flowCore

Extra Credit builds an outline of flowCore's docs the first time your work uses it. Until then, start at the official documentation.

• Rsamtools Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import
• rtracklayer R interface to genome annotation files and the UCSC genome browser
• biomaRt Interface to BioMart databases (i.e. Ensembl)
• KEGGREST Client-side REST access to the Kyoto Encyclopedia of Genes and Genomes (KEGG)
• GenomicAlignments Representation and manipulation of short genomic alignments
• annotate Annotation for microarrays
• DESeq2 Differential gene expression analysis based on the negative binomial distribution
• edgeR Empirical Analysis of Digital Gene Expression Data in R
• GenomicFeatures Query the gene models of a given organism/assembly
• genefilter genefilter: methods for filtering genes from high-throughput experiments
• Rhtslib HTSlib high-throughput sequencing library as an R package
• graph graph: A package to handle graph data structures