Man pages for leekgroup/derfinder
Differential expression analysis of RNA-seq data at base-pair resolution
| derfinder-package | Differential expression analysis of RNA-seq data at base-pair... |
| findclosest.ahead | Find closest long region downstream |
| findclosest.behind | Find closest long region upstream |
| find.mean | Optional helper function for getParams |
| find.mean.down | Helper function for getParams |
| find.mean.up | Helper function for getParams |
| find.sd | Helper function for getParams |
| getAnnotation | Download exon information for a given genome |
| getColmeds | Calculate the medians of the database. |
| getExons | Find closest exon(s) to a genomic region |
| getF | F statistic from comparing nested limma models |
| getFlags | Flag regions with genomic events of interest |
| getLimmaInput | Fit a linear model to each nucleotide |
| getLimmaInput.DF | Fit a linear model to each nucleotide |
| get.numalts | Helper function for getParams |
| getParams | Calculate parameters to use as input for HMM |
| getParams.failsafe | Helper function for getParams |
| get.pvals | Permutation-based significance tests for differentially... |
| get.pvals.DF | Permutation-based significance tests for differentially... |
| getRegions | Generate list of regions, classify each as differentially... |
| getSvs | Do SVA on matrix stored in database |
| getTstats | Calculate moderated t statistic for each nucleotide |
| gsubfn | Helper function for read.csv.sql |
| last | Get the last element |
| locfdrFit | Modified version of Efron's locfdr |
| makeDb | Create SQLite database from text file |
| makeDF | Merge the coverage information for a group of samples |
| match.funfn | Generic extended version of R match.fun |
| mergeRegions | Merge close regions |
| ostrapply | Helper function for read.csv.sql |
| plotExon | Plot pipeline data/results for a given exon |
| plotGene | Plot pipeline data/results for a given gene |
| plotRegion | Plot pipeline data/results for a given region |
| read.csv.sql | Main workhorse of makeDb |
| sqldf | Helper function for read.csv.sql |
| strapply | Helper function for read.csv.sql |
| supportedTables | Print list of supported (downloadable) tables for a given... |
