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Repository Details

The official repository of the Bioconductor 2019 Conference Workshops 🎊

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1

Contributions

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

Course material for CSAMA: Statistical Data Analysis for Genome Scale Biology
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GenomicDataCommons

Provide R access to the NCI Genomic Data Commons portal.
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BiocWorkshops

⚠️ 2018 ⚠️ Bioconductor Workshops
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bioconductor_docker

Docker Containers for Bioconductor
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BiocParallel

Bioconductor facilities for parallel evaluation
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BiocManager

CRAN Package For Managing Bioconductor Packages
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OrchestratingSingleCellAnalysis

Content for the OSCA Book.
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LearnBioconductor

Training material for introductory R / Bioconductor courses
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bioc_docker

[DEPRECATED] Docker containers for Bioconductor
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12

Biostrings

Efficient manipulation of biological strings
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13

GoogleGenomics

[DEPRECATED] An R package for Google Genomics API queries.
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14

BiocIntro

Course material for introductory R / Bioconductor courses
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15

OrchestratingSingleCellAnalysis-release

An online companion to the OSCA manuscript demonstrating Bioconductor resources and workflows for single-cell RNA-seq analysis.
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16

GenomicRanges

Representation and manipulation of genomic intervals
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17

basilisk

Clone of the Bioconductor repository for the basilisk package.
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18

bioconductor_full

[DEPRECATED] Docker Images which include a complete installation of all software needed to build all Bioconductor packages
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19

SummarizedExperiment

SummarizedExperiment container
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20

GenomicFeatures

Conveniently import and query gene models
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21

copy-number-analysis

Explore, compare, and evaluate Bioconductor packages related to genomic copy number analysis
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22

BiocAdvanced

Advanced R / Bioconductor training material
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23

DelayedArray

A unified framework for working transparently with on-disk and in-memory array-like datasets
R
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24

Rsamtools

Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import
R
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25

bioconductor.org

Source code for the Bioconductor website
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19
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26

BuildABiocWorkshop

Template for building a bioconductor workshop package using github actions
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19
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27

IRanges

Foundation of integer range manipulation in Bioconductor
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18
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28

VariantAnnotation

Annotation of Genetic Variants
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18
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29

S4Vectors

Foundation of vector-like and list-like containers in Bioconductor
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30

UseBioconductor

Training material for intermediate R / Bioconductor courses
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31

GenomeInfoDb

Utilities for manipulating chromosome names, including modifying them to follow a particular naming style
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15
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32

bioc_git_transition

This python package is for transitioning bioconductor from SVN to git
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14
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33

BiocStyle

Issues and pull requests for BiocStyle should go here.
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12
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34

bioconductor-teaching

Bioconductor teaching and education committee
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12
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35

MatrixGenerics

S4 Generic Summary Statistic Functions that Operate on Matrix-Like Objects
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12
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36

TENxBrainAnalysis

R scripts for analyzing the 1.3 million brain cell data set from 10X Genomics
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37

BioC2020

BioC2020: Where Software and Biology Connect
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38

CSAMA2015

Course material for CSAMA 2015: Statistics and Computing in Genome Data Science
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11
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39

BiocGenerics

Defines many S4 generic functions used in Bioconductor
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10
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40

AnnotationHub

Client for the Bioconductor AnnotationHub web resource
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10
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41

biocblog

A Quarto blog for Bioconductor community
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9
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42

BBS

The Bioconductor Build System
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9
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43

HDF5Array

HDF5 backend for DelayedArray objects
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9
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44

BiocFileCache

Manage Files Across Sessions
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9
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45

Rhtslib

HTSlib high-throughput sequencing library as an R package
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9
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46

AnVIL

Interact with AnVIL and Leonardo projects
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8
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47

BiocCheck

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8
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48

HCABrowser

Browse the Human Cell Atlas data portal
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8
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49

sweave2rmd

A project for converting Bioconductor Sweave documents to Rmd
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8
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50

EuroBioc2017

European Bioconductor Meeting 2017
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51

SparseArray

High-performance sparse data representation and manipulation in R
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52

EuroBioC2023

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53

pkgrevdocs

Training Material for Community Reviewers
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54

BiocWorkingGroups

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.
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55

BSgenome

Software infrastructure for efficient representation of full genomes and their SNPs
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7
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56

ShortRead

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57

CSAMA2016

Repository for CSAMA 2016 course material
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58

IntermediateR

Intermediate R course offered to members of RPCI / SUNY at Buffalo
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59

GenomicAlignments

Representation and manipulation of short genomic alignments
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60

BiocGithubHelp

Notes and tips for using github with Biocondcutor
7
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61

TENxBrainData

An ExperimentHub package for the 1.3 million brain cell 10X single-cell RNA-seq data set.
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7
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62

BioC2021

BioC2021: Where Software and Biology Connect
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6
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63

AnnotationDbi

Manipulation of SQLite-based annotations in Bioconductor
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6
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64

BioC2019

BioC2019: Where Software and Biology Connect
6
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65

ExperimentHub

Client to access ExperimentHub resources
R
6
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66

BiocInstaller

Install / Update Bioconductor, CRAN, and github Packages
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6
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67

Biobase

Biobase: Base functions for Bioconductor
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6
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68

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/
R
6
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69

BiocAsia2020

BiocAsia2020 repository
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70

genefilter

genefilter: methods for filtering genes from high-throughput experiments
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5
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71

packagebuilder

JavaScript
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72

BioC2018

BioC 2018: Where Software and Biology Connect
5
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73

GDSArray

Representing GDS files as array-like objects
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74

GSE62944

Experiment Data Package for TCGA processed RNA-Seq data
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75

S4Arrays

Foundation of array-like containers in Bioconductor
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76

workshop-contributions

Repository for managing contributions to workshop.bioconductor.org
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77

AnnotationFilter

Facilities for Filtering Bioconductor Annotation Resources
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78

UniProt.ws

R Interface to UniProt Web Services
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79

EuroBioc2020

European Bioconductor Conference, December, 2020
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80

KEGGREST

Client-side REST access to KEGG
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81

ensemblVEP

R Interface to Ensembl Variant Effect Predictor
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82

BioC2015Introduction

Introduction to R and Bioconductor session at BioC2015 July 20-22, Seattle, Wa
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83

VCFArray

Extension of DelayedArray with on-disk/remote VCF backend
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84

BioconductorMeta

Central repository for meta-information about the Bioconductor project
4
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85

BioconductorAnnotationPipeline

build and push Bioconductor annotation packages
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86

BiocBaseUtils

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87

BiocAsia2021

BiocAsia2021 repository
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88

EuroBioC2022

European Bioconductor conference website 2022
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89

biocViews

Categorized views of R package repositories
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4
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90

RaggedExperiment

Matrix-like representations of mutation and CN data
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4
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91

AnnotationForge

Tools for building SQLite-based annotation data packages
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4
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92

GOstats

Tools for manipulating GO and microarrays.
TeX
4
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93

BSgenomeForge

Tools to forge BSgenome data packages
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4
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94

GSEABase

Gene set enrichment data structures and methods
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95

HubPub

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96

ISMB.OSCA

OSCA tutorial at the ISMB 2023
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97

BiocUruguay2015

R / Bioconductor Training Material for Uruguay R Bio Course
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98

HCAMatrixBrowser

⚠️ DEPRECATED ⚠️ Download Matrix Data using the HCA API
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3
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99

BioC2016Introduction

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3
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100

hca

Human Cell Atlas data discovery and retrieval
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