Files in coripenrod/MAGNAMWAR
A Pipeline for Meta-Genome Wide Association
.Rbuildignore
.gitignore
.travis.yml
DESCRIPTION
LICENSE
MAGNAMWAR.Rproj
NAMESPACE
NEWS.md
R/AnalyzeOrthoMCL.R
R/CalculatePrincipalCoordinates.R
R/FormatAfterOrtho.R
R/FormatMCLFastas.R
R/JoinRepSeq.R
R/PrintOGSeqs.R
R/RASTtogbk.R
R/SurvAppendMatrix.R
R/WriteMCL.R
R/doc.R
R/graphics.R
README.md
cran-comments.md
data/after_ortho_format.rda
data/after_ortho_format_grps.rda
data/joined_mtrx.rda
data/joined_mtrx_grps.rda
data/mcl_mtrx.rda
data/mcl_mtrx_grps.rda
data/pheno_data.rda
data/starv_pheno_data.rda
inst/extdata/RASTtoGBK/lfrc.fasta
inst/extdata/RASTtoGBK/lfrc_lookup.csv
inst/extdata/RASTtoGBK/lfrc_out.fasta
inst/extdata/fasta_dir/MCLformatted_all.fasta
inst/extdata/fasta_dir/aace.fasta
inst/extdata/fasta_dir/apap.fasta
inst/extdata/fasta_dir/apas.fasta
inst/extdata/fasta_dir/atro.fasta
inst/extdata/fasta_dir/bsub.fasta
inst/extdata/fasta_dir/dmos.fasta
inst/extdata/fasta_dir/ecol.fasta
inst/extdata/fasta_dir/efao.fasta
inst/extdata/fasta_dir/efav.fasta
inst/extdata/fasta_dir/ehor.fasta
inst/extdata/fasta_dir/geur.fasta
inst/extdata/fasta_dir/geur.fasta~
inst/extdata/fasta_dir/gfra.fasta
inst/extdata/fasta_dir/ghan.fasta
inst/extdata/fasta_dir/ghan.fasta~
inst/extdata/fasta_dir/gobo.fasta
inst/extdata/fasta_dir/gxyl.fasta
inst/extdata/fasta_dir/lani.fasta
inst/extdata/fasta_dir/lbre.fasta
inst/extdata/fasta_dir/lbuc.fasta
inst/extdata/fasta_dir/lcas.fasta
inst/extdata/fasta_dir/lfal.fasta
inst/extdata/fasta_dir/lfer.fasta
inst/extdata/fasta_dir/lfru.fasta
inst/extdata/fasta_dir/lgas.fasta
inst/extdata/fasta_dir/llac.fasta
inst/extdata/fasta_dir/lmai.fasta
inst/extdata/fasta_dir/lmal.fasta
inst/extdata/fasta_dir/lpla.fasta
inst/extdata/fasta_dir/lrha.fasta
inst/extdata/fasta_dir/lver.fasta
inst/extdata/fasta_dir/pbur.fasta
inst/extdata/fasta_dir/pput.fasta
inst/extdata/fasta_dir/smar.fasta
inst/extdata/fasta_dir/smut.fasta
inst/extdata/fasta_dir/spar.fasta
inst/extdata/fasta_dir/swit.fasta
inst/extdata/groups_example_r.txt
inst/extdata/matrix.csv
inst/extdata/muscle_tree2.dnd
inst/extdata/orthologGroups.txt
inst/extdata/outputs/OG5_126801data.csv
inst/extdata/outputs/OG5_126968data.csv
inst/extdata/outputs/OG5_127007data.csv
inst/extdata/outputs/OG5_127151data.csv
inst/extdata/outputs/OG5_127267data.csv
inst/extdata/outputs/OG5_127532data.csv
inst/extdata/outputs/OG5_130166data.csv
inst/extdata/outputs/OG5_130794data.csv
inst/extdata/outputs/OG5_131047data.csv
inst/extdata/outputs/OG5_131512data.csv
inst/extdata/outputs/OG5_132018data.csv
inst/extdata/outputs/OG5_136502data.csv
inst/extdata/outputs/OG5_138794data.csv
inst/extdata/outputs/OG5_163100data.csv
inst/extdata/outputs/OG5_164941data.csv
man/.Rapp.history
man/AnalyzeOrthoMCL.Rd
man/CalculatePrincipalCoordinates.Rd
man/FormatAfterOrtho.Rd
man/FormatMCLFastas.Rd
man/JoinRepSeq.Rd
man/ManhatGrp.Rd
man/PDGvOG.Rd
man/RASTtogbk.Rd
man/SurvAppendMatrix.Rd
man/WriteMCL.Rd
man/after_ortho_format.Rd
man/after_ortho_format_grps.Rd
man/joined_mtrx.Rd
man/joined_mtrx_grps.Rd
man/mcl_mtrx.Rd
man/mcl_mtrx_grps.Rd
man/pdgplot.Rd
man/pheno_data.Rd
man/phydataerror.Rd
man/printOGseqs.Rd
man/qqplotter.Rd
man/starv_pheno_data.Rd
revdep/README.md
revdep/check.R
revdep/checks.rds
revdep/problems.md
vignettes/using_mag.R
vignettes/using_mag.Rmd
