Files in florian0512/sarlacc

Pipeline for Oxford Nanopore RNA-Seq Data Analysis

DESCRIPTION

NAMESPACE

R/adaptorAlign.R R/barcodeAlign.R R/consensusReadSeq.R R/errorFinder.R R/expectedDist.R R/extractSubseq.R R/filterReads.R R/getAdaptorThresholds.R R/getBarcodeThresholds.R R/homopolymerFinder.R R/homopolymerMatcher.R R/mockReads.R R/multiReadAlign.R R/namespace.R R/qualityAlign.R R/qualityMask.R R/realizeReads.R R/sam2ranges.R R/tuneAlignment.R R/umiGroup.R man/adaptorAlign.Rd man/barcodeAlign.Rd man/consensusReadSeq.Rd man/errorFinder.Rd man/expectedDist.Rd man/extractSubseq.Rd man/filterReads.Rd man/getAdaptorThresholds.Rd man/getBarcodeThresholds.Rd man/homopolymerFinder.Rd man/homopolymerMatcher.Rd man/multiReadAlign.Rd man/qualityAlign.Rd man/qualityMask.Rd man/realizeReads.Rd man/sam2ranges.Rd man/tuneAlignment.Rd man/umiGroup.Rd

src/Biostrings_stubs.c

src/DNA_input.cpp

src/DNA_input.h

src/adaptor_align.cpp

src/barcode_align.cpp

src/cluster_umis.cpp

src/cluster_umis.h

src/cluster_umis_test.cpp

src/compute_lev_masked.cpp

src/create_consensus.cpp

src/find_errors.cpp

src/general_align.cpp

src/homopolymer.cpp

src/init.cpp

src/mask_bad_bases.cpp

src/quality_encoding.cpp

src/quality_encoding.h

src/quick_msa.cpp

src/reference_align.cpp

src/reference_align.h

src/sarlacc.h

src/sorted_trie.cpp

src/sorted_trie.h

src/umi_group.cpp

src/unmask_alignment.cpp

src/utils.cpp

src/utils.h

tests/testthat.R tests/testthat/test-adaptor-align.R tests/testthat/test-consensus.R tests/testthat/test-error.R tests/testthat/test-general-align.R tests/testthat/test-homopolymer.R tests/testthat/test-levenshtein.R tests/testthat/test-masking.R tests/testthat/test-tuning.R tests/testthat/test-umicluster.R vignettes/correction.Rmd vignettes/profiling.Rmd

florian0512/sarlacc documentation built on May 28, 2019, 8:39 p.m.