Files in ShortRead
FASTQ input and manipulation
configure.ac
configure
.Rinstignore
NEWS
NAMESPACE
DESCRIPTION
cleanup
build/vignette.rds
src/ShortRead.h
src/io_bowtie.c
src/read_maq_map.cc
src/io_soap.c
src/trim.c
src/alphabet.c
src/trim.h
src/readBfaToc.cc
src/Makevars.win
src/Makevars.in
src/maqmap_m.h
src/util.c
src/S4Vectors_stubs.c
src/IRanges_stubs.c
src/XVector_stubs.c
src/io.c
src/const.h
src/sampler.c
src/count.c
src/xsnap.c
src/R_init_ShortRead.c
src/call.h
src/Biostrings_stubs.c
R/trimEnds.R
R/renew.R
R/methods-SolexaIntensity.R
R/readPrb.R
R/methods-SRList.R
R/methods-FastqSampler.R
R/methods-.QA.R
R/methods-FastqStreamer.R
R/methods-QualityScore.R
R/methods-QA.R
R/AllClasses-Base.R
R/methods-BowtieQA.R
R/readAligned.R
R/methods-RochePath.R
R/SnapshotFunction-helpers.R
R/methods-ShortReadQ.R
R/readBaseQuality.R
R/methods-Intensity.R
R/methods-RtaIntensity.R
R/spViewPerFeature.R
R/SpTrellis.R
R/readQseq.R
R/AllGenerics-Base.R
R/methods-ShortRead.R
R/methods-.ShortReadBase.R
R/methods-SRFilterResult.R
R/readIntensities.R
R/AllGenerics-QA.R
R/report.R
R/AllClasses-QA.R
R/SnapshotFunction.R
R/methods-AlignedDataFrame.R
R/methods-ShortReadFile.R
R/readXStringColumns.R
R/methods-ExperimentPath.R
R/methods-MAQMapQA.R
R/methods-SolexaPath.R
R/methods-FastqFileReader.R
R/methods-FastqFile.R
R/methods-SRSet.R
R/methods-FastqQA.R
R/methods-SolexaExportQA.R
R/qa.R
R/filterFastq.R
R/readBfaToc.R
R/Snapshot.R
R/methods-RocheSet.R
R/AllUtilities.R
R/qa_utilities.R
R/methods-SRFilter.R
R/methods-SolexaRealignQA.R
R/methods-SRError.R
R/methods-AlignedRead.R
R/methods-SRVector.R
R/methods-Misc.R
R/methods-SolexaSet.R
vignettes/ShortRead_and_HilbertVis.pdf
vignettes/qa_E-MTAB-1147.Rda
vignettes/simon2.bst
vignettes/ShortRead_and_HilbertVis.Rnw_
vignettes/README
vignettes/Overview.Rnw
vignettes/hilbert.bib
vignettes/images/HilbertDisplay_GUI.png
vignettes/images/hilbert_3col.png
vignettes/images/HilbertPlot_H3K4me3.pdf
vignettes/images/HilbertDisplay_GUI.pdf
vignettes/images/HilbertPlot_H3K4me1.pdf
vignettes/images/Strand_and_Dir.pdf
vignettes/images/hilbert_3col.pdf
vignettes/images/HilbertPlot_H3K4me3.png
vignettes/images/HilbertPlot_H3K4me1.png
man/srduplicated.Rd
man/MAQMapQA-class.Rd
man/SolexaPath-class.Rd
man/deprecated.Rd
man/RtaIntensity-class.Rd
man/SolexaIntensity.Rd
man/readIntensities.Rd
man/readFasta.Rd
man/AlignedRead-class.Rd
man/SRSet-class.Rd
man/readAligned.Rd
man/readBaseQuality.Rd
man/QualityScore-class.Rd
man/AlignedRead.Rd
man/RochePath-class.Rd
man/BowtieQA-class.Rd
man/SRUtil-class.Rd
man/srFilter.Rd
man/ShortRead-class.Rd
man/ExperimentPath-class.Rd
man/spViewPerFeature.Rd
man/readXStringColumns.Rd
man/srdistance.Rd
man/FastqQA-class.Rd
man/readQseq.Rd
man/dustyScore.Rd
man/report.Rd
man/QualityScore.Rd
man/tables.Rd
man/dotQA-class.Rd
man/ShortRead-deprecated.Rd
man/RtaIntensity.Rd
man/RocheSet-class.Rd
man/QA-class.Rd
man/readFastq.Rd
man/alphabetByCycle.Rd
man/countLines.Rd
man/Sampler-class.Rd
man/SpTrellis-class.Rd
man/SRFilter-class.Rd
man/renew.Rd
man/accessors.Rd
man/SRFilterResult-class.Rd
man/AlignedDataFrame-class.Rd
man/readPrb.Rd
man/qa.Rd
man/AlignedDataFrame.Rd
man/Snapshot-class.Rd
man/SnapshotFunction-class.Rd
man/SolexaExportQA-class.Rd
man/trimTails.Rd
man/SolexaIntensity-class.Rd
man/ShortRead-package.Rd
man/Intensity-class.Rd
man/SolexaSet-class.Rd
man/readBfaToc.Rd
man/polyn.Rd
man/filterFastq.Rd
man/ShortReadQ-class.Rd
man/alphabetScore.Rd
man/clean.Rd
man/qa2.Rd
tests/ShortRead_unit_tests.R
inst/CITATION
inst/doc/Overview.pdf
inst/doc/Overview.R
inst/doc/Overview.Rnw
inst/extdata/bowtie/s_1_aligned_bowtie.txt
inst/extdata/Data/C1-36Firecrest/s_1_0001_nse.txt
inst/extdata/Data/C1-36Firecrest/s_1_0001_int.txt
inst/extdata/Data/C1-36Firecrest/Bustard/s_1_0001_prb.txt
inst/extdata/Data/C1-36Firecrest/Bustard/s_1_0001_seq.txt
inst/extdata/Data/C1-36Firecrest/Bustard/s_1_1_0001_qseq.txt
inst/extdata/Data/C1-36Firecrest/Bustard/GERALD/s_1_sequence.txt
inst/extdata/Data/C1-36Firecrest/Bustard/GERALD/s_2_export.txt
inst/extdata/Data/C1-36Firecrest/Bustard/GERALD/s_5_0001_realign.txt
inst/extdata/E-MTAB-1147/ERR127302_1_subset.fastq.gz
inst/extdata/E-MTAB-1147/ERR127302_2_subset.fastq.gz
inst/extdata/maq/out.aln.1.txt
inst/extdata/maq/out.aln.2.txt
inst/script/qa-test.R
inst/template/5000-PerTile.html
inst/template/QA.css
inst/template/QANucleotideUse.html
inst/template/1000-Overview.html
inst/template/1100-Overview-SolexaRealign.html
inst/template/7000-MultipleAlignment.html
inst/template/4000-CycleSpecific.html
inst/template/QANucleotideByCycle.html
inst/template/QAReadQuality.html
inst/template/3000-ReadDistribution.html
inst/template/QAAdapterContamination.html
inst/template/QAFooter.html
inst/template/QASources.html
inst/template/9999-Footer.html
inst/template/8000-DepthOfCoverage.html
inst/template/qa_solexa.Rnw
inst/template/0000-Header.html
inst/template/QAHeader.html
inst/template/QAFiltered.html
inst/template/2000-RunSummary.html
inst/template/QAQualityByCycle.html
inst/template/9000-AdapterContamination.html
inst/template/QAFlagged.html
inst/template/QASequenceUse.html
inst/template/QAQualityUse.html
inst/template/6000-Alignment.html
inst/template/QAFrequentSequence.html
inst/template/image/bioclogo-small.gif
inst/unitTests/test_SRError.R
inst/unitTests/test_qa.R
inst/unitTests/test_AllClasses.R
inst/unitTests/test_SolexaIntensity.R
inst/unitTests/test_readQseq.R
inst/unitTests/test_trimEnds.R
inst/unitTests/test_functions.R
inst/unitTests/test_filterFastq.R
inst/unitTests/test_writeFastq.R
inst/unitTests/test_trimTails.R
inst/unitTests/test_SRList.R
inst/unitTests/test_append.R
inst/unitTests/test_FastqFile.R
inst/unitTests/test_coverage.R
inst/unitTests/test_readXStringColumns.R
inst/unitTests/test_ShortRead.R
inst/unitTests/test_readPrb.R
inst/unitTests/test_SRFilterResult.R
inst/unitTests/test_renew.R
inst/unitTests/test_SRFilter.R
inst/unitTests/test_ShortReadQ.R
inst/unitTests/test_Intensity.R
inst/unitTests/test_AlignedRead.R
inst/unitTests/test_SRVector.R
inst/unitTests/cases/s_2_export_run_as_factor.txt
inst/unitTests/cases/solexa.fastq
inst/unitTests/cases/s_2_0001_realign_3col_head.txt
inst/unitTests/cases/sanger.fastq
inst/unitTests/cases/s_1_sequence.8_lines_illegal_nucleotide.txt
inst/unitTests/cases/s_1_sequence.8_lines_read_quality_mismatch.txt
inst/unitTests/cases/s_1_results_head.txt
inst/unitTests/cases/s_1_0001_int_head.txt.p
inst/unitTests/cases/s_2_0001_realign_head.txt
inst/unitTests/cases/s_1_sequence.8_lines_read_mismatch.txt
inst/unitTests/cases/s_1_0001_pos_head.txt
inst/unitTests/cases/s_2_export_toIUPAC.txt
inst/unitTests/cases/s_1_sequence.txt
inst/unitTests/cases/s_1_0001_nse_head.txt.p
inst/unitTests/cases/soap.txt
inst/unitTests/cases/s_1_sequence.9_lines.txt
inst/unitTests/cases/PE_export.txt.gz
