scPCA — Peer-reviewed • Rank 13.7 • Science 95%

scPCA: A toolbox for sparse contrastive principal component analysis in R - Published in JOSS (2020)

biotmle — Peer-reviewed • Rank 4.0 • Science 93%

biotmle: Targeted Learning for Biomarker Discovery - Published in JOSS (2017)

MuData • Rank 12.5 • Science 77%

MuData-compatible storage for bioconductor's MultiAssayExperiment

xcms • Rank 23.8 • Science 59%

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

TCGAbiolinks • Rank 23.1 • Science 59%

TCGAbiolinks

MSnbase • Rank 21.7 • Science 59%

Base Classes and Functions for Mass Spectrometry and Proteomics

GEOquery • Rank 23.0 • Science 54%

The bridge between the NCBI Gene Expression Omnibus and Bioconductor

pRoloc • Rank 17.9 • Science 59%

A unifying bioinformatics framework for organelle proteomics

tripr • Rank 11.7 • Science 64%

T-cell Receptor/Immunoglobulin Profiler {tripr}

GeneTonic • Rank 16.5 • Science 59%

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

psichomics • Rank 15.8 • Science 59%

Interactive R package to quantify, analyse and visualise alternative splicing

NormalyzerDE • Rank 15.2 • Science 59%

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

qsvaR • Rank 13.6 • Science 59%

Quality Surrogate Variable Analysis for Degradation Correction

epialleleR • Rank 12.1 • Science 59%

Fast, epiallele-aware methylation caller and reporter — an R/Bioconductor package

tximport • Rank 20.8 • Science 49%

Transcript quantification import for modular pipelines

karyoploteR • Rank 20.1 • Science 49%

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

Spectra • Rank 18.4 • Science 49%

Low level infrastructure to handle MS spectra

BaseSet • Rank 10.4 • Science 57%

Provides classes for working with sets

bambu • Rank 18.3 • Science 49%

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

pcaExplorer • Rank 17.9 • Science 49%

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

SingleR • Rank 20.6 • Science 46%

Clone of the Bioconductor repository for the SingleR package.

tidybulk • Rank 17.4 • Science 49%

Brings bulk and pseudobulk transcriptomics to the tidyverse

ideal • Rank 15.8 • Science 49%

Interactive Differential Expression AnaLysis - DE made accessible and reproducible

scp • Rank 15.5 • Science 49%

Single cell proteomics data processing

TargetSearch • Rank 14.5 • Science 49%

R package for the analysis of GC-MS metabolite profiling data. This git repository mirrors the TargetSearch git repository on bioconductor.

cTRAP • Rank 13.2 • Science 49%

Identification of candidate causal perturbations from differential gene expression data

Structstrings • Rank 12.8 • Science 49%

:package: Structstrings: implementation of Biostrings to work with dot bracket annotations

rmelting • Rank 12.1 • Science 49%

R Interface to MELTING 5

TREG • Rank 12.5 • Science 46%

Tools for finding Total RNA Expression Genes in single nucleus RNA-seq data

splatter • Rank 8.7 • Science 49%

Simple simulation of single-cell RNA sequencing data

GenomicDataCommons • Rank 19.3 • Science 36%

Provide R access to the NCI Genomic Data Commons portal.

zellkonverter • Rank 19.0 • Science 36%

Conversion between scRNA-seq objects

recount3 • Rank 6.0 • Science 49%

Explore and download data from the recount3 project

ProtGenerics • Rank 18.9 • Science 36%

S4 generic functions for Bioconductor mass spectrometry infrastructure

biocthis • Rank 17.0 • Science 36%

Automate package and project setup for Bioconductor packages

cytoviewer • Rank 3.9 • Science 49%

An interactive multi-channel image viewer for R

BiocPkgTools • Rank 16.0 • Science 36%

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

mistyR • Rank 15.8 • Science 36%

Multiview Intercellular SpaTial modeling framework

rworkflows • Rank 12.4 • Science 39%

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

rBLAST • Rank 14.9 • Science 36%

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

trna • Rank 1.6 • Science 49%

:package: tRNA: Analyzing tRNA sequences and structures

fishpond • Rank 16.4 • Science 33%

Differential expression and allelic analysis, nonparametric statistics

https://github.com/cbg-ethz/dce • Rank 13.1 • Science 36%

Finding the causality in biological pathways

RNAmodR.RiboMethSeq • Rank 9.9 • Science 39%

:package: RNAmodR.RiboMethSeq: detection of 2'-O methylations by RiboMethSeq

orthogene • Rank 15.6 • Science 33%

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

bioc-actions • Rank 4.0 • Science 44%

GitHub Actions for developing and maintaining Bioconductor packages

BiocHail • Rank 11.6 • Science 36%

Using hail via Basilisk

crisprDesign • Rank 14.5 • Science 33%

Comprehensive design of CRISPR gRNAs for nucleases and base editors

geneXtendeR • Rank 13.6 • Science 33%

R/Bioconductor package for optimized functional annotation of ChIP-seq data

dada2 • Rank 23.6 • Science 23%

Accurate sample inference from amplicon data with single nucleotide resolution

https://github.com/bioconductor/biocstickers • Rank 9.4 • Science 36%

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

https://github.com/bioconductor/bioconductor.org • Rank 8.2 • Science 36%

Source code for the Bioconductor website

ensembldb • Rank 21.2 • Science 23%

This is the ensembldb development repository.

https://github.com/bioconductor/bioconductor_docker • Rank 7.2 • Science 36%

Docker Containers for Bioconductor

Rhdf5lib • Rank 20.1 • Science 23%

Distribution of the HDF5 library in an R package

mia • Rank 19.6 • Science 23%

Microbiome analysis

isomirs • Rank 6.1 • Science 36%

analyze isomiRs from seqbuster tool

illuminaio • Rank 18.2 • Science 23%

🔬 R package: This is the Bioconductor devel version of the illuminaio package.

derfinder • Rank 18.0 • Science 23%

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

flowcatchr • Rank 4.4 • Science 36%

A framework for tracking and analyzing flowing blood cells in time lapse microscopy images

recount • Rank 17.4 • Science 23%

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

rpx • Rank 16.8 • Science 23%

R Interface to the ProteomeXchange Repository

CopyNumberPlots • Rank 13.3 • Science 26%

R package to create plots representing copy number data using karyoploteR

POMA • Rank 12.9 • Science 26%

:package: Omics Data Analysis Tools

signeR • Rank 15.1 • Science 23%

RBioFormats • Rank 14.9 • Science 23%

:books: R interface to the Bio-Formats library

cmapR • Rank 17.5 • Science 20%

Tools for manipulating annotated data matrices

derfinderPlot • Rank 13.7 • Science 23%

Plotting functions for derfinder results

rRDP • Rank 13.2 • Science 23%

Seamlessly interfaces RDP classifier.

RJMCMCNucleosomes • Rank 13.0 • Science 23%

Bioconductor Package - Genome-Wide Nucleosome Positioning in R with an optimized section in C++

RNAmodR • Rank 12.1 • Science 23%

:package: RNAmodR: detection of post-transcriptional RNA modifications based on HTS data

iSEEde • Rank 11.7 • Science 23%

iSEE extension for panels related to differential expression analysis

sfda-carpentries-workshop • Rank 5.4 • Science 28%

Workshop delivered by OSCSA to Saudi FDA

https://github.com/bioconductor/contributions • Rank 7.3 • Science 26%

Contribute Packages to Bioconductor

DEGreport • Rank 18.0 • Science 13%

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

https://github.com/bioconductor/biocworkinggroups • Rank 4.8 • Science 26%

Bioconductor working group guidelines. Also, a list of active, suggested, and inactive working groups for bioconductor for the community to volunteer to be apart of. The community is also welcome to suggest new working groups.

https://github.com/bioconductor/bioconductor_salt • Rank 4.4 • Science 26%

Salt to configure Linux and Mac (x86_64, arm64) for the BBS

voyager • Rank 6.7 • Science 23%

From geospatial to spatial -omics

categoryCompare • Rank 15.8 • Science 13%

Github repo of the categoryCompare meta-analysis package

affxparser • Rank 18.7 • Science 10%

🔬 R package: This is the Bioconductor devel version of the affxparser package.

cogena • Rank 15.0 • Science 13%

co-expressed gene-set enrichment analysis

TnT • Rank 14.4 • Science 13%

Interactive visulizations for track-based genomic data in R

DiscoRhythm • Rank 13.6 • Science 13%

An R Package for Discovering Rhythmicity in Biological Data with an Interactive Web Interface

regutools • Rank 13.4 • Science 13%

R package to extract and process data from RegulonDB

ImmuneSpaceR • Rank 16.2 • Science 10%

An R Interface to the ImmuneSpace database portal

aroma.light • Rank 15.6 • Science 10%

🔬 R package: This is the Bioconductor devel version of the aroma.light package.

regionReport • Rank 15.6 • Science 10%

Generate HTML report for a set of genomic regions or DESeq2/edgeR results

lipidr • Rank 15.3 • Science 10%

Data Mining and Analysis of Lipidomics datasets in R

chromswitch • Rank 11.9 • Science 13%

An R/Bioconductor package for detecting chromatin state switches

flowPloidy • Rank 13.7 • Science 10%

An R package for flow cytometry histogram analysis

plotGrouper • Rank 13.5 • Science 10%

A shiny app-based GUI wrapper for ggplot2 with built-in statistical analysis.

crisprViz • Rank 12.8 • Science 10%

Visualization of CRISPR guide RNAs (gRNAs)

iSEEhex • Rank 9.7 • Science 13%

iSEE extension for summarising data points in hexagonal bins

fedup • Rank 11.5 • Science 10%

Bioconductor package for pathway enrichment and depletion analysis via a Fisher's exact test on custom test sets and annotations

crisprBwa • Rank 10.2 • Science 10%

BWA-based alignment of CRISPR gRNA spacer sequences

nucleosim • Rank 3.3 • Science 13%

Bioconductor Package - Simulate synthetic nucleosome maps

https://github.com/bernatgel/regioner • Rank 5.6 • Science 10%

An R/Bioconfuctor package for association analysis of genomic regions based on permutation tests

https://github.com/erictleung/phyloseq-cheatsheet • Rank 1.8 • Science 13%

:notebook: Minimal cheatsheet for functions in the phyloseq R package

https://github.com/dalmolingroup/easylayout • Science 13%

interactive force-directed graph layouts within RStudio

bioc-intro-translation • Science 18%

The md files converted from https://github.com/carpentries-incubator/bioc-intro Rmd files (for translation with Crowdin).