Files in HajkD/LTRpred

De novo functional annotation of retrotransposons

.Rbuildignore

DESCRIPTION

Dockerfile

LICENSE

NAMESPACE

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

Sc_LTRpred.png

docs/.DS_Store

docs/404.html

docs/LICENSE-text.html

docs/articles/Introduction.html

docs/articles/Introduction_files/accessible-code-block-0.0.1/empty-anchor.js

docs/articles/Introduction_files/header-attrs-2.11/header-attrs.js

docs/articles/LTRfeatures.png

docs/articles/index.html

docs/authors.html

docs/bootstrap-toc.css

docs/bootstrap-toc.js

docs/docsearch.css

docs/docsearch.js

docs/index.html

docs/inst/LTRpred_logo.png

docs/jquery.sticky-kit.min.js

docs/link.svg

docs/paper.html

docs/pkgdown.css

docs/pkgdown.js

docs/pkgdown.yml

docs/reference/AllPairwiseAlign.html

docs/reference/CLUSTpred.html

docs/reference/LTRdigest.html

docs/reference/LTRharvest.html

docs/reference/LTRpred.html

docs/reference/LTRpred.meta.html

docs/reference/ORFpred.html

docs/reference/Rplot001.png

docs/reference/SimMatAbundance.html

docs/reference/assign.short.sci.name.html

docs/reference/bcolor.html

docs/reference/check_annotation_ltrpred.html

docs/reference/chromoMapChromosomeFile.html

docs/reference/clust2fasta.html

docs/reference/cluster.members.html

docs/reference/cn2bed.html

docs/reference/combinePreds.html

docs/reference/dfam.query.html

docs/reference/file.move.html

docs/reference/filter.jumpers.html

docs/reference/filter.uc.html

docs/reference/generate.multi.quality.filter.meta.html

docs/reference/genome.summary.html

docs/reference/get.pred.filenames.html

docs/reference/get.seqs.html

docs/reference/gridPlotAssemblyVersions.html

docs/reference/index.html

docs/reference/join.with.genome.tbl.html

docs/reference/ltr.cn.html

docs/reference/ltr_age_estimation.html

docs/reference/meta.apply.html

docs/reference/meta.seq.space.html

docs/reference/meta.summarize.html

docs/reference/motif.count.html

docs/reference/output

docs/reference/output.csv

docs/reference/plotCN.html

docs/reference/plotChromoMap.html

docs/reference/plotCluster.html

docs/reference/plotDomain-1.png

docs/reference/plotDomain.html

docs/reference/plotFamily-1.png

docs/reference/plotFamily.html

docs/reference/plotInterSpeciesCluster.html

docs/reference/plotLTRRange.html

docs/reference/plotLTRSim.html

docs/reference/plotLTRSpace.html

docs/reference/plotMainInterSpeciesCluster.html

docs/reference/plotProteinSpace.html

docs/reference/plotRanges.html

docs/reference/plotRepeatSpace.html

docs/reference/plotRepeatSpaceCval.html

docs/reference/plotSimCount.html

docs/reference/plotSize.html

docs/reference/plotSizeJumpers.html

docs/reference/plotSizeMulti.html

docs/reference/plot_copynumber_individual.html

docs/reference/plot_copynumber_kingdom.html

docs/reference/plot_copynumber_species.html

docs/reference/plot_element_distr_along_chromosome.html

docs/reference/plot_ltrwidth_individual.html

docs/reference/plot_ltrwidth_kingdom.html

docs/reference/plot_ltrwidth_species.html

docs/reference/plot_pbswidth_kingdom.html

docs/reference/pred2GRanges.html

docs/reference/pred2bed.html

docs/reference/pred2chromoMap.html

docs/reference/pred2csv.html

docs/reference/pred2fasta.html

docs/reference/pred2gff.html

docs/reference/pred2orfseqs.html

docs/reference/pred2tsv.html

docs/reference/quality.filter.html

docs/reference/quality.filter.meta.html

docs/reference/quant.cds.space.html

docs/reference/quant.protein.space.html

docs/reference/quant.repeat.space.html

docs/reference/quant.space.meta.html

docs/reference/read.blast6out.html

docs/reference/read.dfam.html

docs/reference/read.ltrpred.html

docs/reference/read.orfs.html

docs/reference/read.prediction.html

docs/reference/read.seqs.html

docs/reference/read.tabout.html

docs/reference/read.uc.html

docs/reference/rename.fasta.html

docs/reference/rename.fasta.meta.html

docs/reference/rename.organisms.html

docs/reference/repbase.clean.html

docs/reference/repbase.filter.html

docs/reference/repbase.query.html

docs/reference/test.gff

docs/reference/tidy.datasheet.html

docs/reference/totalRepeatSpace.html

docs/reference/ws.wrap.path.html

inst/Athaliana_TAIR10_chr_all_LTRpred_DataSheet.csv

inst/GenomeMatrix.csv

inst/HMMs/hmm_Gypsy.hmm

inst/HMMs/hmm_IN_DBD_C.hmm

inst/HMMs/hmm_Integrase_Zn.hmm

inst/HMMs/hmm_RNase_H.hmm

inst/HMMs/hmm_RVT_1.hmm

inst/HMMs/hmm_RVT_2.hmm

inst/HMMs/hmm_RdRP_1.hmm

inst/HMMs/hmm_RdRP_2.hmm

inst/HMMs/hmm_RdRP_3.hmm

inst/HMMs/hmm_RdRP_4.hmm

inst/HMMs/hmm_TLV_coat.hmm

inst/HMMs/hmm_retrotrans_gag.hmm

inst/HMMs/hmm_rve.hmm

inst/Hsapiens_ChrY-ltrdigest_3ltr.fas

inst/Hsapiens_ChrY-ltrdigest_5ltr.fas

inst/Hsapiens_ChrY.fa

inst/Hsapiens_ChrY_LTRpred_DataSheet.tsv

inst/LTRpred_logo.png

inst/LTRseqs.fas

inst/SimMatrix.csv

inst/TAIR10_chr_all-ltrdigest_tabout.csv

inst/TAIR10_chr_all_LTRdigestPrediction.gff

inst/example_dfam.out

inst/hg38-tRNAs.fa

inst/nt.fa

inst/tRNAs/eukaryotic-tRNAs.fa

inst/tRNAs/hg38-tRNAs.fa

inst/tRNAs/plants-tRNA_cat.fa

inst/tRNAs/sacCer3-tRNAs.fa

inst/tRNAs/tRNA_library.fa

inst/test.blast6out

inst/test.uc

man/AllPairwiseAlign.Rd man/CLUSTpred.Rd man/LTRdigest.Rd man/LTRharvest.Rd man/LTRpred.Rd man/LTRpred.meta.Rd man/ORFpred.Rd man/SimMatAbundance.Rd man/assign.short.sci.name.Rd man/bcolor.Rd man/clust2fasta.Rd man/cluster.members.Rd man/cn2bed.Rd man/combinePreds.Rd man/dfam.query.Rd man/file.move.Rd man/filter.jumpers.Rd man/filter.uc.Rd man/generate.multi.quality.filter.meta.Rd man/genome.summary.Rd man/get.pred.filenames.Rd man/get.seqs.Rd man/gridPlotAssemblyVersions.Rd man/join.with.genome.tbl.Rd man/ltr.cn.Rd man/ltr_age_estimation.Rd man/meta.apply.Rd man/meta.seq.space.Rd man/meta.summarize.Rd man/motif.count.Rd man/plotLTRSim.Rd man/plot_element_distr_along_chromosome.Rd man/pred2GRanges.Rd man/pred2bed.Rd man/pred2csv.Rd man/pred2fasta.Rd man/pred2gff.Rd man/pred2orfseqs.Rd man/pred2tsv.Rd man/quality.filter.Rd man/quality.filter.meta.Rd man/quant.cds.space.Rd man/quant.protein.space.Rd man/quant.repeat.space.Rd man/quant.space.meta.Rd man/read.blast6out.Rd man/read.dfam.Rd man/read.ltrpred.Rd man/read.orfs.Rd man/read.prediction.Rd man/read.seqs.Rd man/read.tabout.Rd man/read.uc.Rd man/rename.fasta.Rd man/rename.fasta.meta.Rd man/rename.organisms.Rd man/repbase.clean.Rd man/repbase.filter.Rd man/repbase.query.Rd man/tidy.datasheet.Rd man/totalRepeatSpace.Rd man/ws.wrap.path.Rd

paper.bib

paper.md tests/testthat.R tests/testthat/test-read.blast6out.R vignettes/Introduction.Rmd

vignettes/LTRfeatures.png

HajkD/LTRpred documentation built on April 22, 2022, 4:35 p.m.