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127 search results found
Dada2
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428
Accurate sample inference from amplicon data with single nucleotide resolution
Karyoploter
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278
karyoploteR - An R/Bioconductor package to plot arbitrary data along the genome
Tcgabiolinks
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255
TCGAbiolinks
Splatter
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195
Simple simulation of single-cell RNA sequencing data
Bioc Refcard
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170
Bioconductor cheat sheet
Xcms
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160
This is the git repository matching the Bioconductor package xcms: LC/MS and GC/MS Data Analysis
Tidybulk
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153
Brings bulk and pseudobulk transcriptomics to the tidyverse
Bambu
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150
Reference-guided transcript discovery and quantification for long read RNA-Seq data
Singler
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147
Clone of the Bioconductor repository for the SingleR package.
Tximport
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128
Transcript quantification import for modular pipelines
Mixomics
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126
Development repository for the Bioconductor package 'mixOmics '
Biocstickers
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115
Stickers for some Bioconductor packages - feel free to contribute and/or modify.
Msnbase
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115
Base Classes and Functions for Mass Spectrometry and Proteomics
Zellkonverter
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112
Conversion between scRNA-seq objects
Curatedmetagenomicdata
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109
Curated Metagenomic Data of the Human Microbiome
Rblast
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91
Interface for the Basic Local Alignment Search Tool (BLAST) - R-Package
Maaslin2
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86
MaAsLin2: Microbiome Multivariate Association with Linear Models
Genomicdatacommons
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80
Provide R access to the NCI Genomic Data Commons portal.
Genetonic
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74
Enjoy your transcriptomic data and analysis responsibly - like sipping a cocktail
Geoquery
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73
The bridge between the NCBI Gene Expression Omnibus and Bioconductor
Oma
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69
Orchestrating Microbiome Analysis
Rforproteomics
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69
Using R and Bioconductor packages for the analysis and comprehension of proteomics data.
Ggnomics
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69
A small project to add ggplot2 extensions
Multiassayexperiment
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67
Bioconductor package for management of multi-assay data
Cmapr
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56
Tools for manipulating annotated data matrices
Singlecellexperiment
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52
Clone of the Bioconductor repository for the SingleCellExperiment package, see https://bioconductor.org/packages/devel/bioc/html/ for the official development version.
Pcaexplorer
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51
pcaExplorer - Interactive exploration of Principal Components of Samples and Genes in RNA-seq data
Rworkflows
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50
Continuous integration for R packages. 🔀 Automates testing ✅, documentation website building 📦, & containerised deployment 🐳.
Voyager
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49
From geospatial to spatial -omics
Dmrseq
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47
R package for Inference of differentially methylated regions (DMRs) from bisulfite sequencing
Biocthis
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47
Automate package and project setup for Bioconductor packages
Mia
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42
Microbiome analysis
Derfinder
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42
Annotation-agnostic differential expression analysis of RNA-seq data via expressed regions-level or single base-level approaches
Recount
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40
R package for the recount2 project. Documentation website: http://leekgroup.github.io/recount/
Wdlrunr
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34
Elastic, reproducible, and reusable genomic data science tools from R backed by cloud resources
Ensembldb
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33
This is the ensembldb development repository.
Psichomics
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33
Interactive R package to quantify, analyse and visualise alternative splicing
Systempipeshiny
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32
A Shiny framework for workflow management and data visualization
Tidysinglecellexperiment
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32
Brings SingleCellExperiment objects to the tidyverse
Orthogene
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31
🧬 o r t h o g e n e 🧬✨✨✨✨✨✨✨ Interspecies gene mapping✨✨✨✨✨ 🦠 🔁 🌱 🔁 🌳 🔁 🍎 🔁 🍊 🔁 🪱 🔁 🪰 🔁 🐟 🔁 🦎 🔁 🐓 🔁 🦇 🔁 🐄 🔁 🐖 🔁 🐐 🔁 🐎 🔁 🐈 🔁 🐕 🔁 🐁 🔁 🐒 🔁 🦧 🔁 🦍 🔁 🏃♀️
Tcgabiolinksgui
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31
TCGAbiolinksGUI code development for R/Bioconductor submission http://tcgabiolinks.fmrp.usp.br:3838/
Pipecomp
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31
A R framework for pipeline benchmarking, with application to single-cell RNAseq
Spectra
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29
Low level infrastructure to handle MS spectra
Rcpi
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28
Molecular informatics toolkit with a comprehensive integration of bioinformatics and cheminformatics tools for drug discovery.
Tidysq
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28
tidy processing of biological sequences in R
Ideal
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28
Interactive Differential Expression AnaLysis - DE made accessible and reproducible
Biomart
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27
R package providing query functionality to BioMart instances like Ensembl
Mistyr
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27
Multiview Intercellular SpaTial modeling framework
Sevenbridges R
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27
Seven Bridges API Client, CWL Schema, Meta Schema, and SDK Helper in R
Immunespacer
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25
An R Interface to the ImmuneSpace database portal
Pacs
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24
Supplementary R packages utils
Recount3
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24
Explore and download data from the recount3 project
Melonnpan
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24
Model-based Genomically Informed High-dimensional Predictor of Microbial Community Metabolic Profiles
Nullranges
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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.
Lipidr
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23
Data Mining and Analysis of Lipidomics datasets in R
Bioc Intro
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23
Bioconductor data science introduction
Alpine
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22
Modeling and correcting fragment sequence bias for RNA-seq
Degreport
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21
Create a cromphensive report of DEG list coming from any analysis of RNAseq data
Rbioformats
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20
📚 R interface to the Bio-Formats library
Biocpkgtools
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19
Computable build reports, package metadata, and download stats from the Bioconductor project
Qfeatures
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19
Quantitative features for mass spectrometry data
Bioc_2020_tidytranscriptomics
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18
Workshop on tidytranscriptomics: Performing tidy transcriptomics analyses with tidybulk, tidyverse and tidyheatmap
Scp
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18
Single cell proteomics data processing
Risa
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17
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).
Mscoreutils
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16
Core Utils for Mass Spectrometry Data
Cd4 Csaw
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15
Reproducible reanalysis of a combined ChIP-Seq & RNA-Seq data set
Bioc Project
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15
Introduction to the Bioconductor project
Crisprdesign
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14
Comprehensive design of CRISPR gRNAs for nucleases and base editors
Normalyzerde
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14
Tools for normalization, evaluation of outliers, technical biases and batch effects and differential expression analysis.
Bioc Rnaseq
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14
Analysis and Interpretation of Bulk RNA-Seq Data using Bioconductor
Artms
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13
Analytical R Tools for Mass Spectrometry
Singlecellworkflow
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13
Tutorial for the analysis of scRNA-seq data in R
Cogena
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12
co-expressed gene-set enrichment analysis
Alps
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12
AnaLysis routines for ePigenomicS data.
Tnt
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12
Interactive visulizations for track-based genomic data in R
Signer
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12
Recount Website
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12
Code for the Recount project
Proloc
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11
A unifying bioinformatics framework for organelle proteomics
Piano
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11
piano - An R/Bioconductor package for gene set analysis
Hpgltools
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10
A collection of R functions to aid in host-pathogen genomic research
Isoformic
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10
Isoform-level functional RNA-Seq analysis
Epicompare
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10
Comparison, benchmarking & QC of epigenetic datasets
Biocchallenges
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9
Challenges for the Biocoductor community.
Enrichr
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9
Functional Enrichment Analysis and Network Construction
Regionreport
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9
Generate HTML report for a set of genomic regions or DESeq2/edgeR results
Hmp16sdata
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9
16S rRNA Sequencing Data from the Human Microbiome Project
Curatedmetagenomicdataanalyses
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9
Analyses in R and Python Using curatedMetagenomicData
Bioc Actions
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8
GitHub Actions for developing and maintaining Bioconductor packages
Poma
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8
📦 Tools for Omics Data Analysis
Hcabrowser
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8
Browse the Human Cell Atlas data portal
Scpca
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8
A toolbox for sparse contrastive principal component analysis
Genextender
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8
R/Bioconductor package for optimized functional annotation of ChIP-seq data
Baseset
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8
Provides classes for working with sets
Hpar
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8
A simple interface to the Human Protein Atlas
Eurobioc2017
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8
European Bioconductor Meeting 2017
Course R Mol Data
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8
R is nowadays probably the most powerful tool for calculations of all kinds. There are plenty of modules available for work with molecular data. Those will be introduced during the course.
Discorhythm
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7
An R Package for Discovering Rhythmicity in Biological Data with an Interactive Web Interface
Multiassayexperiment.tcga
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7
Isomirs
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7
analyze isomiRs from seqbuster tool
R Advisory Database
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7
Advisory database for R packages published on cran.r-project.org or bioconductor.org
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