aggregateAlignment | Generate summaries on sliding windows over an alignment. |
alignment2Genome | Map alignment positions to genomic positions. |
alignSegments | Align orthologous genome segments with 'fsa' |
aln2map | [INTERNAL] Map a alignment ranges to genomes |
anchors | Access anchor files |
annotatedAlignment | Construct an 'annotatedAlignment'. |
annotatedAlignment-class | Construct an 'annotatedAlignment'. |
annotationList-class | Construct an "annotationList". |
file_size | Quickly look up the size of a file |
findAnnotation | Find annotation associated with alignment positions. |
fsa | Sequence alignment with fsa |
genome2Alignment | Map genomic positions to alignment positions. |
genome2Genome | Map genomic positions in one genome to genomic positions in... |
genoslideR | Genome Alignments and Annotation. |
glimmer3 | Ab initio genome annotation using glimmer3 |
has_command | Test if an external executable is available |
importAlignment | Import a genome alignment |
importAnnotation | Import annotation information into 'GRanges'. |
install_genoslider_dependencies | Install external dependencies for genoslideR |
labels | Access labels |
linebreak | Format paragraphs |
make_tree | [INTERNAL] conctruct NJ or BIONJ tree from one or more... |
map2aln | [INTERNAL] Map a genomic range to the alignment |
maskSequence | Softmask repeats and low-complexity regions using RepeatScout... |
mercator | Run mercator to build a homology map and create orthologous... |
mergeOrthologyMatrix | Merge a list of pairwise orthology matrices into an... |
minimum | INTERNAL: Map a genomic range to the alignment |
ncbi_bacteria | Retrieve bacterial genomes from NCBI FTP site |
orthologyMatrix | Construct orthology matrices |
plot.OrthoMatrix | Plot an orthology matrix |
rbh | Find Reciprocal Best Hits using Blat |
sliceAlignment | Slice genomic ranges from an alignment. |
sliceGR | [INTERNAL] Slice GRanges from an alignment |
sliceGRL | [INTERNAL] Slice GRangesList from an alignment |
strip_ext | Strip file extensions |
substituteCDSNumbers | Replace CDS indices in an oframe by the corresponding... |
SysCall | Wrapper for system commands |
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