bioconductor有它自己的统计，在http://bioconductor.org/packages/stats/index.html。其中有top50的统计。但是这是全部下载的统计，体现不出一些新的软件包的快速成长。所以本人制作了一个统计表。本着本表，本博客会逐步介绍一些使用率高的软件包。
| Package | Maintainer | Title | last Month downloads | total Downloads |
| BiocInstaller | Bioconductor Package Maintainer | Install/Update Bioconductor and CRAN Packages | 12236 | 86043 |
| Biobase | Bioconductor Package Maintainer | Biobase: Base functions for Bioconductor | 9328 | 70855 |
| AnnotationDbi | Bioconductor Package Maintainer | Annotation Database Interface | 9020 | 61763 |
| BiocGenerics | Bioconductor Package Maintainer | Generic functions for Bioconductor | 8656 | 64868 |
| IRanges | Bioconductor Package Maintainer | Infrastructure for manipulating intervals on sequences | 8380 | 63344 |
| limma | Gordon Smyth | Linear Models for Microarray Data | 5885 | 46651 |
| Biostrings | H. Pages | String objects representing biological sequences, and matching algorithms | 5026 | 38688 |
| zlibbioc | Bioconductor Package Maintainer | An R packaged zlib-1.2.5 | 4951 | 38101 |
| GenomicRanges | Bioconductor Package Maintainer | Representation and manipulation of genomic intervals | 4788 | 34009 |
| annotate | Bioconductor Package Maintainer | Annotation for microarrays | 4451 | 35754 |
| graph | Bioconductor Package Maintainer | graph: A package to handle graph data structures | 4229 | 29110 |
| genefilter | Bioconductor Package Maintainer | genefilter: methods for filtering genes from microarray experiments | 4095 | 31717 |
| affy | Rafael A. Irizarry | Methods for Affymetrix Oligonucleotide Arrays | 4051 | 32927 |
| preprocessCore | Benjamin Milo Bolstad | A collection of pre-processing functions | 3865 | 31136 |
| affyio | Benjamin Milo Bolstad | Tools for parsing Affymetrix data files | 3657 | 29974 |
| biomaRt | Steffen Durinck | Interface to BioMart databases (e.g. Ensembl, COSMIC ,Wormbase and Gramene) | 3628 | 26999 |
| Rsamtools | Bioconductor Package Maintainer | Binary alignment (BAM), variant call (BCF), or tabix file import | 3482 | 25261 |
| GenomicFeatures | Bioconductor Package Maintainer | Tools for making and manipulating transcript centric annotations | 3267 | 19416 |
| multtest | Katherine S. Pollard | Resampling-based multiple hypothesis testing | 2949 | 21246 |
| BSgenome | H. Pages | Infrastructure for Biostrings-based genome data packages | 2879 | 22372 |
| rtracklayer | Michael Lawrence | R interface to genome browsers and their annotation tracks | 2832 | 21912 |
| geneplotter | Bioconductor Package Maintainer | Graphics related functions for Bioconductor | 2615 | 19376 |
| edgeR | Mark Robinson, Davis McCarthy, Yunshun Chen, Gordon Smyth | Empirical analysis of digital gene expression data in R | 2308 | 16809 |
| DESeq | Simon Anders | Differential gene expression analysis based on the negative binomial distribution | 2230 | 15204 |
| RBGL | Bioconductor Package Maintainer | An interface to the BOOST graph library | 2151 | 17334 |
| Rgraphviz | Kasper Daniel Hansen | Provides plotting capabilities for R graph objects | 2078 | 15031 |
| gcrma | Z. Wu | Background Adjustment Using Sequence Information | 1917 | 16491 |
| biovizBase | Tengfei Yin | Basic graphic utilities for visualization of genomic data. | 1696 | 8930 |
| vsn | Wolfgang Huber | Variance stabilization and calibration for microarray data | 1628 | 13508 |
| impute | Balasubramanian Narasimhan | impute: Imputation for microarray data | 1608 | 13383 |
| simpleaffy | Crispin Miller | Very simple high level analysis of Affymetrix data | 1590 | 11657 |
| AnnotationForge | Bioconductor Package Maintainer | Code for Building Annotation Database Packages | 1503 | 8795 |
| ShortRead | Bioconductor Package Maintainer | Classes and methods for high-throughput short-read sequencing data. | 1460 | 11826 |
| affyPLM | Ben Bolstad | Methods for fitting probe-level models | 1454 | 12901 |
| GEOquery | Sean Davis | Get data from NCBI Gene Expression Omnibus (GEO) | 1435 | 10443 |
| GSEABase | Bioconductor Package Maintainer | Gene set enrichment data structures and methods | 1298 | 10828 |
| qvalue | John D. Storey | Q-value estimation for false discovery rate control | 1293 | 10157 |
| affxparser | Kasper Daniel Hansen | Affymetrix File Parsing SDK | 1289 | 8945 |
| Gviz | Florian Hahne | Plotting data and annotation information along genomic coordinates | 1285 | 7220 |
| annaffy | Colin A. Smith | Annotation tools for Affymetrix biological metadata | 1194 | 10993 |
| marray | Yee Hwa (Jean) Yang | Exploratory analysis for two-color spotted microarray data | 1171 | 10629 |
| Category | Bioconductor Package Maintainer | Category Analysis | 1169 | 9212 |
| VariantAnnotation | Valerie Obenchain | Annotation of Genetic Variants | 1153 | 6747 |
| DynDoc | Bioconductor Package Maintainer | Dynamic document tools | 1128 | 9993 |
| GOstats | Bioconductor Package Maintainer | Tools for manipulating GO and microarrays. | 1103 | 8558 |
| siggenes | Holger Schwender | Multiple testing using SAM and Efron’s empirical Bayes approaches | 1102 | 6695 |
| cummeRbund | Loyal A. Goff | Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data. | 1090 | 8086 |
