├── .Rbuildignore ├── .gitattributes ├── .gitignore ├── .travis.yml ├── CONDUCT.md ├── DESCRIPTION ├── NAMESPACE ├── NEWS ├── R ├── ask_uniprot.R ├── check_khdel.R ├── external_imports.R ├── helper_functions.R ├── m_slicer.R ├── manage_paths.R ├── objects.R ├── parse_signalp.R ├── signalp_parallel.R ├── targetp_parallel.R ├── tmhmm.R ├── topcons.R └── wolfpsort.R ├── README.md ├── SecretSanta.Rproj ├── index.md ├── inst └── extdata │ ├── er_prot.fasta │ ├── multiple_seqs │ ├── query.fasta │ ├── seq_0 │ │ ├── DG1.txt │ │ ├── Homology │ │ │ ├── query.fa.total_aligns │ │ │ └── query.top │ │ ├── OCTOPUS │ │ │ ├── NN_PRF_FILES │ │ │ │ └── query.prf │ │ │ └── query.top │ │ ├── PolyPhobius │ │ │ └── query.top │ │ ├── SCAMPI_MSA │ │ │ └── query.top │ │ ├── SPOCTOPUS │ │ │ ├── NN_PRF_FILES │ │ │ │ └── query.nnprf │ │ │ └── query.top │ │ ├── Topcons │ │ │ ├── reliability.final │ │ │ ├── reliability.txt │ │ │ ├── topcons.gnu │ │ │ ├── topcons.large.png │ │ │ ├── topcons.png │ │ │ ├── topcons.top │ │ │ ├── total_image.gnu │ │ │ ├── total_image.large.png │ │ │ └── total_image.png │ │ ├── dg.txt │ │ ├── nicetop.html │ │ ├── philius │ │ │ └── query.top │ │ └── seq.fa │ ├── seq_1 │ │ ├── DG1.txt │ │ ├── Homology │ │ │ ├── query.fa.total_aligns │ │ │ └── query.top │ │ ├── OCTOPUS │ │ │ ├── NN_PRF_FILES │ │ │ │ └── query.prf │ │ │ └── query.top │ │ ├── PolyPhobius │ │ │ └── query.top │ │ ├── SCAMPI_MSA │ │ │ └── query.top │ │ ├── SPOCTOPUS │ │ │ ├── NN_PRF_FILES │ │ │ │ └── query.nnprf │ │ │ └── query.top │ │ ├── Topcons │ │ │ ├── reliability.final │ │ │ ├── reliability.txt │ │ │ ├── topcons.gnu │ │ │ ├── topcons.large.png │ │ │ ├── topcons.png │ │ │ ├── topcons.top │ │ │ ├── total_image.gnu │ │ │ ├── total_image.large.png │ │ │ └── total_image.png │ │ ├── dg.txt │ │ ├── nicetop.html │ │ ├── philius │ │ │ └── query.top │ │ └── seq.fa │ ├── seq_2 │ │ ├── DG1.txt │ │ ├── Homology │ │ │ ├── query.fa.total_aligns │ │ │ └── query.top │ │ ├── OCTOPUS │ │ │ ├── NN_PRF_FILES │ │ │ │ └── query.prf │ │ │ └── query.top │ │ ├── PolyPhobius │ │ │ └── query.top │ │ ├── SCAMPI_MSA │ │ │ └── query.top │ │ ├── SPOCTOPUS │ │ │ ├── NN_PRF_FILES │ │ │ │ └── query.nnprf │ │ │ └── query.top │ │ ├── Topcons │ │ │ ├── reliability.final │ │ │ ├── reliability.txt │ │ │ ├── topcons.gnu │ │ │ ├── topcons.large.png │ │ │ ├── topcons.png │ │ │ ├── topcons.top │ │ │ ├── total_image.gnu │ │ │ ├── total_image.large.png │ │ │ └── total_image.png │ │ ├── dg.txt │ │ ├── nicetop.html │ │ ├── philius │ │ │ └── query.top │ │ └── seq.fa │ ├── seq_3 │ │ ├── DG1.txt │ │ ├── Homology │ │ │ ├── query.fa.total_aligns │ │ │ └── query.top │ │ ├── OCTOPUS │ │ │ ├── NN_PRF_FILES │ │ │ │ └── query.prf │ │ │ └── query.top │ │ ├── PolyPhobius │ │ │ └── query.top │ │ ├── SCAMPI_MSA │ │ │ └── query.top │ │ ├── SPOCTOPUS │ │ │ ├── NN_PRF_FILES │ │ │ │ └── query.nnprf │ │ │ └── query.top │ │ ├── Topcons │ │ │ ├── reliability.final │ │ │ ├── reliability.txt │ │ │ ├── topcons.gnu │ │ │ ├── topcons.large.png │ │ │ ├── topcons.png │ │ │ ├── topcons.top │ │ │ ├── total_image.gnu │ │ │ ├── total_image.large.png │ │ │ └── total_image.png │ │ ├── dg.txt │ │ ├── nicetop.html │ │ ├── philius │ │ │ └── query.top │ │ └── seq.fa │ └── time.txt │ ├── rst_7gaVh2.zip │ ├── rst_SVw4hG.zip │ ├── sample_dna.fasta │ ├── sample_paths │ ├── sample_prot_100.fasta │ ├── sample_prot_signalp2_out2 │ ├── sample_prot_sp2_hmm_out │ ├── sample_prot_sp2_nn_out │ ├── sample_prot_sp3_hmm_out │ ├── sample_prot_sp3_nn_out │ ├── santa_paths │ ├── small_prot.fasta │ ├── summary_tools.csv │ ├── tail2_prot.fasta │ └── tail_prot.fasta ├── man ├── CBS_methods.Rd ├── ErResult_methods.Rd ├── SecretSanta_man.Rd ├── SignalpResult_methods.Rd ├── TMhmmResult_methods.Rd ├── TargetpResult_methods.Rd ├── TopconsResult_methods.Rd ├── WolfResult_methods.Rd ├── ask_uniprot.Rd ├── check_khdel.Rd ├── combine_SpResult.Rd ├── combine_TpResult.Rd ├── crop_names.Rd ├── estimate_lim.Rd ├── m_slicer.Rd ├── manage_paths.Rd ├── parse_signalp.Rd ├── signalp.Rd ├── split_XStringSet.Rd ├── targetp.Rd ├── tmhmm.Rd ├── topcons.Rd ├── truncate_seq.Rd └── wolfpsort.Rd ├── tests ├── testthat.R └── testthat │ ├── test_ask_uniprot.R │ ├── test_check_khdel.R │ ├── test_m_slicer.R │ ├── test_manage_paths.R │ ├── test_parallel_helpers.R │ ├── test_parse_signalp.R │ ├── test_piping.R │ ├── test_run_signalp.R │ ├── test_run_targetp.R │ ├── test_run_tmhmm.R │ ├── test_topcons.R │ └── test_wolfpsort.R └── vignettes ├── Santa.bib ├── Santa_hexagon.png ├── SecretSanta-vignette.Rmd ├── SecretSanta-vignette.html ├── bioinformatics.csl ├── biomed-central.csl ├── class_structure.png ├── motifs_and_domains.png ├── pipes_long.png ├── pipes_short.png ├── secretome_out.fasta └── sp_out.fasta /.Rbuildignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gogleva/SecretSanta/HEAD/.Rbuildignore -------------------------------------------------------------------------------- /.gitattributes: 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