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

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