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Accurate sample inference from amplicon data with single nucleotide resolution

Karyoploter ⭐ 278

karyoploteR - An R/Bioconductor package to plot arbitrary data along the genome

Tcgabiolinks ⭐ 255

Rdocumentation 2.0 ⭐ 249

📚 RDocumentation provides an easy way to search the documentation for every version of every R package on CRAN and Bioconductor.

Splatter ⭐ 195

Simple simulation of single-cell RNA sequencing data

Bioc Refcard ⭐ 170

Bioconductor cheat sheet

This is the git repository matching the Bioconductor package xcms: LC/MS and GC/MS Data Analysis

Tidybulk ⭐ 153

Brings bulk and pseudobulk transcriptomics to the tidyverse

Reference-guided transcript discovery and quantification for long read RNA-Seq data

Singler ⭐ 147

Clone of the Bioconductor repository for the SingleR package.

Tximport ⭐ 128

Transcript quantification import for modular pipelines

Mixomics ⭐ 126

Development repository for the Bioconductor package 'mixOmics '

Contributions ⭐ 123

Contribute Packages to Bioconductor

Msnbase ⭐ 115

Base Classes and Functions for Mass Spectrometry and Proteomics

Biocstickers ⭐ 115

Stickers for some Bioconductor packages - feel free to contribute and/or modify.

Zellkonverter ⭐ 112

Conversion between scRNA-seq objects

Curatedmetagenomicdata ⭐ 109

Curated Metagenomic Data of the Human Microbiome

Anndata2ri ⭐ 104

Convert between AnnData and SingleCellExperiment

Interface for the Basic Local Alignment Search Tool (BLAST) - R-Package

Maaslin2 ⭐ 86

MaAsLin2: Microbiome Multivariate Association with Linear Models

Genomicdatacommons ⭐ 80

Provide R access to the NCI Genomic Data Commons portal.

Genetonic ⭐ 74

Enjoy your transcriptomic data and analysis responsibly - like sipping a cocktail

Geoquery ⭐ 73

The bridge between the NCBI Gene Expression Omnibus and Bioconductor

Bioconductor_docker ⭐ 70

Docker Containers for Bioconductor - NEW!

Ggnomics ⭐ 69

A small project to add ggplot2 extensions

Rforproteomics ⭐ 69

Using R and Bioconductor packages for the analysis and comprehension of proteomics data.

Orchestrating Microbiome Analysis

Multiassayexperiment ⭐ 67

Bioconductor package for management of multi-assay data

Tools for manipulating annotated data matrices

Spatiallibd ⭐ 53

Code for the spatialLIBD R/Bioconductor package and shiny app

Singlecellexperiment ⭐ 52

Clone of the Bioconductor repository for the SingleCellExperiment package, see https://bioconductor.org/packages/devel/bioc/html/ for the official development version.

Pcaexplorer ⭐ 51

pcaExplorer - Interactive exploration of Principal Components of Samples and Genes in RNA-seq data

Rworkflows ⭐ 50

Continuous integration for R packages. 🔀 Automates testing ✅, documentation website building 📦, & containerised deployment 🐳.

From geospatial to spatial -omics

R package for Inference of differentially methylated regions (DMRs) from bisulfite sequencing

Biocthis ⭐ 47

Automate package and project setup for Bioconductor packages

Microbiome analysis

Derfinder ⭐ 42

Annotation-agnostic differential expression analysis of RNA-seq data via expressed regions-level or single base-level approaches

R package for the recount2 project. Documentation website: http://leekgroup.github.io/recount/

Tcgaworkflow ⭐ 37

TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages

Elastic, reproducible, and reusable genomic data science tools from R backed by cloud resources

Ensembldb ⭐ 33

This is the ensembldb development repository.

Psichomics ⭐ 33

Interactive R package to quantify, analyse and visualise alternative splicing

Systempipeshiny ⭐ 32

A Shiny framework for workflow management and data visualization

Tidysinglecellexperiment ⭐ 32

Brings SingleCellExperiment objects to the tidyverse

Microarray Analysis ⭐ 32

Materials on the analysis of microarray expression data; focus on re-analysis of public data ( http://tinyurl.com/cruk-microarray)

Orthogene ⭐ 31

🧬 o r t h o g e n e 🧬✨✨✨✨✨✨✨ Interspecies gene mapping✨✨✨✨✨ 🦠 🔁 🌱 🔁 🌳 🔁 🍎 🔁 🍊 🔁 🪱 🔁 🪰 🔁 🐟 🔁 🦎 🔁 🐓 🔁 🦇 🔁 🐄 🔁 🐖 🔁 🐐 🔁 🐎 🔁 🐈 🔁 🐕 🔁 🐁 🔁 🐒 🔁 🦧 🔁 🦍 🔁 🏃‍♀️

Pipecomp ⭐ 31

A R framework for pipeline benchmarking, with application to single-cell RNAseq

Tcgabiolinksgui ⭐ 31

TCGAbiolinksGUI code development for R/Bioconductor submission http://tcgabiolinks.fmrp.usp.br:3838/

Low level infrastructure to handle MS spectra

Molecular informatics toolkit with a comprehensive integration of bioinformatics and cheminformatics tools for drug discovery.

Interactive Differential Expression AnaLysis - DE made accessible and reproducible

tidy processing of biological sequences in R

Sevenbridges R ⭐ 27

Seven Bridges API Client, CWL Schema, Meta Schema, and SDK Helper in R

R package providing query functionality to BioMart instances like Ensembl

Multiview Intercellular SpaTial modeling framework

Bioconductor_full ⭐ 26

DEPRECATED - Docker Images which include a complete installation of all software needed to build all Bioconductor packages

Immunespacer ⭐ 25

An R Interface to the ImmuneSpace database portal

Supplementary R packages utils

Recount3 ⭐ 24

Explore and download data from the recount3 project

Melonnpan ⭐ 24

Model-based Genomically Informed High-dimensional Predictor of Microbial Community Metabolic Profiles

Data Mining and Analysis of Lipidomics datasets in R

Nullranges ⭐ 23

Modular package for generation of sets of ranges representing the null hypothesis. These can take the form of bootstrap samples of ranges (using the block bootstrap framework of Bickel et al 2010), or set of control ranges that are matched across one or more covariates.

Bioc Intro ⭐ 23

Bioconductor data science introduction

Fishpond ⭐ 23

Differential expression and allelic analysis, nonparametric statistics

Circtools ⭐ 22

circtools: a modular, python-based framework for circRNA-related tools that unifies several functionalities in a single, command line driven software.

Modeling and correcting fragment sequence bias for RNA-seq

Imcdataanalysis ⭐ 22

R based workflow for multiplexed imaging data

Bioconductor.org ⭐ 21

Source code for the Bioconductor website

Degreport ⭐ 21

Create a cromphensive report of DEG list coming from any analysis of RNAseq data

Rbioformats ⭐ 20

📚 R interface to the Bio-Formats library

Biocpkgtools ⭐ 19

Computable build reports, package metadata, and download stats from the Bioconductor project

Qfeatures ⭐ 19

Quantitative features for mass spectrometry data

Bestpracticesst ⭐ 19

'Best Practices for Spatial Transcriptomics Analysis with Bioconductor' online book

Single cell proteomics data processing

Bioc_2020_tidytranscriptomics ⭐ 18

Workshop on tidytranscriptomics: Performing tidy transcriptomics analyses with tidybulk, tidyverse and tidyheatmap

Risa allows to access metadata/data in ISA-tab format and builds Bioconductor data structures. Apart from parsing ISA-tab files, the package also provides functionality to save the ISA-tab dataset, or each of its individual files. Additionally, it is also possible to update assay files. Currently, metadata associated to proteomics and metabolomics-based assays (i.e. mass spectrometry) can be processed into an xcmsSet object (from the xcms R package).

Multiassayworkshop ⭐ 17

Multi-omic Integration and Analysis of cBioPortal and TCGA data with MultiAssayExperiment

Mscoreutils ⭐ 16

Core Utils for Mass Spectrometry Data

Bioc Project ⭐ 15

Introduction to the Bioconductor project

Cd4 Csaw ⭐ 15

Reproducible reanalysis of a combined ChIP-Seq & RNA-Seq data set

Normalyzerde ⭐ 14

Tools for normalization, evaluation of outliers, technical biases and batch effects and differential expression analysis.

Bioc Rnaseq ⭐ 14

Analysis and Interpretation of Bulk RNA-Seq Data using Bioconductor

Crisprdesign ⭐ 14

Comprehensive design of CRISPR gRNAs for nucleases and base editors

Bioc_git_transition ⭐ 14

This python package is for transitioning bioconductor from SVN to git

Analytical R Tools for Mass Spectrometry

Singlecellworkflow ⭐ 13

Tutorial for the analysis of scRNA-seq data in R

Recount Website ⭐ 12

Code for the Recount project

co-expressed gene-set enrichment analysis

Interactive visulizations for track-based genomic data in R

AnaLysis routines for ePigenomicS data.

Graphical GUI for Docker (Bioconductor, R, Cytoscape, NetworkBMA)

piano - An R/Bioconductor package for gene set analysis

A unifying bioinformatics framework for organelle proteomics

Isoformic ⭐ 10

Isoform-level functional RNA-Seq analysis

Hpgltools ⭐ 10

A collection of R functions to aid in host-pathogen genomic research

Rformassspectrometry.org ⭐ 10

The R for Mass Spectrometry Initiative home page

Epicompare ⭐ 10

Comparison, benchmarking & QC of epigenetic datasets

Biocchallenges ⭐ 9

Challenges for the Biocoductor community.

1-100 of 152 search results

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