Files in philliplab/hypermutR
Detects hypermutation in DNA
.Rbuildignore
.gitignore
DESCRIPTION
NAMESPACE
R/RcppExports.R
R/ancestor_processing.R
R/consensusMatrix.R
R/data.R
R/deduplicate.R
R/hypermutR.R
R/random_utils.R
R/scan_seq.R
R/sim_data.R
README.md
data/hd_seqs.rda
data/ld_seqs.rda
inst/CITATION
inst/hypermutR.R
inst/old/hypermut_sim.R
inst/old/sim_test_data.R
inst/old/unhypermutoR.R
inst/removeHypermutatedSequences.R
inst/simulate_founder_call.sh
inst/test_data/test_file1.fasta
inst/test_data/test_file_1111.fasta
inst/test_data/test_file_4x2.fasta
inst/test_data/test_file_4x2_ref.fasta
inst/test_data/test_file_4x2_seq.fasta
inst/test_data/test_file_4x2_seq_removeDuplicateSequences.fasta
inst/test_data/test_file_4x2_seq_removeHypermutatedSequences.fasta
man/ancestor_processing.Rd
man/consensusMatrix_seqinr.Rd
man/convert_alignment_to_matrix.Rd
man/deduplicate_seqs.Rd
man/hd_seqs.Rd
man/ld_seqs.Rd
man/make_list_SeqFastadna.Rd
man/rcpp_scan_seq.Rd
man/remove_hypermut.Rd
man/restart_r.Rd
man/scan_seq.Rd
man/sim_hyper.Rd
src/RcppExports.cpp
src/scan_seq.cpp
tests/testthat.R
tests/testthat/test_consensusMatrix.R
tests/testthat/test_datasets.R
tests/testthat/test_deduplicate.R
tests/testthat/test_rcpp_scan_seq.R
tests/testthat/test_remove_hypermut.R
tests/testthat/test_scan_seq.R
tests/testthat/test_sim_data.R
vignettes/hiv-founder-id_compatibility.Rmd
vignettes/hypermut_vignette.pdf
vignettes/hypermut_vignette.pdf.asis
