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| Software | Description | in common.yaml | in library() |
|---|---|---|---|
| affy | Methods for Affymetrix Oligonucleotide Arrays | y | y |
| affyio | GNU R package “Tools for parsing Affymetrix data files” | y | |
| annotate | GNU R package “Annotation for microarrays” | y | |
annotationdbi | GNU R package “Annotation Database Interface” | y | |
| arrayQualityMetrics | Quality metrics report for microarray data sets | y | y |
| ballgown | Flexible, isoform-level differential expression analysis | y | y |
| biobase | GNU R package “Biobase: Base functions for Bioconductor” | y | |
biocgenerics | GNU R package “S4 generic functions for Bioconductor” | y | |
biocinstaller | GNU R package “Install/Update Bioconductor and CRAN | ||
biocparallel | GNU R package “Bioconductor facilities for parallel | y | |
biomart | GNU R Interface to BioMart databases (Ensembl, COSMIC, Wormbase and Gramene) | y | |
biostrings | GNU R package “String objects representing biological | y | |
| BSgenome | Efficient genome searching | y | y |
| BSgenome.Hsapiens.UCSC.hg19 | Full genome sequences for Homo sapiens (UCSC version hg19) | y | y |
| ChIPseeker | annotating ChIP-seq data analysis | y | y |
| cummeRbund | analyzing Cufflinks RNA-Seq output | y | y |
| 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 | y | y |
| devtools | Collection of package development tools | y | y |
| DEXSeq | finding differential exon usage using RNA-seq exon counts between samples | y | y |
| EnhancedVolcano | Publication-ready volcano plots with enhanced colouring and labeling | y | |
| genefilter | GNU R package “genefilter: methods for filtering genes | y | |
geneplotter | Graphics related functions for Bioconductor | y | |
genomeinfodb | GNU R package “Utilities for manipulating chromosome and | y | |
genomicalignments | GNU R package “Representation and manipulation of short | y | |
genomicranges | GNU R package “Representation and manipulation of genomic | y | |
| ggplot2movies | Movies Data | y | |
| GISPA | GISPA: Method for Gene Integrated Set Profile Analysis | y | y |
| GOstats | tools for interacting with GO and microarray data | y | y |
| GO.db | y | ||
hilbertvis | GNU R package to visualise long vector data | ||
| httpuv | HTTP and WebSocket Server Library | y | y |
iranges | GNU R package “Infrastructure for manipulating intervals | ||
| JunctionSeq | JunctionSeq: A Utility for Detection of Differential Exon and Splice-Junction Usage in RNA-Seq data | y | y |
limma | GNU R package “Linear Models for Microarray Data” | y | |
| mirbase.db | miRBase: the microRNA database | y | y |
multtest | GNU R package “Resampling-based multiple hypothesis | ||
| org.Hs.eg.db | Genome wide annotation for Human | y | y |
| org.Sc.sgd.db | Genome wide annotation for Yeast | y | y |
| org.Mm.eg.db | Genome wide annotation for Mouse | y | y |
| org.Rn.eg.db | Genome wide annotation for Rat | y | y |
preprocesscore | GNU R package “A collection of pre-processing functions” | y | |
| processx | Execute and Control System Processes | y | y |
| pkgload | y | ||
| qvalue | Bioconductor package “Q-value estimation for false discovery rate control” | y | |
| rhdf5 | provides an interface between HDF5 and R | y | y |
| readr | Read Rectangular Text Data | y | y |
| ReportingTools | Tools for making reports in various formats | y | y |
| RIPSeeker | identify protein-associated transcripts from RIP-seq experiments | y | y |
| roxygen2 | In-Line Documentation for R | y | y |
| rsamtools | GNU R package “Binary alignment (BAM), variant call (BCF), | y | |
s4vectors | GNU R package “S4 implementation of vectors and lists” | y | |
| SISPA | SISPA: Method for Sample Integrated Set Profile Analysis | y | y |
| sleuth | analysis of RNA-Seq experiments for which transcript abundances have been quantified with kallisto | y | y |
| ShortRead | sampling, iteration, and input of FASTQ files | y | y |
| topGO | Enrichment Analysis for Gene Ontology | y | y |
| TxDb.Scerevisiae.UCSC.sacCer3.sgdGene | Annotation package for TxDb object(s) | y | y |
| TxDb.Hsapiens.UCSC.hg38.knownGene | Annotation package for TxDb object(s) | y | y |
| tximport | Import and summarize transcript-level estimates for transcript- and gene-level analysis | y | y |
| WGCNA | Weighted Correlation Network Analysis | y | y |
xvector | GNU R package “Representation and manpulation of external | y | |
| yardstick | Tidy Characterizations of Model Performance | y | y |
zlibbioc | GNU R package “An R packaged zlib-1.2.5″ | y |
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