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| Software | Description |
|---|---|
| affy | |
| arrayQualityMetrics | |
| ballgown | Flexible, isoform-level differential expression analysis |
| BSgenome | Efficient genome searching |
| BSgenome.Hsapiens.UCSC.hg19 | |
| ChIPseeker | annotating ChIP-seq data analysis |
| cummeRbund | analyzing Cufflinks RNA-Seq output |
| 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 |
| GISPA | |
| GOstats | tools for interacting with GO and microarray data |
| GO.db | |
| JunctionSeq | |
| mirbase.db | |
| org.Sc.sgd.db | |
| org.Mm.eg.db | |
| rhdf5 | provides an interface between HDF5 and R |
| readr | |
| ReportingTools | |
| rhdf5 | |
| RIPSeeker | identify protein-associated transcripts from RIP-seq experiments |
| 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 |
...