Files in HIVDiversity/MotifBinner2
Processes NGS Primer ID Datasets
.Rbuildignore
.Rhistory
.Rproj.user/E88F0AD5/build_options
.Rproj.user/E88F0AD5/cpp-complilation-config
.Rproj.user/E88F0AD5/cpp-definition-cache
.Rproj.user/E88F0AD5/pcs/debug-breakpoints.pper
.Rproj.user/E88F0AD5/pcs/source-pane.pper
.Rproj.user/E88F0AD5/pcs/windowlayoutstate.pper
.Rproj.user/E88F0AD5/pcs/workbench-pane.pper
.Rproj.user/E88F0AD5/persistent-state
.Rproj.user/E88F0AD5/saved_source_markers
.Rproj.user/E88F0AD5/sdb/prop/3F8FF719
.Rproj.user/E88F0AD5/sdb/prop/55D71D91
.Rproj.user/E88F0AD5/sdb/prop/B99E0E17
.Rproj.user/E88F0AD5/sdb/prop/FF9190ED
.Rproj.user/E88F0AD5/sdb/prop/INDEX
.gitignore
DESCRIPTION
MotifBinner2.Rproj
NAMESPACE
R/RcppExports.R
R/alignBins.R
R/alignBinsMSA.R
R/alignBinsSP.R
R/allResults.R
R/ambigSeqs.R
R/basicQC.R
R/binSeqErr.R
R/binSizeCheck.R
R/blastTrim.R
R/buildConfig.R
R/buildConsensus.R
R/computeMetrics.R
R/consensus_cutoff.R
R/dataTracing.R
R/doubleClusterTally.R
R/extractData.R
R/extractPIDs.R
R/genReport.R
R/genSummary.R
R/loadData.R
R/makeIUPACScoreMat.R
R/matchPairs.R
R/mergePEAR.R
R/pairwiseMSA.R
R/prepConfig.R
R/primerDimer.R
R/primerSeqErr.R
R/processBadPIDs.R
R/processPrimers.R
R/qualTrim.R
R/regionSplit.R
R/removeChars.R
R/saveToDisk.R
R/seqLength.R
R/test_n_debug.R
R/timing.R
R/trimAffixes.R
R/trimFront.R
R/vacuumPIDs.R
R/vsearchCluster.R
README.md
inst/MotifBinner2.R
inst/reports/alignBins.Rmd
inst/reports/alignBinsMSA.Rmd
inst/reports/alignBinsSP.Rmd
inst/reports/allResults.Rmd
inst/reports/ambigSeqs.Rmd
inst/reports/basicQC.Rmd
inst/reports/binSeqErr.Rmd
inst/reports/binSizeCheck.Rmd
inst/reports/blastTrim.Rmd
inst/reports/buildConsensus.Rmd
inst/reports/dataTracing.Rmd
inst/reports/dataTracing_internal.Rmd
inst/reports/doubleClusterTally.Rmd
inst/reports/extractData.Rmd
inst/reports/extractPIDs.Rmd
inst/reports/loadData.Rmd
inst/reports/matchPairs.Rmd
inst/reports/mergePEAR.Rmd
inst/reports/prepConfig.Rmd
inst/reports/primerDimer.Rmd
inst/reports/primerSeqErr.Rmd
inst/reports/primerSeqErr_internal.Rmd
inst/reports/processBadPIDs.Rmd
inst/reports/qualTrim.Rmd
inst/reports/regionSplit.Rmd
inst/reports/removeChars.Rmd
inst/reports/seqLength.Rmd
inst/reports/trimAffixes.Rmd
inst/reports/vsearchCluster.Rmd
inst/test_dat.fastq
man/alignBins.Rd
man/alignBinsMSA.Rd
man/alignBinsMSA_internal.Rd
man/alignBinsSP.Rd
man/alignBinsSP_internal.Rd
man/alignBins_internal.Rd
man/allResults.Rd
man/ambigSeqs.Rd
man/applyOperation.Rd
man/apply_consensus_cutoff.Rd
man/basicQC.Rd
man/binSeqErr.Rd
man/binSeqErr_internal.Rd
man/binSizeCheck.Rd
man/blastTrim.Rd
man/buildConfig.Rd
man/buildConfig_nol_test.Rd
man/buildConfig_ol_prod.Rd
man/buildConsensus.Rd
man/build_cutoff_models.Rd
man/computeMetrics.Rd
man/dataTracing.Rd
man/doubleClusterTally.Rd
man/extractData.Rd
man/extractPIDs.Rd
man/genKeptVector.Rd
man/genReport.Rd
man/genSummary.Rd
man/genSummary_case1.Rd
man/genSummary_case3.Rd
man/genSummary_case4.Rd
man/getKept.Rd
man/getTrimmed.Rd
man/get_consensus_cutoff.Rd
man/get_cutoff_models.Rd
man/group_cons_bins_internal.Rd
man/kable_summary.Rd
man/loadData.Rd
man/makeIUPACScoreMat.Rd
man/make_monotonic.Rd
man/matchPairs.Rd
man/mergePEAR.Rd
man/moving_statistic.Rd
man/mutate_letter.Rd
man/pairwiseMSA.Rd
man/plot_consensus_cutoff_model.Rd
man/plot_consensus_cutoff_sim.Rd
man/prepConfig.Rd
man/primerDimer.Rd
man/primerSeqErr.Rd
man/processBadPIDs.Rd
man/processPrimers.Rd
man/qualTrim.Rd
man/reformat_tallies.Rd
man/regionSplit.Rd
man/removeChars.Rd
man/saveToDisk.Rd
man/seqLength.Rd
man/shortReadQ_forced_append.Rd
man/sim_all_parents_main_off.Rd
man/sim_one_parent_main_off.Rd
man/sim_wrapper.Rd
man/sliceTime.Rd
man/timingTable.Rd
man/trimAffixes.Rd
man/vsearchCluster.Rd
src/Makevars
src/RcppExports.cpp
src/trimFront.cpp
vignettes/MotifBinner2_design.Rmd
