on FD-Environment relationship, which tests to what extent we can expect FD-Environment trait relationship in function of number of traits included and type of environmental filtering.
Maintained by Matthias Grenié. Last updated 2 years ago.
1.70 score
emptyfield-ds
shunyata:Deploy Empty Field Teaching Material
This package helps set up new teaching material and deploy courses based on the Empty Field teaching workflow.
Maintained by Malcolm Barrett. Last updated 1 years ago.
1 stars 1.70 score 2 scriptsdnme-minturdep
d4t4tur:Herramientas para el Trabajo con Datos y Análisis Turístico de Argentina
Manera sencilla de instalar y cargar los paquetes de 'dnme-minturdep'.
Maintained by Juan Pablo Ruiz Nicolini. Last updated 3 years ago.
argentinaestadisticasturismoopenjdk
1.70 score 6 scriptsemptyfield-ds
rrr.workshop:Install Materials for Reproducible Research in R
Install learning materials for Reproducible Research in R.
Maintained by Malcolm Barrett. Last updated 4 years ago.
1.70 score 1 scripts
ices-tools-prod
icesdown:ICES Rmarkdown tools
A collection of rmarkdown and pandoc versions of various ICES templates can be found here.
Maintained by Iago Mosqueira. Last updated 3 years ago.
1.70 score 1 scripts