| annotation | Accessing annotation information |
| append | Append elements to a vector-like object |
| as.data.frame | Coerce an object into a data frame |
| as.vector | Coerce an object into a vector |
| BiocGenerics-package | S4 generic functions for Bioconductor |
| boxplot | Box plots |
| cbind | Combine objects by rows or columns |
| clusterApply | Apply operations using clusters |
| combine | Combining or merging different Bioconductor data structures |
| dbconn | Accessing SQLite DB information |
| density | Kernel density estimation |
| dge | Accessors and generic functions used in the context of count... |
| do.call | Execute a function call |
| duplicated | Determine duplicate elements |
| eval | Evaluate an (unevaluated) expression |
| evalq | Evaluate an (unevaluated) expression |
| Extremes | Maxima and minima |
| fileName | Accessing the file name of an object |
| funprog | Common higher-order functions in functional programming... |
| get | Return the value of a named object |
| grep | Pattern Matching and Replacement |
| image | Display a color image |
| IQR | The Interquartile Range |
| is.unsorted | Test if a vector-like object is not sorted |
| lapply | Apply a function over a list-like or vector-like object |
| lengths | Lengths of the list elements of a list-like object |
| mad | Median Absolute Deviation |
| mapply | Apply a function to multiple list-like or vector-like... |
| match | Value matching |
| matrix-summary | Form Row and Column Sums and Means |
| mean | Arithmetic Mean |
| normalize | Normalize an object |
| nrow | The number of rows/columns of an array-like object |
| order | Ordering permutation |
| organism_species | Organism and species accessors |
| paste | Concatenate strings |
| plotMA | MA-plot: plot differences versus averages for high-throughput... |
| plotPCA | PCA-plot: Principal Component Analysis plot |
| rank | Ranks the values in a vector-like object |
| relist | Re-listing an unlist()ed object |
| rep | Replicate elements of a vector-like object |
| residuals | Extract model residuals |
| row_colnames | Row and column names |
| S3-classes-as-S4-classes | S3 classes as S4 classes |
| score | Score accessor |
| sets | Set operations |
| sort | Sorting a vector-like object |
| start | Start, end, width generic getters and setters |
| strand | Accessing strand information |
| subset | Subsetting vector-like, matrix-like and data-frame-like... |
| t | Matrix Transponse |
| table | Cross tabulation and table creation |
| tapply | Apply a function over a ragged array |
| testPackage | Run RUnit package unit tests |
| unique | Extract unique elements |
| unlist | Flatten list-like objects |
| unsplit | Unsplit a list-like object |
| updateObject | Update an object to its current class definition |
| var | Variance and Standard Deviation |
| weights | Extract model weights |
| which | Subscript generators |
| xtabs | Cross tabulation |
