Files in HIVDiversity/MotifBinner2
Process 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/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/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/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
HIVDiversity/MotifBinner2 documentation built on Aug. 15, 2018, 12:22 a.m.