API for gschofl/genoslideR
Create and manipulate multiple genome alignments with annotation.

Global functions
Call Source code
Compose Source code
Eta Source code
Partial Source code
SysCall Man page Source code
aggregateAlignment Man page Source code
aggregateRanges Source code
alignSegmentDir Source code
alignSegments Man page Source code
alignment2Genome Man page Source code
aln2map Man page Source code Source code
anchors Man page Source code
anchors.OrthoFrame Source code
annotatedAlignment Man page Source code
annotatedAlignment-class Man page
annotationList Source code
annotationList-class Man page
are_empty Source code
are_false Source code
are_null Source code
are_true Source code
blat2hits Source code
blat_add_query_length Source code
build_icm Source code
capitalize Source code
check_conflicts Source code
collapse_duplicates Source code
collapse_slices Source code
compact Source code
compactNA Source code
count_lines Source code
create.GRanges Source code
create_if_not_exists Source code
dup Source code
ellipsize Source code
escape Source code
extract Source code
extract_attr Source code
extract_upstream Source code
file_size Man page Source code
findAnnotation Man page Source code
find_breakpoints Source code
find_gaps Source code
fna2fna Source code
fna_for_mercator Source code
fsa Man page Source code
fsaAlignSegmentDirs Source code
ftb2gff Source code
gbk2fna Source code
gbk2gff Source code
genome2Alignment Man page Source code
genome2Genome Man page Source code
genoslideR Man page
genoslideR-package Man page
get_alignment_gaps Source code
get_attr Source code
get_duplicate Source code
get_position_from_gff Source code
gff2anchors Source code
gff2gff Source code
gff_for_mercator Source code
glimmer Source code
glimmer2gff Source code
glimmer3 Man page Source code
guide_tree Source code
has_command Man page Source code
has_dependencies Source code
header2map Source code
importAlignment Man page Source code
importAnnotation Man page Source code
import_annotation_from_ftb Source code
import_annotation_from_genbank Source code
import_annotation_from_gff Source code
import_annotation_from_ptt Source code
import_annotation_from_table Source code
install_genoslider_dependencies Man page Source code
interval Source code
intervals_overlap Source code
is.empty Source code
is_fasta Source code
is_gbk Source code
is_maf Source code
is_mapped_alignment Source code
is_mfa Source code
is_segments_dir Source code
is_sliced_alignment Source code
labeledLine Source code
labels Man page Source code
labels.OrthoFrame Source code
labels<- Man page
linebreak Man page Source code
longorfs Source code
make_gapped_ranges Source code
make_tree Man page Source code
make_ungapped_ranges Source code
map2aln Man page Source code
map2header Source code
map2range Source code
map_max Source code
map_min Source code
maskSequence Man page Source code
match_genes Source code
maximum Source code
mercator Man page Source code
mergeOrthologyMatrix Man page Source code
merge_all Source code
merge_duplicate Source code
merge_hsps Source code
merge_list Source code
merge_mercator_segments Source code
merge_segments Source code
minimum Man page Source code
narrowAlignment Source code
narrowAlnrange Source code
ncbi_bacteria Man page Source code
newAnnotationList Source code
orthoList Source code
orthologyMatrix Man page Source code
pad Source code
pairwiseCombine Source code
parse_attr Source code
plot.OrthoMatrix Man page Source code
print.OrthoFrame Source code
ptt2gff Source code
pwm Source code
rbh Man page Source code
readMAF Source code
reciprocal_blat Source code
repeatmasker Source code
replace_ext Source code
run_glimmer Source code
run_mercator Source code
segments_dir Source code
selectSome Source code
show_AnnotationList Source code
slice Source code
sliceAlignment Man page Source code
sliceGR Man page Source code
sliceGRL Man page Source code
slidingWindows Source code
strip_ext Man page Source code
strsplitN Source code
subl Source code
substituteCDSNumbers Man page Source code
sw Source code
trim Source code
unescape Source code
ungap_alignment_position Source code
update_alignment_position_cpp Source code
update_genomic_position_cpp Source code
update_position Source code
venn_groups Source code
gschofl/genoslideR documentation built on May 14, 2017, 4:11 p.m.