Files in almeidasilvaf/syntenet
Inference And Analysis Of Synteny Networks
.Rbuildignore
.github/.gitignore
.github/CODE_OF_CONDUCT.md
.github/ISSUE_TEMPLATE/issue_template.md
.github/SUPPORT.md
.github/workflows/check-bioc.yml
.gitignore
DESCRIPTION
NAMESPACE
NEWS.md
R/01_data_import.R
R/02_data_preprocessing.R
R/03_similarity_searches.R
R/04_synteny_detection.R
R/05_phylogenomic_profiling.R
R/06_dataviz.R
R/07_microsynteny-based_phylogeny.R
R/RcppExports.R
R/catch-routine-registration.R
R/data.R
R/syntenet-package.R
R/utils.R
R/utils_synteny.R
README.Rmd
README.md
codecov.yml
data/angiosperm_phylogeny.rda
data/annotation.rda
data/blast_list.rda
data/clusters.rda
data/edges.rda
data/network.rda
data/proteomes.rda
data/scerevisiae_annot.rda
data/scerevisiae_diamond.rda
dev/01_create_pkg.R
dev/02_git_github_setup.R
dev/03_core_files.R
dev/04_update.R
inst/CITATION
inst/_pkgdown.yml
inst/extdata/Osp_Osp.tsv
inst/extdata/RefSeq_parsing_example/Aalosa.fa.gz
inst/extdata/RefSeq_parsing_example/Aalosa.gff3.gz
inst/extdata/Scerevisiae.collinearity
inst/extdata/annotation/Olucimarinus.gff3.gz
inst/extdata/annotation/OspRCC809.gff3.gz
inst/extdata/sequences/Olucimarinus.fa.gz
inst/extdata/sequences/OspRCC809.fa.gz
inst/script/data_acquisition.md
man/angiosperm_phylogeny.Rd
man/annotation.Rd
man/binarize_and_transpose.Rd
man/blast_list.Rd
man/check_input.Rd
man/cluster_network.Rd
man/clusters.Rd
man/collapse_protein_ids.Rd
man/create_species_id_table.Rd
man/diamond_is_installed.Rd
man/edges.Rd
man/export_sequences.Rd
man/fasta2AAStringSetlist.Rd
man/figures/logo.png
man/find_GS_clusters.Rd
man/gff2GRangesList.Rd
man/infer_microsynteny_phylogeny.Rd
man/infer_syntenet.Rd
man/interspecies_synteny.Rd
man/intraspecies_synteny.Rd
man/iqtree_is_installed.Rd
man/iqtree_version.Rd
man/last_is_installed.Rd
man/network.Rd
man/parse_collinearity.Rd
man/phylogenomic_profile.Rd
man/plot_network.Rd
man/plot_profiles.Rd
man/process_input.Rd
man/profiles2phylip.Rd
man/proteomes.Rd
man/rcpp_mcscanx_file.Rd
man/read_diamond.Rd
man/run_diamond.Rd
man/run_last.Rd
man/scerevisiae_annot.Rd
man/scerevisiae_diamond.Rd
man/syntenet-package.Rd
src/RcppExports.cpp
src/mcscanxr.cpp
src/mcscanxr.h
src/test-runner.cpp
tests/testthat.R
tests/testthat/test-01_data_import.R
tests/testthat/test-02_data_preprocessing.R
tests/testthat/test-03_synteny_detection.R
tests/testthat/test-04_phylogenomic_profiling.R
tests/testthat/test-05_dataviz.R
tests/testthat/test-06_microsynteny-based_phylogeny.R
tests/testthat/test-cpp.R
tests/testthat/test-similarity_searches.R
tests/testthat/test-utils.R
vignettes/.gitignore
vignettes/syntenet.Rmd
vignettes/vignette_bibliography.bib
