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| BiocGenerics-package | Generic functions for Bioconductor |
| annotation | Accessing annotation information |
| annotation<- | Accessing annotation information |
| anyDuplicated | Determine duplicate elements |
| as.data.frame | Coerce to a data frame |
| AsIs-class | S3 classes as S4 classes |
| BiocGenerics | Generic functions for Bioconductor |
| boxplot | Box plots |
| bzfile-class | S3 classes as S4 classes |
| cbind | Combine R objects by rows or columns |
| characterORconnection-class | S3 classes as S4 classes |
| clusterApply | Apply operations using clusters |
| clusterApplyLB | Apply operations using clusters |
| clusterCall | Apply operations using clusters |
| clusterEvalQ | Apply operations using clusters |
| clusterExport | Apply operations using clusters |
| clusterMap | Apply operations using clusters |
| clusterSplit | Apply operations using clusters |
| colnames | Row and column names |
| combine | Combining or merging different Bioconductor data structures |
| combine-method | Combining or merging different Bioconductor data structures |
| connection-class | S3 classes as S4 classes |
| density | Kernel density estimation |
| duplicated | Determine duplicate elements |
| eval | Evaluate an (unevaluated) expression |
| Extremes | Maxima and minima |
| fifo-class | S3 classes as S4 classes |
| file-class | S3 classes as S4 classes |
| Filter | Common higher-order functions in functional programming languages |
| Find | Common higher-order functions in functional programming languages |
| funprog | Common higher-order functions in functional programming languages |
| get | Return the value of a named object |
| getObjectSlots | Update an object to its current class definition |
| gzcon-class | S3 classes as S4 classes |
| gzfile-class | S3 classes as S4 classes |
| image | Display a color image |
| intersect | Set operations |
| lapply | Apply a function over a list-like or vector-like R object |
| Map | Common higher-order functions in functional programming languages |
| mapply | Apply a function to multiple list-like or vector-like arguments |
| match | Value matching |
| mget | Return the value of a named object |
| NCOL | The number of rows/columns of an array-like object |
| ncol | The number of rows/columns of an array-like object |
| NROW | The number of rows/columns of an array-like object |
| nrow | The number of rows/columns of an array-like object |
| order | Ordering permutation |
| parApply | Apply operations using clusters |
| parCapply | Apply operations using clusters |
| parLapply | Apply operations using clusters |
| parLapplyLB | Apply operations using clusters |
| parRapply | Apply operations using clusters |
| parSapply | Apply operations using clusters |
| parSapplyLB | Apply operations using clusters |
| paste | Concatenate strings |
| pipe-class | S3 classes as S4 classes |
| pmax | Maxima and minima |
| pmax.int | Maxima and minima |
| pmin | Maxima and minima |
| pmin.int | Maxima and minima |
| Position | Common higher-order functions in functional programming languages |
| rank | Ranks the values in a vector-like object |
| rbind | Combine R objects by rows or columns |
| Reduce | Common higher-order functions in functional programming languages |
| rep.int | Replicate elements of a vector-like R object |
| residuals | Extract model residuals |
| row+colnames | Row and column names |
| rownames | Row and column names |
| S3-classes-as-S4-classes | S3 classes as S4 classes |
| sapply | Apply a function over a list-like or vector-like R object |
| setdiff | Set operations |
| sets | Set operations |
| sockconn-class | S3 classes as S4 classes |
| sort | Sorting a vector-like object |
| strand | Accessing strand information |
| strand<- | Accessing strand information |
| table | Cross tabulation and table creation |
| tapply | Apply a function over a ragged array |
| terminal-class | S3 classes as S4 classes |
| textConnection-class | S3 classes as S4 classes |
| union | Set operations |
| unique | Extract unique elements |
| unlist | Flatten list-like objects |
| unz-class | S3 classes as S4 classes |
| updateObject | Update an object to its current class definition |
| updateObject-method | Update an object to its current class definition |
| updateObjectFromSlots | Update an object to its current class definition |
| url-class | S3 classes as S4 classes |
| weights | Extract model weights |
| xtabs | Cross tabulation |