Discover Bioconductor/hca Open Source project by @Bioconductor

Provide R access to the NCI Genomic Data Commons portal.

GenomicDataCommons

BiocWorkshops

⚠️ 2018 ⚠️ Bioconductor Workshops

Docker Containers for Bioconductor

bioconductor_docker

Shell

BiocParallel

Bioconductor facilities for parallel evaluation

BiocManager

CRAN Package For Managing Bioconductor Packages

OrchestratingSingleCellAnalysis

Content for the OSCA Book.

Training material for introductory R / Bioconductor courses

LearnBioconductor

bioc_docker

[DEPRECATED] Docker containers for Bioconductor

Biostrings

Efficient manipulation of biological strings

GoogleGenomics

[DEPRECATED] An R package for Google Genomics API queries.

BiocIntro

Course material for introductory R / Bioconductor courses

OrchestratingSingleCellAnalysis-release

An online companion to the OSCA manuscript demonstrating Bioconductor resources and workflows for single-cell RNA-seq analysis.

GenomicRanges

Representation and manipulation of genomic intervals

basilisk

Clone of the Bioconductor repository for the basilisk package.

BiocWorkshops2019

The official repository of the Bioconductor 2019 Conference Workshops 🎊

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

bioconductor_full

SummarizedExperiment container

SummarizedExperiment

GenomicFeatures

Conveniently import and query gene models

copy-number-analysis

Explore, compare, and evaluate Bioconductor packages related to genomic copy number analysis

BiocAdvanced

Advanced R / Bioconductor training material

DelayedArray

A unified framework for working transparently with on-disk and in-memory array-like datasets

Rsamtools

Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import

bioconductor.org

Source code for the Bioconductor website

Template for building a bioconductor workshop package using github actions

BuildABiocWorkshop

Foundation of integer range manipulation in Bioconductor

IRanges

VariantAnnotation

Annotation of Genetic Variants

S4Vectors

Foundation of vector-like and list-like containers in Bioconductor

UseBioconductor

Training material for intermediate R / Bioconductor courses

GenomeInfoDb

Utilities for manipulating chromosome names, including modifying them to follow a particular naming style

bioc_git_transition

This python package is for transitioning bioconductor from SVN to git

Python

BiocStyle

Issues and pull requests for BiocStyle should go here.

bioconductor-teaching

Bioconductor teaching and education committee

S4 Generic Summary Statistic Functions that Operate on Matrix-Like Objects

MatrixGenerics

TENxBrainAnalysis

R scripts for analyzing the 1.3 million brain cell data set from 10X Genomics

BioC2020

BioC2020: Where Software and Biology Connect

CSAMA2015

Course material for CSAMA 2015: Statistics and Computing in Genome Data Science

Defines many S4 generic functions used in Bioconductor

BiocGenerics

AnnotationHub

Client for the Bioconductor AnnotationHub web resource

biocblog

A Quarto blog for Bioconductor community

The Bioconductor Build System

BBS

Shell

HDF5Array

HDF5 backend for DelayedArray objects

BiocFileCache

Manage Files Across Sessions

Rhtslib

HTSlib high-throughput sequencing library as an R package

AnVIL

Interact with AnVIL and Leonardo projects

BiocCheck

HCABrowser

Browse the Human Cell Atlas data portal

sweave2rmd

A project for converting Bioconductor Sweave documents to Rmd

EuroBioc2017

European Bioconductor Meeting 2017

High-performance sparse data representation and manipulation in R

SparseArray

EuroBioC2023

Training Material for Community Reviewers

pkgrevdocs

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.

BiocWorkingGroups

Software infrastructure for efficient representation of full genomes and their SNPs

BSgenome

ShortRead

CSAMA2016

Repository for CSAMA 2016 course material

Intermediate R course offered to members of RPCI / SUNY at Buffalo

IntermediateR

GenomicAlignments

Representation and manipulation of short genomic alignments

BiocGithubHelp

Notes and tips for using github with Biocondcutor

TENxBrainData

An ExperimentHub package for the 1.3 million brain cell 10X single-cell RNA-seq data set.

BioC2021

BioC2021: Where Software and Biology Connect

Manipulation of SQLite-based annotations in Bioconductor

AnnotationDbi

BioC2019

BioC2019: Where Software and Biology Connect

ExperimentHub

Client to access ExperimentHub resources

BiocInstaller

Install / Update Bioconductor, CRAN, and github Packages

Biobase

Biobase: Base functions for Bioconductor

LoomExperiment

A package to read, write, and manipulate loom files using LoomExperiments. Uses the loom file format from the Linnarson Lab. https://linnarssonlab.org/loompy/

BiocAsia2020

BiocAsia2020 repository

genefilter

genefilter: methods for filtering genes from high-throughput experiments

packagebuilder

JavaScript

BioC2018

BioC 2018: Where Software and Biology Connect

GDSArray

Representing GDS files as array-like objects

GSE62944

Experiment Data Package for TCGA processed RNA-Seq data

S4Arrays

Foundation of array-like containers in Bioconductor

workshop-contributions

Repository for managing contributions to workshop.bioconductor.org

Facilities for Filtering Bioconductor Annotation Resources

AnnotationFilter

UniProt.ws

R Interface to UniProt Web Services

EuroBioc2020

European Bioconductor Conference, December, 2020

KEGGREST

Client-side REST access to KEGG

ensemblVEP

R Interface to Ensembl Variant Effect Predictor

BioC2015Introduction

Introduction to R and Bioconductor session at BioC2015 July 20-22, Seattle, Wa

VCFArray

Extension of DelayedArray with on-disk/remote VCF backend

BioconductorMeta

Central repository for meta-information about the Bioconductor project

BioconductorAnnotationPipeline

build and push Bioconductor annotation packages

BiocBaseUtils

BiocAsia2021

BiocAsia2021 repository

European Bioconductor conference website 2022

EuroBioC2022

Categorized views of R package repositories

biocViews

RaggedExperiment

Matrix-like representations of mutation and CN data

AnnotationForge

Tools for building SQLite-based annotation data packages

GOstats

Tools for manipulating GO and microarrays.

Tools to forge BSgenome data packages

BSgenomeForge

GSEABase

Gene set enrichment data structures and methods

HubPub

ISMB.OSCA

OSCA tutorial at the ISMB 2023

R / Bioconductor Training Material for Uruguay R Bio Course

BiocUruguay2015

HCAMatrixBrowser

⚠️ DEPRECATED ⚠️ Download Matrix Data using the HCA API

100

BioC2016Introduction