Bioconductor is a large-scale FLOSS project that provides many individual packages for bioinformatics research. It includes a set of tools for analyzing and understanding genomic data, annotated chip names, annotations of biological sequences, etc., as well as the experimental data themselves.
| Bioconductor | |
|---|---|
 | |
| Type of | Bioinformatics |
| operating system | Linux , Mac OS X , Windows |
| Interface languages | R |
| Latest version | 3.6 |
| License | Artistic License 2.0 |
| Website | bioconductor.org |
It uses the programming language R , due to which it supports cross-platform ( Linux , most UNIX-like systems , Mac OS X , Windows ). It is developed and distributed freely and openly. Release of releases occurs twice a year. It has an active free community of developers and scientists, which is typical of good open source projects. Descriptions of the project and changes in it are issued in the form of an annual report [1] .
Currently contains more than 2000 packages.
Content
- 1 Project Objectives
- 2 Project History
- 3 Importance of the project
- 4 Packs
- 5 Releases
- 6 Usage Examples
- 7 See also
- 8 Notes
- 9 References
Project Goals
The main objectives of Bioconductor are:
- Providing open access to a wide range of powerful statistical and graphical methods for analyzing genomic data.
- Facilitating the inclusion of biological metadata in the analysis of genomic data, for example, literature data from PubMed , annotated data from Entrez .
- Providing a common software platform that allows you to quickly develop and deploy extensible, scalable, and compatible programs.
- Further scientific understanding in creating high-quality documentation for reproducible research.
- Training researchers in computational and statistical methods for analyzing genomic data.
Project History
The project began in 2001 at the Dana Farber Cancer Institute . [2]
Project Importance
Packages
The three main groups of packages are the actual statistical and graphical packages ( Software ), annotation packages ( AnnotationData ) and experimental data ( ExperimentData ).
The number of packets in the group is indicated in parentheses.
Software (936)
AssayDomain (299)
- aCGH (12)
- CellBasedAssays (38)
- ChIPchip (7)
- CopyNumberVariation (43)
- CpGIsland (6)
- DNAMethylation (38)
- ExonArray (6)
- GeneExpression (131)
- GeneticVariability (23)
- SNP (40)
- Transcription (47)
BiologicalQuestion (261)
- AlternativeSplicing (7)
- Coverage (13)
- DifferentialExpression (164)
- DifferentialMethylation (8)
- DifferentialPeakCalling (1)
- DifferentialSplicing (6)
- FunctionalPrediction (1)
- GeneRegulation (21)
- GeneSetEnrichment (41)
- GeneTarget (1)
- GenomeAnnotation (10)
- GenomicVariation (6)
- LinkageDisequilibrium (1)
- MotifAnnotation (3)
- MotifDiscovery (4)
- NetworkEnrichment (13)
- NetworkInference (17)
- SequenceMatching (17)
- SomaticMutation (4)
- VariantDetection (1)
Infrastructure (186)
- DataImport (82)
- DataRepresentation (34)
- GUI (19)
- ThirdPartyClient (9)
ResearchField (193)
- BiomedicalInformatics (2)
- CellBiology (20)
- Cheminformatics (3)
- FunctionalGenomics (1)
- Genetics (96)
- Metabolomics (12)
- Metagenomics (5)
- Proteomics (65)
- SystemsBiology (10)
StatisticalMethod (261)
- Bayesian (15)
- Classification (65)
- Clustering (89)
- DecisionTree (7)
- DimensionReduction (2)
- FeatureExtraction (2)
- GraphAndNetwork (69)
- HiddenMarkovModel (4)
- NeuralNetwork (1)
- PrincipalComponent (2)
- Regression (7)
- StructuralEquationModels (1)
- SupportVectorMachine (1)
- Survival (4)
- TimeCourse (29)
Technology (591)
- FlowCytometry (36)
MassSpectrometry (44)
Microarray (328)
- ChipOnChip (1)
- MethylationArray (7)
- mRNAMicroarray (3)
- MultiChannel (3)
- OneChannel (68)
- ProprietaryPlatforms (2)
- TwoChannel (53)
- MicrotitrePlateAssay (13)
- qPCR (9)
- SAGE (9)
Sequencing (212)
- ChIPSeq (40)
- DNASeq (6)
- ExomeSeq (3)
- MethylSeq (10)
- Microbiome (3)
- miRNA (4)
- RIPSeq (1)
- RNASeq (76)
- TargetedResequencing (2)
- WholeGenome (3)
WorkflowStep (477)
- Alignment (8)
- Annotation (67)
- BatchEffect (5)
- ExperimentalDesign (2)
- MultipleComparison (76)
- Normalization (15)
Pathways (69)
- GO (33)
- Preprocessing (128)
- QualityControl (95)
- ReportWriting (25)
Visualization (218)
- Network (44)
AnnotationData (895)
ChipManufacturer (374)
- AffymetrixChip (336)
- AgilentChip (15)
- IlluminaChip (19)
- INDACChip (1)
- QiagenChip (1)
- RNG_MRCChip (2)
ChipName (195)
- adme16cod (1)
- ag (3)
- ath1121501 (3)
- celegans (3)
- drosgenome1 (3)
- drosophila2 (3)
- h10kcod (1)
- h20kcod (1)
- hcg110 (3)
- hgfocus (3)
- hgu133a (4)
- hgu133a2 (4)
- hgu133b (3)
- hgu133plus2 (4)
- hgu95a (3)
- hgu95av2 (4)
- hgu95b (3)
- hgu95c (3)
- hgu95d (3)
- hgu95e (3)
- hguatlas13k (1)
- hgug4100a (1)
- hgug4101a (1)
- hgug4110b (1)
- hgug4111a (1)
- hgug4112a (1)
- hguqiagenv3 (1)
- hi16cod (1)
- hs25kresogen (1)
- hu35ksuba (3)
- hu35ksubb (3)
- hu35ksubc (3)
- hu35ksubd (3)
- hu6800 (3)
- HuO22 (1)
- hwgcod (1)
- illuminaHumanv1 (1)
- illuminaHumanv2 (1)
- illuminaMousev1 (1)
- illuminaMousev1p1 (1)
- illuminaRatv1 (1)
- indac (1)
- m10kcod (1)
- m20kcod (1)
- mgu74a (3)
- mgu74av2 (3)
- mgu74b (3)
- mgu74bv2 (3)
- mgu74c (3)
- mgu74cv2 (3)
- mguatlas5k (1)
- mgug4121a (1)
- mgug4122a (1)
- mi16cod (1)
- mm24kresogen (1)
- moe430a (3)
- moe430b (3)
- mouse4302 (4)
- mouse430a2 (4)
- mpedbarray (1)
- mu11ksuba (3)
- mu11ksubb (3)
- Mu15v1 (1)
- mu19ksuba (2)
- mu19ksubb (2)
- mu19ksubc (2)
- Mu22v3 (1)
- mwgcod (1)
- Norway981 (1)
- OperonHumanV3 (1)
- PartheenMetaData (1)
- pedbarrayv10 (1)
- pedbarrayv9 (1)
- r10kcod (1)
- rae230a (3)
- rae230b (3)
- rat2302 (3)
- rgu34a (3)
- rgu34b (3)
- rgu34c (3)
- rgug4130a (1)
- ri16cod (1)
- rnu34 (3)
- Roberts2005Annotation (1)
- rtu34 (3)
- rwgcod (1)
- SHDZ (1)
- u133x3p (3)
- xenopuslaevis (2)
- yeast2 (3)
- ygs98 (4)
- zebrafish (3)
- CustomArray (2)
CustomCDF (16)
- GACustomCDF (16)
CustomDBSchema (11)
- GeneCardsCustomSchema (8)
- FunctionalAnnotation (13)
Organism (532)
- Anopheles_gambiae (4)
- Apis_mellifera (3)
- Arabidopsis_thaliana (12)
- Bacillus_subtilis (2)
- Bos_taurus (11)
- Caenorhabditis_elegans (10)
- Canis_familiaris (12)
- Danio_rerio (12)
- Drosophila_melanogaster (15)
- Escherichia_coli (12)
- Gallus_gallus (9)
- Gasterosteus_aculeatus (2)
- Homo_sapiens (201)
- Hordeum_vulgare (2)
- Macaca_mulatta (7)
- Mus_musculus (103)
- Oryza_sativa (1)
- Pan_troglodytes (6)
- Plasmodium_falciparum (4)
- Pseudomonas_aeruginosa (2)
- Rattus_norvegicus (65)
- Saccharomyces_cerevisiae (18)
- Saccharum_officinarum (2)
- Staphylococcus_aureus (2)
- Sus_scrofa (7)
- Taeniopygia_guttata (2)
- Vitis_vinifera (2)
- Xenopus_laevis (3)
- Xenopus_tropicalis (1)
- Zea_mays (2)
PackageType (524)
- BSgenome (69)
- cdf (126)
- ChipDb (155)
- db0 (19)
- InparanoidDb (8)
- MeSHDb (3)
- OrganismDb (3)
- OrgDb (19)
- probe (104)
- SNPlocs (1)
- TxDb (17)
SequenceAnnotation (3)
- miRNA (3)
ExperimentData (223)
Cancer (35)
- Breast (2)
- Colon (2)
- Kidney (1)
- Leukemia (6)
- Lung (1)
- Ovarian (1)
- ChIPchipData (1)
- ChIPseqData (4)
- EColiData (1)
- ExpressionData (4)
- HapMap (7)
- HighThroughputSequencingData (9)
- HIV (1)
- MassSpectrometryData (7)
- NormalTissue (3)
- RNAExpressionData (16)
- RNAseqData (19)
- StemCells (1)
- Yeast (10)
Releases
Releases are released twice a year - in spring and autumn. Each new release as a dependency requires the latest version of the R distribution .
Biocondactor Packet Growth Chart
| Version | date of release | Number of packages (in the "Software" section) | Dependence |
|---|---|---|---|
| 1.0 | May 1, 2001 | fifteen | R 1.5 |
| 1.1 | Nov 19, 2002 | twenty | R 1.6 |
| 1.2 | May 29, 2003 | thirty | R 1.7 |
| 1.3 | Oct 30, 2003 | 49 | R 1.8 |
| 1.4 | May 17, 2004 | 81 | R 1.9 |
| 1.5 | Oct 25, 2004 | one hundred | R 2.0 |
| 1.6 | May 18, 2005 | 123 | R 2.1 |
| 1.7 | Oct 14, 2005 | 141 | R 2.2 |
| 1.8 | Apr 27, 2006 | 172 | R 2.3 |
| 1.9 | October 4, 2006 | 188 | R 2.4 |
| 2.0 | Apr 26, 2007 | 214 | R 2.5 |
| 2.1 | Oct 8, 2007 | 233 | R 2.6 |
| 2.2 | May 1, 2008 | 260 | R 2.7 |
| 2.3 | October 22, 2008 | 294 | R 2.8 |
| 2.4 | Apr 21, 2009 | 320 | R 2.9 |
| 2.5 | October 28, 2009 | 352 | R 2.10 |
| 2.6 | Apr 23, 2010 | 389 | R 2.11 |
| 2.7 | October 18, 2010 | 418 | R 2.12 |
| 2.8 | Apr 14, 2011 | 466 | R 2.13 |
| 2.9 | Nov 1, 2011 | 517 | R 2.14 |
| 2.10 | Nov 2, 2012 | 554 | R 2.15 |
| 2.11 | October 3, 2012 | 610 | R 2.15 |
| 2.12 | Apr 4, 2013 | 671 | R 3.0 |
| 2.13 | October 15, 2013 | 749 | R 3.0 |
| 2.14 | Apr 14, 2014 | 824 | R 3.1 |
| 3.0 | Oct 14, 2014 | 934 | R 3.1 |
Use
See also
- R
- Bioinformatics
- Computational Biology
- Computational Methods
- Free and open source software
- DNA microchip
- List of open source bioinformatics software
- Sequence Alignment Software List
- Affymetrix is an American DNA microarray company.
Notes
- ↑ Annual reports of the project on the official website .
- ↑ R. Gentleman. [ http://www.bioconductor.org/about/annual-reports/AnnRep2002.pdf 2002 Annual Report for the Bioconductor. Project, DFCI]. - May 29, 2008.
Links
Official website - http://www.bioconductor.org/