Rbowtie: R bowtie wrapper

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This package provides an R wrapper around the popular bowtie short read aligner and around SpliceMap, a de novo splice junction discovery and alignment tool. The package is used by the QuasR bioconductor package. We recommend to use the QuasR package instead of using Rbowtie directly.

Author
Florian Hahne, Anita Lerch, Michael B Stadler
Date of publication
None
Maintainer
Michael Stadler <michael.stadler@fmi.ch>
License
Artistic-1.0 | file LICENSE
Version
1.14.0

View on Bioconductor

Man pages

Rbowtie
Interface to bowtie
Rbowtie-package
R bowtie wrapper
SpliceMap
Interface to SpliceMap

Files in this package

Rbowtie/.BBSoptions
Rbowtie/DESCRIPTION
Rbowtie/LICENSE
Rbowtie/NAMESPACE
Rbowtie/R
Rbowtie/R/Rbowtie.R
Rbowtie/R/SpliceMap.R
Rbowtie/build
Rbowtie/build/vignette.rds
Rbowtie/inst
Rbowtie/inst/CITATION
Rbowtie/inst/NEWS
Rbowtie/inst/doc
Rbowtie/inst/doc/Rbowtie-Overview.R
Rbowtie/inst/doc/Rbowtie-Overview.Rnw
Rbowtie/inst/doc/Rbowtie-Overview.pdf
Rbowtie/inst/samples
Rbowtie/inst/samples/reads
Rbowtie/inst/samples/reads/reads.fastq
Rbowtie/inst/samples/refs
Rbowtie/inst/samples/refs/chr1.fa
Rbowtie/inst/samples/refs/chr2.fa
Rbowtie/inst/samples/refs/chr3.fa
Rbowtie/man
Rbowtie/man/Rbowtie-package.Rd
Rbowtie/man/Rbowtie.Rd
Rbowtie/man/SpliceMap.Rd
Rbowtie/src
Rbowtie/src/AUTHORS
Rbowtie/src/LICENSE
Rbowtie/src/MANUAL
Rbowtie/src/MANUAL.markdown
Rbowtie/src/Makefile
Rbowtie/src/Makefile.win
Rbowtie/src/NEWS
Rbowtie/src/SeqAn-1.1
Rbowtie/src/SeqAn-1.1/GPL.txt
Rbowtie/src/SeqAn-1.1/LGPL.txt
Rbowtie/src/SeqAn-1.1/README.txt
Rbowtie/src/SeqAn-1.1/platform_linux_gcc.h
Rbowtie/src/SeqAn-1.1/platform_windows_mingw.h
Rbowtie/src/SeqAn-1.1/platform_windows_vs.h
Rbowtie/src/SeqAn-1.1/seqan
Rbowtie/src/SeqAn-1.1/seqan/basic
Rbowtie/src/SeqAn-1.1/seqan/basic.h
Rbowtie/src/SeqAn-1.1/seqan/basic/basic_aggregates.h
Rbowtie/src/SeqAn-1.1/seqan/basic/basic_allocator_interface.h
Rbowtie/src/SeqAn-1.1/seqan/basic/basic_allocator_multipool.h
Rbowtie/src/SeqAn-1.1/seqan/basic/basic_allocator_simple.h
Rbowtie/src/SeqAn-1.1/seqan/basic/basic_allocator_singlepool.h
Rbowtie/src/SeqAn-1.1/seqan/basic/basic_allocator_to_std.h
Rbowtie/src/SeqAn-1.1/seqan/basic/basic_alphabet_interface.h
Rbowtie/src/SeqAn-1.1/seqan/basic/basic_alphabet_interface2.h
Rbowtie/src/SeqAn-1.1/seqan/basic/basic_alphabet_simple.h
Rbowtie/src/SeqAn-1.1/seqan/basic/basic_alphabet_simple_tabs.h
Rbowtie/src/SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h
Rbowtie/src/SeqAn-1.1/seqan/basic/basic_compare.h
Rbowtie/src/SeqAn-1.1/seqan/basic/basic_converter.h
Rbowtie/src/SeqAn-1.1/seqan/basic/basic_counted_ptr.h
Rbowtie/src/SeqAn-1.1/seqan/basic/basic_debug.h
Rbowtie/src/SeqAn-1.1/seqan/basic/basic_definition.h
Rbowtie/src/SeqAn-1.1/seqan/basic/basic_forwards.h
Rbowtie/src/SeqAn-1.1/seqan/basic/basic_generated_forwards.h
Rbowtie/src/SeqAn-1.1/seqan/basic/basic_holder.h
Rbowtie/src/SeqAn-1.1/seqan/basic/basic_host.h
Rbowtie/src/SeqAn-1.1/seqan/basic/basic_iterator.h
Rbowtie/src/SeqAn-1.1/seqan/basic/basic_iterator_adapt_std.h
Rbowtie/src/SeqAn-1.1/seqan/basic/basic_iterator_adaptor.h
Rbowtie/src/SeqAn-1.1/seqan/basic/basic_iterator_base.h
Rbowtie/src/SeqAn-1.1/seqan/basic/basic_iterator_position.h
Rbowtie/src/SeqAn-1.1/seqan/basic/basic_iterator_simple.h
Rbowtie/src/SeqAn-1.1/seqan/basic/basic_metaprogramming.h
Rbowtie/src/SeqAn-1.1/seqan/basic/basic_operator.h
Rbowtie/src/SeqAn-1.1/seqan/basic/basic_pointer.h
Rbowtie/src/SeqAn-1.1/seqan/basic/basic_profile.h
Rbowtie/src/SeqAn-1.1/seqan/basic/basic_proxy.h
Rbowtie/src/SeqAn-1.1/seqan/basic/basic_tag.h
Rbowtie/src/SeqAn-1.1/seqan/basic/basic_transport.h
Rbowtie/src/SeqAn-1.1/seqan/basic/basic_type.h
Rbowtie/src/SeqAn-1.1/seqan/basic/basic_volatile_ptr.h
Rbowtie/src/SeqAn-1.1/seqan/file
Rbowtie/src/SeqAn-1.1/seqan/file.h
Rbowtie/src/SeqAn-1.1/seqan/file/chunk_collector.h
Rbowtie/src/SeqAn-1.1/seqan/file/cstream.h
Rbowtie/src/SeqAn-1.1/seqan/file/file_array.h
Rbowtie/src/SeqAn-1.1/seqan/file/file_base.h
Rbowtie/src/SeqAn-1.1/seqan/file/file_format.h
Rbowtie/src/SeqAn-1.1/seqan/file/file_format_cgviz.h
Rbowtie/src/SeqAn-1.1/seqan/file/file_format_fasta.h
Rbowtie/src/SeqAn-1.1/seqan/file/file_format_fasta_align.h
Rbowtie/src/SeqAn-1.1/seqan/file/file_format_guess.h
Rbowtie/src/SeqAn-1.1/seqan/file/file_format_raw.h
Rbowtie/src/SeqAn-1.1/seqan/file/file_forwards.h
Rbowtie/src/SeqAn-1.1/seqan/file/file_generated_forwards.h
Rbowtie/src/SeqAn-1.1/seqan/file/meta.h
Rbowtie/src/SeqAn-1.1/seqan/file/stream.h
Rbowtie/src/SeqAn-1.1/seqan/file/stream_algorithms.h
Rbowtie/src/SeqAn-1.1/seqan/find
Rbowtie/src/SeqAn-1.1/seqan/find.h
Rbowtie/src/SeqAn-1.1/seqan/find/find_base.h
Rbowtie/src/SeqAn-1.1/seqan/find/find_generated_forwards.h
Rbowtie/src/SeqAn-1.1/seqan/find/find_horspool.h
Rbowtie/src/SeqAn-1.1/seqan/find/find_multi.h
Rbowtie/src/SeqAn-1.1/seqan/find/find_multiple_shiftand.h
Rbowtie/src/SeqAn-1.1/seqan/find/find_score.h
Rbowtie/src/SeqAn-1.1/seqan/find/find_set_horspool.h
Rbowtie/src/SeqAn-1.1/seqan/index
Rbowtie/src/SeqAn-1.1/seqan/index.h
Rbowtie/src/SeqAn-1.1/seqan/index/index_base.h
Rbowtie/src/SeqAn-1.1/seqan/index/index_find.h
Rbowtie/src/SeqAn-1.1/seqan/index/index_generated_forwards.h
Rbowtie/src/SeqAn-1.1/seqan/index/index_manual_forwards.h
Rbowtie/src/SeqAn-1.1/seqan/index/index_qgram_find.h
Rbowtie/src/SeqAn-1.1/seqan/index/index_sa_lss.h
Rbowtie/src/SeqAn-1.1/seqan/index/shape_base.h
Rbowtie/src/SeqAn-1.1/seqan/index/shape_gapped.h
Rbowtie/src/SeqAn-1.1/seqan/index/shape_predefined.h
Rbowtie/src/SeqAn-1.1/seqan/platform.h
Rbowtie/src/SeqAn-1.1/seqan/sequence
Rbowtie/src/SeqAn-1.1/seqan/sequence.h
Rbowtie/src/SeqAn-1.1/seqan/sequence/lexical.h
Rbowtie/src/SeqAn-1.1/seqan/sequence/segment_base.h
Rbowtie/src/SeqAn-1.1/seqan/sequence/segment_infix.h
Rbowtie/src/SeqAn-1.1/seqan/sequence/segment_prefix.h
Rbowtie/src/SeqAn-1.1/seqan/sequence/segment_suffix.h
Rbowtie/src/SeqAn-1.1/seqan/sequence/sequence_forwards.h
Rbowtie/src/SeqAn-1.1/seqan/sequence/sequence_generated_forwards.h
Rbowtie/src/SeqAn-1.1/seqan/sequence/sequence_interface.h
Rbowtie/src/SeqAn-1.1/seqan/sequence/sequence_multiple.h
Rbowtie/src/SeqAn-1.1/seqan/sequence/sequence_shortcuts.h
Rbowtie/src/SeqAn-1.1/seqan/sequence/std_string.h
Rbowtie/src/SeqAn-1.1/seqan/sequence/string_alloc.h
Rbowtie/src/SeqAn-1.1/seqan/sequence/string_array.h
Rbowtie/src/SeqAn-1.1/seqan/sequence/string_base.h
Rbowtie/src/SeqAn-1.1/seqan/sequence/string_cstyle.h
Rbowtie/src/SeqAn-1.1/seqan/sequence/string_packed.h
Rbowtie/src/SeqAn-1.1/seqan/sequence/string_pointer.h
Rbowtie/src/SeqAn-1.1/seqan/sequence/string_stack.h
Rbowtie/src/SeqAn-1.1/seqan/sequence/string_value_expand.h
Rbowtie/src/SpliceMap
Rbowtie/src/SpliceMap/LICENSE
Rbowtie/src/SpliceMap/Makefile
Rbowtie/src/SpliceMap/Makefile.win
Rbowtie/src/SpliceMap/SpliceMap_utils_QuasR.cpp
Rbowtie/src/SpliceMap/SpliceMap_utils_QuasR.h
Rbowtie/src/SpliceMap/amalgamateSAM.cpp
Rbowtie/src/SpliceMap/amalgamateSAM.h
Rbowtie/src/SpliceMap/cfgfile.cpp
Rbowtie/src/SpliceMap/cfgfile.h
Rbowtie/src/SpliceMap/fuseReorder.cpp
Rbowtie/src/SpliceMap/getSpliceMapUnmapped.cpp
Rbowtie/src/SpliceMap/main.cpp
Rbowtie/src/SpliceMap/main.h
Rbowtie/src/SpliceMap/params.cpp
Rbowtie/src/SpliceMap/params.h
Rbowtie/src/SpliceMap/runSpliceMap_QuasR.cpp
Rbowtie/src/SpliceMap/runSpliceMap_QuasR.h
Rbowtie/src/SpliceMap/sortsam.cpp
Rbowtie/src/SpliceMap/sortsam.h
Rbowtie/src/TUTORIAL
Rbowtie/src/VERSION
Rbowtie/src/aligner.h
Rbowtie/src/aligner_0mm.h
Rbowtie/src/aligner_1mm.h
Rbowtie/src/aligner_23mm.h
Rbowtie/src/aligner_metrics.h
Rbowtie/src/aligner_seed_mm.h
Rbowtie/src/alphabet.cpp
Rbowtie/src/alphabet.h
Rbowtie/src/annot.cpp
Rbowtie/src/annot.h
Rbowtie/src/assert_helpers.h
Rbowtie/src/auto_array.h
Rbowtie/src/binary_sa_search.h
Rbowtie/src/bitpack.h
Rbowtie/src/bitset.h
Rbowtie/src/blockwise_sa.h
Rbowtie/src/bowtie
Rbowtie/src/bowtie-build
Rbowtie/src/bowtie-inspect
Rbowtie/src/bowtie_build_main.cpp
Rbowtie/src/bowtie_inspect.cpp
Rbowtie/src/bowtie_main.cpp
Rbowtie/src/btypes.h
Rbowtie/src/ccnt_lut.cpp
Rbowtie/src/chaincat.cpp
Rbowtie/src/color.cpp
Rbowtie/src/color.h
Rbowtie/src/color_dec.cpp
Rbowtie/src/color_dec.h
Rbowtie/src/diff_sample.h
Rbowtie/src/ebwt.cpp
Rbowtie/src/ebwt.h
Rbowtie/src/ebwt_build.cpp
Rbowtie/src/ebwt_search.cpp
Rbowtie/src/ebwt_search_backtrack.h
Rbowtie/src/ebwt_search_util.cpp
Rbowtie/src/ebwt_search_util.h
Rbowtie/src/edit.cpp
Rbowtie/src/edit.h
Rbowtie/src/endian_swap.h
Rbowtie/src/fast_mutex.h
Rbowtie/src/filebuf.h
Rbowtie/src/formats.h
Rbowtie/src/hit.cpp
Rbowtie/src/hit.h
Rbowtie/src/hit_set.cpp
Rbowtie/src/hit_set.h
Rbowtie/src/log.cpp
Rbowtie/src/log.h
Rbowtie/src/mm.h
Rbowtie/src/multikey_qsort.h
Rbowtie/src/pat.cpp
Rbowtie/src/pat.h
Rbowtie/src/pool.h
Rbowtie/src/processor_support.h
Rbowtie/src/qual.cpp
Rbowtie/src/qual.h
Rbowtie/src/random_source.h
Rbowtie/src/random_test.cpp
Rbowtie/src/range.h
Rbowtie/src/range_cache.h
Rbowtie/src/range_chaser.h
Rbowtie/src/range_source.h
Rbowtie/src/ref_aligner.cpp
Rbowtie/src/ref_aligner.h
Rbowtie/src/ref_read.cpp
Rbowtie/src/ref_read.h
Rbowtie/src/reference.h
Rbowtie/src/refmap.cpp
Rbowtie/src/refmap.h
Rbowtie/src/row_chaser.h
Rbowtie/src/sam.cpp
Rbowtie/src/sam.h
Rbowtie/src/search_1mm_phase1.c
Rbowtie/src/search_1mm_phase2.c
Rbowtie/src/search_23mm_phase1.c
Rbowtie/src/search_23mm_phase2.c
Rbowtie/src/search_23mm_phase3.c
Rbowtie/src/search_exact.c
Rbowtie/src/search_globals.h
Rbowtie/src/search_seeded_phase1.c
Rbowtie/src/search_seeded_phase2.c
Rbowtie/src/search_seeded_phase3.c
Rbowtie/src/search_seeded_phase4.c
Rbowtie/src/sequence_io.h
Rbowtie/src/shmem.cpp
Rbowtie/src/shmem.h
Rbowtie/src/str_util.h
Rbowtie/src/third_party
Rbowtie/src/third_party/cpuid.h
Rbowtie/src/threading.h
Rbowtie/src/timer.h
Rbowtie/src/tinythread.cpp
Rbowtie/src/tinythread.h
Rbowtie/src/tokenize.h
Rbowtie/src/word_io.h
Rbowtie/src/zbox.h
Rbowtie/vignettes
Rbowtie/vignettes/Rbowtie-Overview.Rnw
Rbowtie/vignettes/Rbowtie-refs.bib