A B C D E F G H I L M N O P R S T U V W misc
rphast-package | RPHAST: R interface to PHAST |
addIntrons.feat | Add introns to features... |
addSignals.feat | Add start/stop codon, 3'/5' splice signals to features... |
addUTRs.feat | Add UTRs to features... |
alphabet.msa | MSA Alphabet |
as.data.frame.feat | Features to Data Frame |
as.list.tm | Tree Model to List |
as.pointer.feat | Features To Pointer |
as.pointer.msa | MSA To Pointer |
branchlen.tree | Get the total length of the edges of a tree... |
complement | complement |
composition.feat | Composition of features with respect to annotations... |
concat.msa | Concatenate msa objects... |
copy.feat | Features copy |
copy.msa | MSA copy |
coverage.feat | Features coverage... |
density.feat | Features kernel density... |
depth.tree | Get the distance from a node to the root of a tree... |
dim.feat | Feature dimensions |
dim.msa | Returns the dimensions of an msa object as (# of species, # of columns)... |
enrichment.feat | Enrichment of features with respect to annotation types... |
extract.feature.msa | Extract features from an MSA object... |
feat | Features Objects |
feat.track | Create a features track... |
fix.semicolon.tree | Add a semi-colon to end of tree string... |
fixStartStop.feat | Fix start and stop signals... |
from.pointer.msa | MSA From Pointer |
gene.track | Create a gene track... |
get4d.msa | Extract fourfold degenerate sites from an MSA object... |
guess.format.msa | MSA Format From Filename Extension |
hist.feat | plot histogram of feature lengths... |
hmm | Create an rphast HMM object |
informative.regions.msa | Get informative regions of an alignment... |
inverse.feat | Get inverse features... |
is.msa | Check an MSA object... |
is.ordered.msa | MSA is Ordered? |
is.tm | Tree Models |
is.track | Is this a track? |
isSubstMod.tm | Check Substitution Model Strings |
likelihood.msa | MSA Likelihood |
msa | MSA Objects |
name.ancestors | Name Ancestral Nodes |
names.msa | MSA Sequence Names |
ncol.feat | Number of Columns in Features |
ncol.msa | MSA Sequence Length. |
ninf.msa | The number of informative columns in an alignment... |
nrow.feat | Number of Features |
nrow.msa | MSA Number of Sequences |
nstate.hmm | HMM number of states... |
numnodes.tree | Number of Nodes in a Tree |
offset.msa | MSA Index Offset |
overlap.feat | Feature overlap... |
phastCons | Produce conservation scores and identify conserved elements,... |
phyloFit | Fit a Phylogenetic model to an alignment... |
phyloP | phyloP (basewise or by feature) |
phyloP.prior | phyloP prior |
phyloP.sph | phyloP SPH |
plot.feat | Features plot |
plot.gene | Gene plot |
plot.track | Make browser-like plot in rphast... |
print.feat | Printing a features Object |
print.msa | Printing MSA objects |
print.tm | Printing Tree Models |
prune.tree | Prune a Tree |
range.feat | Features range |
range.track | Get the coordinate range of a list of RPHAST results... |
rbind.feat | concatenate feature objects... |
read.feat | Read a Feature File (GFF, BED, or GenePred) |
read.hmm | Read an HMM object from a file... |
read.msa | Reading an MSA Object |
read.newick.tree | Read a Newick Tree from a File |
read.tm | Read a Tree Model |
rename.tree | Tree Node Renaming |
rescale.tree | Scale a Tree or Subtree |
reverse.complement | Reverse complement a multiple sequence alignment... |
rphast | RPHAST: R interface to PHAST |
sample.msa | Sample columns from an MSA... |
score.hmm | Score an alignment using a general phylo-HMM |
simulate.msa | Simulate a MSA given a tree model and HMM. |
smooth.wig | Smooth a wig plot in rphast... |
sort.feat | Sort a GFF... |
split.by.feature.msa | Split an MSA by feature... |
split.feat | Split features by length... |
strip.gaps.msa | MSA Strip Gaps |
sub.msa | MSA Subset |
subst.mods | List PHAST Substitution Models |
subtree | Subtree |
summary.feat | Features Summary |
summary.msa | MSA Summary |
summary.tm | Tree Model Summary |
tagval | Extract value from tag-value formatted attributes... |
tagval.feat | Extract value from tag-value formatted attribute in features object... |
tm | Tree Models |
unique.feat | Remove overlapping genes... |
validFormatStr.msa | Check an MSA Format String |
wig.track | Create a wig track... |
write.feat | Writing a features Object |
write.hmm | Write an HMM object to a file... |
write.msa | Writing MSA Objects to Files |
write.tm | Wrting Tree Models |
[.msa | Extract, replace, reorder MSA... |