API for HajkD/LTRpred
De novo functional annotation of retrotransposons

Global functions
AlignmentMatrix	Source code
AllPairwiseAlign	Man page Source code
CLUSTpred	Man page Source code
LTRdigest	Man page Source code
LTRharvest	Man page Source code
LTRpred	Man page Source code
LTRpred.meta	Man page Source code
NW.Align	Source code
ORFpred	Man page Source code
SimMatAbundance	Man page Source code
assign.short.sci.name	Man page Source code
bcolor	Man page Source code
clust2fasta	Man page Source code
cluster.members	Man page Source code
cn2bed	Man page Source code
combinePreds	Man page Source code
customColors	Source code
dfam.query	Man page Source code
file.check	Source code
file.move	Man page Source code
filter.jumpers	Man page Source code
filter.uc	Man page Source code
generate.multi.quality.filter.meta	Man page Source code
genome.summary	Man page Source code
get.pred.filenames	Man page Source code
get.seqs	Man page Source code
gridPlotAssemblyVersions	Man page Source code
join.with.genome.tbl	Man page Source code
ltr.cn	Man page Source code
ltr_age_estimation	Man page Source code
meta.apply	Man page Source code
meta.seq.space	Man page Source code
meta.summarize	Man page Source code
motif.count	Man page Source code
pairwise.wilcox.test	Source code
pairwise.z.test	Source code
plotLTRSim	Man page Source code
plot_element_distr_along_chromosome	Man page Source code
pred2GRanges	Man page Source code
pred2bed	Man page Source code
pred2csv	Man page Source code
pred2fasta	Man page Source code
pred2gff	Man page Source code
pred2orfseqs	Man page Source code
pred2tsv	Man page Source code
quality.filter	Man page Source code
quality.filter.meta	Man page Source code
quant.cds.space	Man page Source code
quant.protein.space	Man page Source code
quant.repeat.space	Man page Source code
quant.space.meta	Man page Source code
read.blast6out	Man page Source code
read.dfam	Man page Source code
read.ltrpred	Man page Source code
read.orfs	Man page Source code
read.prediction	Man page Source code
read.seqs	Man page Source code
read.tabout	Man page Source code
read.uc	Man page Source code
rename.fasta	Man page Source code
rename.fasta.meta	Man page Source code
rename.organisms	Man page Source code
repbase.clean	Man page Source code
repbase.filter	Man page Source code
repbase.query	Man page Source code
str_chop_vec	Source code
superfamilyDistr	Source code
test_installation_blast	Source code
test_installation_gt	Source code
test_installation_hmmer	Source code
test_installation_perl	Source code
test_installation_usearch	Source code
test_installation_vsearch	Source code
tidy.datasheet	Man page Source code
totalRepeatSpace	Man page Source code
ws.wrap.path	Man page Source code