Rbowtie: R bowtie wrapper
Version 1.16.0

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.

AuthorFlorian Hahne, Anita Lerch, Michael B Stadler
Bioconductor views Alignment Sequencing
Date of publicationNone
MaintainerMichael Stadler <michael.stadler@fmi.ch>
LicenseArtistic-1.0 | file LICENSE
Version1.16.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("Rbowtie")

Getting started

Package overview

Popular man pages

Rbowtie: Interface to bowtie
Rbowtie-package: R bowtie wrapper
SpliceMap: Interface to SpliceMap
See all...

All man pages Function index File listing

Man pages

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

Functions

Rbowtie Man page
Rbowtie-package Man page
SpliceMap Man page Source code
bowtie Man page Source code
bowtieBin Source code
bowtie_build Man page Source code
bowtie_build_usage Man page Source code
bowtie_usage Man page Source code
bowtie_version Man page Source code
createFlags Source code
execute Source code
write_cfg Source code

Files

.BBSoptions
DESCRIPTION
LICENSE
NAMESPACE
R
R/Rbowtie.R
R/SpliceMap.R
build
build/vignette.rds
inst
inst/CITATION
inst/NEWS
inst/doc
inst/doc/Rbowtie-Overview.R
inst/doc/Rbowtie-Overview.Rnw
inst/doc/Rbowtie-Overview.pdf
inst/samples
inst/samples/reads
inst/samples/reads/reads.fastq
inst/samples/refs
inst/samples/refs/chr1.fa
inst/samples/refs/chr2.fa
inst/samples/refs/chr3.fa
man
man/Rbowtie-package.Rd
man/Rbowtie.Rd
man/SpliceMap.Rd
src
src/AUTHORS
src/LICENSE
src/MANUAL
src/MANUAL.markdown
src/Makefile
src/Makefile.win
src/NEWS
src/SeqAn-1.1
src/SeqAn-1.1/GPL.txt
src/SeqAn-1.1/LGPL.txt
src/SeqAn-1.1/README.txt
src/SeqAn-1.1/platform_linux_gcc.h
src/SeqAn-1.1/platform_windows_mingw.h
src/SeqAn-1.1/platform_windows_vs.h
src/SeqAn-1.1/seqan
src/SeqAn-1.1/seqan/basic
src/SeqAn-1.1/seqan/basic.h
src/SeqAn-1.1/seqan/basic/basic_aggregates.h
src/SeqAn-1.1/seqan/basic/basic_allocator_interface.h
src/SeqAn-1.1/seqan/basic/basic_allocator_multipool.h
src/SeqAn-1.1/seqan/basic/basic_allocator_simple.h
src/SeqAn-1.1/seqan/basic/basic_allocator_singlepool.h
src/SeqAn-1.1/seqan/basic/basic_allocator_to_std.h
src/SeqAn-1.1/seqan/basic/basic_alphabet_interface.h
src/SeqAn-1.1/seqan/basic/basic_alphabet_interface2.h
src/SeqAn-1.1/seqan/basic/basic_alphabet_simple.h
src/SeqAn-1.1/seqan/basic/basic_alphabet_simple_tabs.h
src/SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h
src/SeqAn-1.1/seqan/basic/basic_compare.h
src/SeqAn-1.1/seqan/basic/basic_converter.h
src/SeqAn-1.1/seqan/basic/basic_counted_ptr.h
src/SeqAn-1.1/seqan/basic/basic_debug.h
src/SeqAn-1.1/seqan/basic/basic_definition.h
src/SeqAn-1.1/seqan/basic/basic_forwards.h
src/SeqAn-1.1/seqan/basic/basic_generated_forwards.h
src/SeqAn-1.1/seqan/basic/basic_holder.h
src/SeqAn-1.1/seqan/basic/basic_host.h
src/SeqAn-1.1/seqan/basic/basic_iterator.h
src/SeqAn-1.1/seqan/basic/basic_iterator_adapt_std.h
src/SeqAn-1.1/seqan/basic/basic_iterator_adaptor.h
src/SeqAn-1.1/seqan/basic/basic_iterator_base.h
src/SeqAn-1.1/seqan/basic/basic_iterator_position.h
src/SeqAn-1.1/seqan/basic/basic_iterator_simple.h
src/SeqAn-1.1/seqan/basic/basic_metaprogramming.h
src/SeqAn-1.1/seqan/basic/basic_operator.h
src/SeqAn-1.1/seqan/basic/basic_pointer.h
src/SeqAn-1.1/seqan/basic/basic_profile.h
src/SeqAn-1.1/seqan/basic/basic_proxy.h
src/SeqAn-1.1/seqan/basic/basic_tag.h
src/SeqAn-1.1/seqan/basic/basic_transport.h
src/SeqAn-1.1/seqan/basic/basic_type.h
src/SeqAn-1.1/seqan/basic/basic_volatile_ptr.h
src/SeqAn-1.1/seqan/file
src/SeqAn-1.1/seqan/file.h
src/SeqAn-1.1/seqan/file/chunk_collector.h
src/SeqAn-1.1/seqan/file/cstream.h
src/SeqAn-1.1/seqan/file/file_array.h
src/SeqAn-1.1/seqan/file/file_base.h
src/SeqAn-1.1/seqan/file/file_format.h
src/SeqAn-1.1/seqan/file/file_format_cgviz.h
src/SeqAn-1.1/seqan/file/file_format_fasta.h
src/SeqAn-1.1/seqan/file/file_format_fasta_align.h
src/SeqAn-1.1/seqan/file/file_format_guess.h
src/SeqAn-1.1/seqan/file/file_format_raw.h
src/SeqAn-1.1/seqan/file/file_forwards.h
src/SeqAn-1.1/seqan/file/file_generated_forwards.h
src/SeqAn-1.1/seqan/file/meta.h
src/SeqAn-1.1/seqan/file/stream.h
src/SeqAn-1.1/seqan/file/stream_algorithms.h
src/SeqAn-1.1/seqan/find
src/SeqAn-1.1/seqan/find.h
src/SeqAn-1.1/seqan/find/find_base.h
src/SeqAn-1.1/seqan/find/find_generated_forwards.h
src/SeqAn-1.1/seqan/find/find_horspool.h
src/SeqAn-1.1/seqan/find/find_multi.h
src/SeqAn-1.1/seqan/find/find_multiple_shiftand.h
src/SeqAn-1.1/seqan/find/find_score.h
src/SeqAn-1.1/seqan/find/find_set_horspool.h
src/SeqAn-1.1/seqan/index
src/SeqAn-1.1/seqan/index.h
src/SeqAn-1.1/seqan/index/index_base.h
src/SeqAn-1.1/seqan/index/index_find.h
src/SeqAn-1.1/seqan/index/index_generated_forwards.h
src/SeqAn-1.1/seqan/index/index_manual_forwards.h
src/SeqAn-1.1/seqan/index/index_qgram_find.h
src/SeqAn-1.1/seqan/index/index_sa_lss.h
src/SeqAn-1.1/seqan/index/shape_base.h
src/SeqAn-1.1/seqan/index/shape_gapped.h
src/SeqAn-1.1/seqan/index/shape_predefined.h
src/SeqAn-1.1/seqan/platform.h
src/SeqAn-1.1/seqan/sequence
src/SeqAn-1.1/seqan/sequence.h
src/SeqAn-1.1/seqan/sequence/lexical.h
src/SeqAn-1.1/seqan/sequence/segment_base.h
src/SeqAn-1.1/seqan/sequence/segment_infix.h
src/SeqAn-1.1/seqan/sequence/segment_prefix.h
src/SeqAn-1.1/seqan/sequence/segment_suffix.h
src/SeqAn-1.1/seqan/sequence/sequence_forwards.h
src/SeqAn-1.1/seqan/sequence/sequence_generated_forwards.h
src/SeqAn-1.1/seqan/sequence/sequence_interface.h
src/SeqAn-1.1/seqan/sequence/sequence_multiple.h
src/SeqAn-1.1/seqan/sequence/sequence_shortcuts.h
src/SeqAn-1.1/seqan/sequence/std_string.h
src/SeqAn-1.1/seqan/sequence/string_alloc.h
src/SeqAn-1.1/seqan/sequence/string_array.h
src/SeqAn-1.1/seqan/sequence/string_base.h
src/SeqAn-1.1/seqan/sequence/string_cstyle.h
src/SeqAn-1.1/seqan/sequence/string_packed.h
src/SeqAn-1.1/seqan/sequence/string_pointer.h
src/SeqAn-1.1/seqan/sequence/string_stack.h
src/SeqAn-1.1/seqan/sequence/string_value_expand.h
src/SpliceMap
src/SpliceMap/LICENSE
src/SpliceMap/Makefile
src/SpliceMap/Makefile.win
src/SpliceMap/SpliceMap_utils_QuasR.cpp
src/SpliceMap/SpliceMap_utils_QuasR.h
src/SpliceMap/amalgamateSAM.cpp
src/SpliceMap/amalgamateSAM.h
src/SpliceMap/cfgfile.cpp
src/SpliceMap/cfgfile.h
src/SpliceMap/fuseReorder.cpp
src/SpliceMap/getSpliceMapUnmapped.cpp
src/SpliceMap/main.cpp
src/SpliceMap/main.h
src/SpliceMap/params.cpp
src/SpliceMap/params.h
src/SpliceMap/runSpliceMap_QuasR.cpp
src/SpliceMap/runSpliceMap_QuasR.h
src/SpliceMap/sortsam.cpp
src/SpliceMap/sortsam.h
src/TUTORIAL
src/VERSION
src/aligner.h
src/aligner_0mm.h
src/aligner_1mm.h
src/aligner_23mm.h
src/aligner_metrics.h
src/aligner_seed_mm.h
src/alphabet.cpp
src/alphabet.h
src/annot.cpp
src/annot.h
src/assert_helpers.h
src/auto_array.h
src/binary_sa_search.h
src/bitpack.h
src/bitset.h
src/blockwise_sa.h
src/bowtie
src/bowtie-build
src/bowtie-inspect
src/bowtie_build_main.cpp
src/bowtie_inspect.cpp
src/bowtie_main.cpp
src/btypes.h
src/ccnt_lut.cpp
src/chaincat.cpp
src/color.cpp
src/color.h
src/color_dec.cpp
src/color_dec.h
src/diff_sample.h
src/ebwt.cpp
src/ebwt.h
src/ebwt_build.cpp
src/ebwt_search.cpp
src/ebwt_search_backtrack.h
src/ebwt_search_util.cpp
src/ebwt_search_util.h
src/edit.cpp
src/edit.h
src/endian_swap.h
src/fast_mutex.h
src/filebuf.h
src/formats.h
src/hit.cpp
src/hit.h
src/hit_set.cpp
src/hit_set.h
src/log.cpp
src/log.h
src/mm.h
src/multikey_qsort.h
src/pat.cpp
src/pat.h
src/pool.h
src/processor_support.h
src/qual.cpp
src/qual.h
src/random_source.h
src/random_test.cpp
src/range.h
src/range_cache.h
src/range_chaser.h
src/range_source.h
src/ref_aligner.cpp
src/ref_aligner.h
src/ref_read.cpp
src/ref_read.h
src/reference.h
src/refmap.cpp
src/refmap.h
src/row_chaser.h
src/sam.cpp
src/sam.h
src/search_1mm_phase1.c
src/search_1mm_phase2.c
src/search_23mm_phase1.c
src/search_23mm_phase2.c
src/search_23mm_phase3.c
src/search_exact.c
src/search_globals.h
src/search_seeded_phase1.c
src/search_seeded_phase2.c
src/search_seeded_phase3.c
src/search_seeded_phase4.c
src/sequence_io.h
src/shmem.cpp
src/shmem.h
src/str_util.h
src/third_party
src/third_party/cpuid.h
src/threading.h
src/timer.h
src/tinythread.cpp
src/tinythread.h
src/tokenize.h
src/word_io.h
src/zbox.h
vignettes
vignettes/Rbowtie-Overview.Rnw
vignettes/Rbowtie-refs.bib
Rbowtie documentation built on May 20, 2017, 9:23 p.m.

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