Files in felipepratalima/gunga
.Rbuildignore
.gitignore
CentrifugeShSpingoQiime.R
CentrifugeShSpingoQiime.md
CentrifugeShSpingoQiime_files/figure-markdown_github/unnamed-chunk-10-1.png
CentrifugeShSpingoQiime_files/figure-markdown_github/unnamed-chunk-11-1.png
CentrifugeShSpingoQiime_files/figure-markdown_github/unnamed-chunk-12-1.png
CentrifugeShSpingoQiime_files/figure-markdown_github/unnamed-chunk-13-1.png
CentrifugeShSpingoQiime_files/figure-markdown_github/unnamed-chunk-14-1.png
CentrifugeShSpingoQiime_files/figure-markdown_github/unnamed-chunk-15-1.png
CentrifugeShSpingoQiime_files/figure-markdown_github/unnamed-chunk-16-1.png
DESCRIPTION
Ext.ods
NAMESPACE
R/Kraken2.R
R/assignCentrifugeProfileAsMetatranscriptomics.R
R/assignCentrifugeProfileAsShotgun.R
R/assignQiimeProfileAsAmplicons.R
R/assignSpingoProfileAsAmplicons.R
R/clasifyCentrifugeShSpingoAndQiimeGungaProfile.R
R/getMLPerformanceMeasuresForSingleRankAsDataFrame.R
R/getPerformanceMeasuresForSingleRankAsDataFrame.R
R/getStandardIdsDataFrame.R
R/getStandardParentIdsAsDataFrame.R
R/loadRawCentrifugeClassifications.R
R/loadRawCentrifugeProfile.R
R/loadRawMajorityVoteProfile.R
R/loadRawQiimeClassifications.R
R/loadRawQiimeOtuTable.R
R/loadRawQiimeProfile.R
R/loadRawSpingoClassifications.R
R/loadRawSpingoProfile.R
R/makeCentrifugeProfileForMetatranscriptomics.R
R/makeCentrifugeProfileForShotgun.R
R/makeQiimeProfileForAmplicon.R
R/makeSpingoProfileForAmplicon.R
R/mergeProfiles.R
R/processCentrifugeClassifications.R
R/processCentrifugeProfile.R
R/processQiimeClassifications.R
R/processQiimeProfile.R
R/processSpingoClassifications.R
R/processSpingoProfile.R
R/sayHelloGunga.R
R/summarizeCentrifugeClassifications.R
R/summarizeQiimeClassifications.R
R/summarizeSpingoClassifications.R
README.R
README.md
Rmd/MajorityVoteDevelopment.html
Sel.ods
data/CentrifugeRf_TrainSet.rds
data/CentrifugeShRf_TrainSet.rds
data/CentrifugeSh_Spingo_Qiime_RF.rds
data/CentrifugeSh_Spingo_Qiime_RF_ntree1000.rds
data/ClarkRf_TrainSet.rds
data/ClarkSRf_TrainSet.rds
data/DudesRf_TrainSet.rds
data/GottchaRf_TrainSet.rds
data/Kraken2StandardRf_TrainSet.rds
data/KrakenRf_TrainSet.rds
data/LmatRf_TrainSet.rds
data/Metaphlan2Rf_TrainSet_CV.rds
data/MotusRf_TrainSet.rds
data/TippRf_TrainSet_CV.rds
gunga.Rproj
scripts/addSrrToTipp.R
scripts/clarkToWevote.R
scripts/join2WevoteN3.R
scripts/join2WevoteN5.R
scripts/krakenToWevote.R
scripts/makeMetaphlan2Map.R
scripts/meganToWevote.R
scripts/metaphlan2ToWevote.R
scripts/runWevote.sh
scripts/tippToWevote.R
tests/testthat.R
tests/testthat/test-loadRawCentrifugeClassifications.R
tests/testthat/test-loadRawCentrifugeProfile.R
tests/testthat/test-makeCentrifugeProfileForShotgun.R
tests/testthat/test-makeQiimeProfileForAmplicon.R
tests/testthat/test-makeSpingoProfileForAmplicon.R
tests/testthat/test-mergeProfiles.R
