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Additional R BioConductor Tools
| Software | Description | |
|---|---|---|
| affy | ||
| affyio | GNU R package “Tools for parsing Affymetrix data files” | |
| annotate | GNU R package “Annotation for microarrays” | |
annotationdbi | GNU R package “Annotation Database Interface” | |
| arrayQualityMetrics | ||
| ballgown | Flexible, isoform-level differential expression analysis | |
| biobase | GNU R package “Biobase: Base functions for Bioconductor” | |
biocgenerics | GNU R package “S4 generic functions for Bioconductor” | |
biocinstaller | GNU R package “Install/Update Bioconductor and CRAN | |
biocparallel | GNU R package “Bioconductor facilities for parallel | |
biomart | GNU R Interface to BioMart databases (Ensembl, COSMIC, Wormbase and Gramene) | |
biostrings | GNU R package “String objects representing biological | |
| BSgenome | Efficient genome searching | |
| BSgenome.Hsapiens.UCSC.hg19 | ||
| ChIPseeker | annotating ChIP-seq data analysis | |
| cummeRbund | analyzing Cufflinks RNA-Seq output | |
| deseq | ||
| DESeq2 | Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution | |
| devtools | Collection of package development tools | |
| DEXSeq | finding differential exon usage using RNA-seq exon counts between samples | |
| genfilter | GNU R package “genefilter: methods for filtering genes | |
geneplotter | Graphics related functions for Bioconductor | |
genomeinfodb | GNU R package “Utilities for manipulating chromosome and | |
genomicalignments | GNU R package “Representation and manipulation of short | |
genomicranges | GNU R package “Representation and manipulation of genomic | |
| GISPA | ||
| GOstats | tools for interacting with GO and microarray data | |
| GO.db | ||
hilbertvis | GNU R package to visualise long vector data | |
iranges | GNU R package “Infrastructure for manipulating intervals | |
| JunctionSeq | ||
limma | GNU R package “Linear Models for Microarray Data” | |
| mirbase.db | ||
multtest | GNU R package “Resampling-based multiple hypothesis | |
| org.Sc.sgd.db | ||
| org.Mm.eg.db | ||
preprocesscore | GNU R package “A collection of pre-processing functions” | |
| qvalue | Bioconductor package “Q-value estimation for false discovery rate control” | |
| rhdf5 | provides an interface between HDF5 and R | |
| readr | ||
| ReportingTools | rhdf5 | |
| RIPSeeker | identify protein-associated transcripts from RIP-seq experiments | |
| rsamtools | GNU R package “Binary alignment (BAM), variant call (BCF), | |
s4vectors | GNU R package “S4 implementation of vectors and lists” | |
| SISPA | ||
| sleuth | analysis of RNA-Seq experiments for which transcript abundances have been quantified with kallisto | |
| ShortRead | sampling, iteration, and input of FASTQ files | |
| topGO | ||
| TxDb.Scerevisiae.UCSC.sacCer3.sgdGene | ||
| TxDb.Hsapiens.UCSC.hg38.knownGene | ||
| tximport | ||
| WGCNA | ||
xvector | GNU R package “Representation and manpulation of external | |
zlibbioc | GNU R package “An R packaged zlib-1.2.5″ |
Additional Perl CPAN modules
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