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Additional R Tools
| Software | Description |
|---|---|
| abind | |
| cargo | |
| cowplot | |
| curl | |
| foreach | |
| gganimate | |
| GGally | |
| ggpubr | |
| ggrepel | |
| gifski | |
| gridSVG | |
| igraph | |
| jpeg | |
| leaps | |
| lme4 | |
| lubridate | |
| mirbase.db | |
| mixdist | |
| multcomp | |
| mvtnorm | |
| network | |
| pheatmap | |
| plotly | |
| plotROC | |
| plotrix | |
| quantmod | |
| RMySQL | |
| sna | |
| sqldf | |
| tidyr | |
| VGAM | |
| vioplot |
Additional R BioConductor Tools
| 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 | ||
| readr | ||
| ReportingTools | ||
| rhdf5 | provides an interface between HDF5 and R | |
| RIPSeeker | identify protein-associated transcripts from RIP-seq experiments | |
| ShortRead | sampling, iteration, and input of FASTQ files | |
| sleuth | analysis of RNA-Seq experiments for which transcript abundances have been quantified with kallisto | |
| RIPSeeker | ||
| SISPA | ||
| sleuth | ||
| ShortRead | ||
| topGO | ||
| TxDb.Scerevisiae.UCSC.sacCer3.sgdGene | ||
| TxDb.Hsapiens.UCSC.hg38.knownGene | BSgenome.Hsapiens.UCSC.hg19 | |
| ballgown | Flexible, isoform-level differential expression analysistximport | |
| WGCNA |
Additional Perl CPAN modules
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