API for HajkD/LTRpred
De novo annotation of potentially active LTR 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
PlotRanges2 Source code
PlotRangesLTRharvestPrediction2 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
plotCN Man page Source code
plotCluster Man page Source code
plotDomain Man page Source code
plotFamily Man page Source code
plotInterSpeciesCluster Man page Source code
plotLTRRange Man page Source code
plotLTRSim Man page Source code
plotLTRSpace Man page Source code
plotMainInterSpeciesCluster Man page Source code
plotProteinSpace Man page Source code
plotRanges Man page Source code
plotRepeatSpace Man page Source code
plotRepeatSpaceCval Man page Source code
plotSimCount Man page Source code
plotSize Man page Source code
plotSizeJumpers Man page Source code
plotSizeMulti Man page Source code
plot_copynumber_individual Man page Source code
plot_copynumber_kingdom Man page Source code
plot_copynumber_species Man page Source code
plot_ltrwidth_individual Man page Source code
plot_ltrwidth_kingdom Man page Source code
plot_ltrwidth_species Man page Source code
plot_pbswidth_kingdom Man page Source code
pred2bed Man page Source code
pred2csv Man page Source code
pred2fasta Man page Source code
pred2gff 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
HajkD/LTRpred documentation built on Oct. 20, 2018, 12:39 a.m.