Biobase - Biobase: Base functions for Bioconductor
Functions that are needed by many other packages or which replace R functions.
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infrastructurebioconductor-packagecore-package
16.56 score 9 stars 2.2k dependents 7.2k scripts 126k downloadsBiocGenerics - S4 generic functions used in Bioconductor
The package defines many S4 generic functions used in Bioconductor.
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infrastructurebioconductor-packagecore-package
15.22 score 13 stars 2.9k dependents 1.3k scripts 159k downloadsDirichletMultinomial - Dirichlet-Multinomial Mixture Model Machine Learning for Microbiome Data
Dirichlet-multinomial mixture models can be used to describe variability in microbial metagenomic data. This package is an interface to code originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): 1-15, as discussed further in the man page for this package, ?DirichletMultinomial.
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immunooncologymicrobiomesequencingclusteringclassificationmetagenomicsgsl
11.37 score 12 stars 29 dependents 171 scripts 10k downloadsRhtslib - HTSlib high-throughput sequencing library as an R package
This package provides version 1.18 of the 'HTSlib' C library for high-throughput sequence analysis. The package is primarily useful to developers of other R packages who wish to make use of HTSlib. Motivation and instructions for use of this package are in the vignette, vignette(package="Rhtslib", "Rhtslib").
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dataimportsequencingbioconductor-packagecore-packagecurlbzip2xz-utilszlib
11.22 score 11 stars 706 dependents 4 scripts 59k downloadsontoProc - processing of ontologies of anatomy, cell lines, and so on
Support harvesting of diverse bioinformatic ontologies, making particular use of the ontologyIndex package on CRAN. We provide snapshots of key ontologies for terms about cells, cell lines, chemical compounds, and anatomy, to help analyze genome-scale experiments, particularly cell x compound screens. Another purpose is to strengthen development of compelling use cases for richer interfaces to emerging ontologies.
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infrastructuregobioinformaticsgenomicsontology
7.74 score 5 stars 2 dependents 102 scripts 656 downloadsOSCA - Orchestrating Single Cell Analysis with Bioconductor
Online book for orchestrating single cell analysis with Bioconductor. Contains plenty of worked examples, theoretical background and some philosophical discussions on the nature of single-cell data analysis.
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immunooncologyworkflowworkflowsinglecellworkflowbookbook-baserna-seqsingle-cellsingle-cell-rna-seq
6.92 score 69 starsOSTA - Orchestrating Spatial Transcriptomics Analysis with Bioconductor
This package contains source files for the "Orchestrating Spatial Transcriptomics Analysis with Bioconductor" online book. This book provides interactive examples and discussion on key principles of computational analysis workflows for spatial transcriptomics data using Bioconductor in R. The book contains chapters describing individual analysis steps as well as extended workflows, each with examples including R code and datasets.
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spatialsinglecellgeneexpressiontranscriptomicsanalysis-workflowsbioconductorspatial-transcriptomicsspatially-resolved-transcriptomicsopenjdk
6.27 score 114 starsOSCA.basic - Single-Cell Analysis Basics
Most of the content in this book has been migrated to scrapbook (https://bioconductor.org/books/release/scrapbook). This book is only retained to provide redirections to the relevant scrapbook chapters.
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immunooncologyworkflowworkflowsinglecellworkflow
5.31 score 17 starsOSCA.multisample - OSCA for Multiple Samples
Deploys the multi-sample analysis chapters for the "Orchestrating Single Cell Analysis with Bioconductor" book. This describes the handling of multiple samples in a single-cell RNA-seq analysis, starting with integration of multiple datasets into a common space for consistent analyses, differential expression comparisons between conditions based on pseudo-bulk samples, and differential abundance analyses for cell subpopulations. It is intended for readers who are already familiar with basic single-cell analyses, possibly after reading some of the prior books in this collection.
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immunooncologyworkflowworkflowsinglecellworkflow
4.80 score 7 starsOSCA.intro - Introduction to OSCA
Deploys the introduction to the "Orchestrating Single Cell Analysis with Bioconductor" book. This describes how to install R and Bioconductor packages, links out to some resources to learn R, describes how to load datasets into an R session, provides an overview of the SingleCellExperiment class, and performs a "quick start" demonstration for basic single-cell RNA-seq analyses. It is intended for readers with little-to-no computational background who are just getting started with analyses in R.
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immunooncologyworkflowworkflowsinglecellworkflow
4.80 score 7 stars 1 scriptsOHCA - Orchestrating Hi-C analysis with Bioconductor
The primary aim of this book is to introduce the R user to Hi-C analysis. This book starts with key concepts important for the analysis of chromatin conformation capture and then presents Bioconductor tools that can be leveraged to process, analyze, explore and visualize Hi-C data.
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hicdna3dstructurefunctionalgenomics
4.52 score 11 stars 2 scriptsscrapbook - Single-cell RNA-seq analyses with scrapper
Demonstrates some basic analysis of single-cell RNA-seq data with scrapper. This includes quality control, normalization, feature selection, various forms of dimensionality reduction, clustering into subpopulations, and detection of marker genes. It is intended for users who already have some familiarity with R and want to get hands-on with some basic single-cell analyses.
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workflowsinglecellworkflow
3.74 score 1 starsOSCA.workflows - OSCA Workflows
Deploys the workflows of the "Orchestrating Single Cell Analysis with Bioconductor" book. This contains worked case studies of analyses of a variety of single-cell datasets, each proceeding from a SingleCellExperiment object. Exposition is generally minimal other than for dataset-specific justifications for parameter tweaks; refer to the other books in the OCSA collection for a detailed explanation of the theoretical basis of each step. It is intended for readers who already know the background and just want some code to copy and paste into their own analyses.
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immunooncologyworkflowworkflowsinglecellworkflow
3.60 score 4 starsRNAseq123 - RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR
R package that supports the F1000Research workflow article on RNA-seq analysis using limma, Glimma and edgeR by Law et al. (2016).
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workflowgeneexpressionworkflowimmunooncologyworkflow
2.34 score 11 scriptsyeastNagalakshmi - Yeast genome RNA sequencing data based on Nagalakshmi et. al.
The yeast genome data was retrieved from the sequence read archive, aligned with bwa, and converted to BAM format with samtools.
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experimentdatagenomesaccharomyces_cerevisiae_datasequencingdatabiocviewschipseqdata
2.30 scoreAHEnsDbs - EnsDbs for AnnotationHub
Supplies AnnotationHub with EnsDb Ensembl-based annotation databases for all species. EnsDb SQLite databases are generated separately from Ensembl MySQL databases using functions from the ensembldb package employing the Ensembl Perl API.
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dataimportsequencingcoverageannotationhubsoftware
2.00 scoremyTestPkg - myTestPkg with a workflow
A test package with a Github Action Workflow.
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software
1.00 score 1 scripts