Files in gogleva/SecretSanta

flexible pipelines for secretome prediction

.Rbuildignore

.gitattributes

.gitignore

.travis.yml

CONDUCT.md

DESCRIPTION

NAMESPACE

NEWS

R/ask_uniprot.R R/check_khdel.R R/external_imports.R R/helper_functions.R R/m_slicer.R R/manage_paths.R R/objects.R R/parse_signalp.R R/signalp_parallel.R R/targetp_parallel.R R/tmhmm.R R/topcons.R R/wolfpsort.R README.md

SecretSanta.Rproj

index.md

inst/extdata/er_prot.fasta

inst/extdata/multiple_seqs/query.fasta

inst/extdata/multiple_seqs/seq_0/DG1.txt

inst/extdata/multiple_seqs/seq_0/Homology/query.fa.total_aligns

inst/extdata/multiple_seqs/seq_0/Homology/query.top

inst/extdata/multiple_seqs/seq_0/OCTOPUS/NN_PRF_FILES/query.prf

inst/extdata/multiple_seqs/seq_0/OCTOPUS/query.top

inst/extdata/multiple_seqs/seq_0/PolyPhobius/query.top

inst/extdata/multiple_seqs/seq_0/SCAMPI_MSA/query.top

inst/extdata/multiple_seqs/seq_0/SPOCTOPUS/NN_PRF_FILES/query.nnprf

inst/extdata/multiple_seqs/seq_0/SPOCTOPUS/query.top

inst/extdata/multiple_seqs/seq_0/Topcons/reliability.final

inst/extdata/multiple_seqs/seq_0/Topcons/reliability.txt

inst/extdata/multiple_seqs/seq_0/Topcons/topcons.gnu

inst/extdata/multiple_seqs/seq_0/Topcons/topcons.large.png

inst/extdata/multiple_seqs/seq_0/Topcons/topcons.png

inst/extdata/multiple_seqs/seq_0/Topcons/topcons.top

inst/extdata/multiple_seqs/seq_0/Topcons/total_image.gnu

inst/extdata/multiple_seqs/seq_0/Topcons/total_image.large.png

inst/extdata/multiple_seqs/seq_0/Topcons/total_image.png

inst/extdata/multiple_seqs/seq_0/dg.txt

inst/extdata/multiple_seqs/seq_0/nicetop.html

inst/extdata/multiple_seqs/seq_0/philius/query.top

inst/extdata/multiple_seqs/seq_0/seq.fa

inst/extdata/multiple_seqs/seq_1/DG1.txt

inst/extdata/multiple_seqs/seq_1/Homology/query.fa.total_aligns

inst/extdata/multiple_seqs/seq_1/Homology/query.top

inst/extdata/multiple_seqs/seq_1/OCTOPUS/NN_PRF_FILES/query.prf

inst/extdata/multiple_seqs/seq_1/OCTOPUS/query.top

inst/extdata/multiple_seqs/seq_1/PolyPhobius/query.top

inst/extdata/multiple_seqs/seq_1/SCAMPI_MSA/query.top

inst/extdata/multiple_seqs/seq_1/SPOCTOPUS/NN_PRF_FILES/query.nnprf

inst/extdata/multiple_seqs/seq_1/SPOCTOPUS/query.top

inst/extdata/multiple_seqs/seq_1/Topcons/reliability.final

inst/extdata/multiple_seqs/seq_1/Topcons/reliability.txt

inst/extdata/multiple_seqs/seq_1/Topcons/topcons.gnu

inst/extdata/multiple_seqs/seq_1/Topcons/topcons.large.png

inst/extdata/multiple_seqs/seq_1/Topcons/topcons.png

inst/extdata/multiple_seqs/seq_1/Topcons/topcons.top

inst/extdata/multiple_seqs/seq_1/Topcons/total_image.gnu

inst/extdata/multiple_seqs/seq_1/Topcons/total_image.large.png

inst/extdata/multiple_seqs/seq_1/Topcons/total_image.png

inst/extdata/multiple_seqs/seq_1/dg.txt

inst/extdata/multiple_seqs/seq_1/nicetop.html

inst/extdata/multiple_seqs/seq_1/philius/query.top

inst/extdata/multiple_seqs/seq_1/seq.fa

inst/extdata/multiple_seqs/seq_2/DG1.txt

inst/extdata/multiple_seqs/seq_2/Homology/query.fa.total_aligns

inst/extdata/multiple_seqs/seq_2/Homology/query.top

inst/extdata/multiple_seqs/seq_2/OCTOPUS/NN_PRF_FILES/query.prf

inst/extdata/multiple_seqs/seq_2/OCTOPUS/query.top

inst/extdata/multiple_seqs/seq_2/PolyPhobius/query.top

inst/extdata/multiple_seqs/seq_2/SCAMPI_MSA/query.top

inst/extdata/multiple_seqs/seq_2/SPOCTOPUS/NN_PRF_FILES/query.nnprf

inst/extdata/multiple_seqs/seq_2/SPOCTOPUS/query.top

inst/extdata/multiple_seqs/seq_2/Topcons/reliability.final

inst/extdata/multiple_seqs/seq_2/Topcons/reliability.txt

inst/extdata/multiple_seqs/seq_2/Topcons/topcons.gnu

inst/extdata/multiple_seqs/seq_2/Topcons/topcons.large.png

inst/extdata/multiple_seqs/seq_2/Topcons/topcons.png

inst/extdata/multiple_seqs/seq_2/Topcons/topcons.top

inst/extdata/multiple_seqs/seq_2/Topcons/total_image.gnu

inst/extdata/multiple_seqs/seq_2/Topcons/total_image.large.png

inst/extdata/multiple_seqs/seq_2/Topcons/total_image.png

inst/extdata/multiple_seqs/seq_2/dg.txt

inst/extdata/multiple_seqs/seq_2/nicetop.html

inst/extdata/multiple_seqs/seq_2/philius/query.top

inst/extdata/multiple_seqs/seq_2/seq.fa

inst/extdata/multiple_seqs/seq_3/DG1.txt

inst/extdata/multiple_seqs/seq_3/Homology/query.fa.total_aligns

inst/extdata/multiple_seqs/seq_3/Homology/query.top

inst/extdata/multiple_seqs/seq_3/OCTOPUS/NN_PRF_FILES/query.prf

inst/extdata/multiple_seqs/seq_3/OCTOPUS/query.top

inst/extdata/multiple_seqs/seq_3/PolyPhobius/query.top

inst/extdata/multiple_seqs/seq_3/SCAMPI_MSA/query.top

inst/extdata/multiple_seqs/seq_3/SPOCTOPUS/NN_PRF_FILES/query.nnprf

inst/extdata/multiple_seqs/seq_3/SPOCTOPUS/query.top

inst/extdata/multiple_seqs/seq_3/Topcons/reliability.final

inst/extdata/multiple_seqs/seq_3/Topcons/reliability.txt

inst/extdata/multiple_seqs/seq_3/Topcons/topcons.gnu

inst/extdata/multiple_seqs/seq_3/Topcons/topcons.large.png

inst/extdata/multiple_seqs/seq_3/Topcons/topcons.png

inst/extdata/multiple_seqs/seq_3/Topcons/topcons.top

inst/extdata/multiple_seqs/seq_3/Topcons/total_image.gnu

inst/extdata/multiple_seqs/seq_3/Topcons/total_image.large.png

inst/extdata/multiple_seqs/seq_3/Topcons/total_image.png

inst/extdata/multiple_seqs/seq_3/dg.txt

inst/extdata/multiple_seqs/seq_3/nicetop.html

inst/extdata/multiple_seqs/seq_3/philius/query.top

inst/extdata/multiple_seqs/seq_3/seq.fa

inst/extdata/multiple_seqs/time.txt

inst/extdata/rst_7gaVh2.zip

inst/extdata/rst_SVw4hG.zip

inst/extdata/sample_dna.fasta

inst/extdata/sample_paths

inst/extdata/sample_prot_100.fasta

inst/extdata/sample_prot_signalp2_out2

inst/extdata/sample_prot_sp2_hmm_out

inst/extdata/sample_prot_sp2_nn_out

inst/extdata/sample_prot_sp3_hmm_out

inst/extdata/sample_prot_sp3_nn_out

inst/extdata/santa_paths

inst/extdata/small_prot.fasta

inst/extdata/summary_tools.csv

inst/extdata/tail2_prot.fasta

inst/extdata/tail_prot.fasta

man/CBS_methods.Rd man/ErResult_methods.Rd man/SecretSanta_man.Rd man/SignalpResult_methods.Rd man/TMhmmResult_methods.Rd man/TargetpResult_methods.Rd man/TopconsResult_methods.Rd man/WolfResult_methods.Rd man/ask_uniprot.Rd man/check_khdel.Rd man/combine_SpResult.Rd man/combine_TpResult.Rd man/crop_names.Rd man/estimate_lim.Rd man/m_slicer.Rd man/manage_paths.Rd man/parse_signalp.Rd man/signalp.Rd man/split_XStringSet.Rd man/targetp.Rd man/tmhmm.Rd man/topcons.Rd man/truncate_seq.Rd man/wolfpsort.Rd tests/testthat.R tests/testthat/test_ask_uniprot.R tests/testthat/test_check_khdel.R tests/testthat/test_m_slicer.R tests/testthat/test_manage_paths.R tests/testthat/test_parallel_helpers.R tests/testthat/test_parse_signalp.R tests/testthat/test_piping.R tests/testthat/test_run_signalp.R tests/testthat/test_run_targetp.R tests/testthat/test_run_tmhmm.R tests/testthat/test_topcons.R tests/testthat/test_wolfpsort.R

vignettes/Santa.bib

vignettes/Santa_hexagon.png

vignettes/SecretSanta-vignette.Rmd

vignettes/SecretSanta-vignette.html

vignettes/bioinformatics.csl

vignettes/biomed-central.csl

vignettes/class_structure.png

vignettes/motifs_and_domains.png

vignettes/pipes_long.png

vignettes/pipes_short.png

vignettes/secretome_out.fasta

vignettes/sp_out.fasta

gogleva/SecretSanta documentation built on May 30, 2019, 8:02 a.m.