Files in Bioconductor-mirror/ShortRead
FASTQ input and manipulation

.Rinstignore
.gitignore
DESCRIPTION
NAMESPACE
NEWS
R/AllClasses-Base.R R/AllClasses-QA.R R/AllGenerics-Base.R R/AllGenerics-QA.R R/AllUtilities.R R/Snapshot.R R/SnapshotFunction-helpers.R R/SnapshotFunction.R R/SpTrellis.R R/filterFastq.R R/methods-.QA.R R/methods-.ShortReadBase.R R/methods-AlignedDataFrame.R R/methods-AlignedRead.R R/methods-BowtieQA.R R/methods-ExperimentPath.R R/methods-FastqFile.R R/methods-FastqFileReader.R R/methods-FastqQA.R R/methods-FastqSampler.R R/methods-FastqStreamer.R R/methods-Intensity.R R/methods-MAQMapQA.R R/methods-Misc.R R/methods-QA.R R/methods-QualityScore.R R/methods-RochePath.R R/methods-RocheSet.R R/methods-RtaIntensity.R R/methods-SRError.R R/methods-SRFilter.R R/methods-SRFilterResult.R R/methods-SRList.R R/methods-SRSet.R R/methods-SRVector.R R/methods-ShortRead.R R/methods-ShortReadFile.R R/methods-ShortReadQ.R R/methods-SolexaExportQA.R R/methods-SolexaIntensity.R R/methods-SolexaPath.R R/methods-SolexaRealignQA.R R/methods-SolexaSet.R R/qa.R R/qa_utilities.R R/readAligned.R R/readBaseQuality.R R/readBfaToc.R R/readIntensities.R R/readPrb.R R/readQseq.R R/readXStringColumns.R R/renew.R R/report.R R/spViewPerFeature.R R/trimEnds.R
cleanup
configure
configure.ac
inst/CITATION
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/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/s_1_0001_int.txt
inst/extdata/Data/C1-36Firecrest/s_1_0001_nse.txt
inst/extdata/E-MTAB-1147/ERR127302_1_subset.fastq.gz
inst/extdata/E-MTAB-1147/ERR127302_2_subset.fastq.gz
inst/extdata/bowtie/s_1_aligned_bowtie.txt
inst/extdata/maq/out.aln.1.txt
inst/extdata/maq/out.aln.2.txt
inst/script/qa-test.R
inst/template/0000-Header.html
inst/template/1000-Overview.html
inst/template/1100-Overview-SolexaRealign.html
inst/template/2000-RunSummary.html
inst/template/3000-ReadDistribution.html
inst/template/4000-CycleSpecific.html
inst/template/5000-PerTile.html
inst/template/6000-Alignment.html
inst/template/7000-MultipleAlignment.html
inst/template/8000-DepthOfCoverage.html
inst/template/9000-AdapterContamination.html
inst/template/9999-Footer.html
inst/template/QA.css
inst/template/QAAdapterContamination.html
inst/template/QAFiltered.html
inst/template/QAFlagged.html
inst/template/QAFooter.html
inst/template/QAFrequentSequence.html
inst/template/QAHeader.html
inst/template/QANucleotideByCycle.html
inst/template/QANucleotideUse.html
inst/template/QAQualityByCycle.html
inst/template/QAQualityUse.html
inst/template/QAReadQuality.html
inst/template/QASequenceUse.html
inst/template/QASources.html
inst/template/image/bioclogo-small.gif
inst/template/qa_solexa.Rnw
inst/unitTests/cases/PE_export.txt.gz
inst/unitTests/cases/s_1_0001_int_head.txt.p
inst/unitTests/cases/s_1_0001_nse_head.txt.p
inst/unitTests/cases/s_1_0001_pos_head.txt
inst/unitTests/cases/s_1_results_head.txt
inst/unitTests/cases/s_1_sequence.8_lines_illegal_nucleotide.txt
inst/unitTests/cases/s_1_sequence.8_lines_read_mismatch.txt
inst/unitTests/cases/s_1_sequence.8_lines_read_quality_mismatch.txt
inst/unitTests/cases/s_1_sequence.9_lines.txt
inst/unitTests/cases/s_1_sequence.txt
inst/unitTests/cases/s_2_0001_realign_3col_head.txt
inst/unitTests/cases/s_2_0001_realign_head.txt
inst/unitTests/cases/s_2_export_run_as_factor.txt
inst/unitTests/cases/s_2_export_toIUPAC.txt
inst/unitTests/cases/sanger.fastq
inst/unitTests/cases/soap.txt
inst/unitTests/cases/solexa.fastq
inst/unitTests/test_AlignedRead.R inst/unitTests/test_AllClasses.R inst/unitTests/test_FastqFile.R inst/unitTests/test_Intensity.R inst/unitTests/test_SRError.R inst/unitTests/test_SRFilter.R inst/unitTests/test_SRFilterResult.R inst/unitTests/test_SRList.R inst/unitTests/test_SRVector.R inst/unitTests/test_ShortRead.R inst/unitTests/test_ShortReadQ.R inst/unitTests/test_SolexaIntensity.R inst/unitTests/test_append.R inst/unitTests/test_coverage.R inst/unitTests/test_filterFastq.R inst/unitTests/test_functions.R inst/unitTests/test_qa.R inst/unitTests/test_readPrb.R inst/unitTests/test_readQseq.R inst/unitTests/test_readXStringColumns.R inst/unitTests/test_renew.R inst/unitTests/test_trimEnds.R inst/unitTests/test_trimTails.R inst/unitTests/test_writeFastq.R man/AlignedDataFrame-class.Rd man/AlignedDataFrame.Rd man/AlignedRead-class.Rd man/AlignedRead.Rd man/BowtieQA-class.Rd man/ExperimentPath-class.Rd man/FastqQA-class.Rd man/Intensity-class.Rd man/MAQMapQA-class.Rd man/QA-class.Rd man/QualityScore-class.Rd man/QualityScore.Rd man/RochePath-class.Rd man/RocheSet-class.Rd man/RtaIntensity-class.Rd man/RtaIntensity.Rd man/SRFilter-class.Rd man/SRFilterResult-class.Rd man/SRSet-class.Rd man/SRUtil-class.Rd man/Sampler-class.Rd man/ShortRead-class.Rd man/ShortRead-deprecated.Rd man/ShortRead-package.Rd man/ShortReadQ-class.Rd man/Snapshot-class.Rd man/SnapshotFunction-class.Rd man/SolexaExportQA-class.Rd man/SolexaIntensity-class.Rd man/SolexaIntensity.Rd man/SolexaPath-class.Rd man/SolexaSet-class.Rd man/SpTrellis-class.Rd man/accessors.Rd man/alphabetByCycle.Rd man/alphabetScore.Rd man/clean.Rd man/countLines.Rd man/deprecated.Rd man/dotQA-class.Rd man/dustyScore.Rd man/filterFastq.Rd man/polyn.Rd man/qa.Rd man/qa2.Rd man/readAligned.Rd man/readBaseQuality.Rd man/readBfaToc.Rd man/readFasta.Rd man/readFastq.Rd man/readIntensities.Rd man/readPrb.Rd man/readQseq.Rd man/readXStringColumns.Rd man/renew.Rd man/report.Rd man/spViewPerFeature.Rd man/srFilter.Rd man/srdistance.Rd man/srduplicated.Rd man/tables.Rd man/trimTails.Rd
src/Biostrings_stubs.c
src/IRanges_stubs.c
src/Makevars.in
src/Makevars.win
src/R_init_ShortRead.c
src/S4Vectors_stubs.c
src/ShortRead.h
src/XVector_stubs.c
src/alphabet.c
src/call.h
src/const.h
src/io.c
src/io_bowtie.c
src/io_soap.c
src/maqmap_m.h
src/readBfaToc.cc
src/read_maq_map.cc
src/sampler.c
src/trim.c
src/trim.h
src/util.c
src/xsnap.c
tests/ShortRead_unit_tests.R
vignettes/Overview.Rnw
vignettes/README
vignettes/ShortRead_and_HilbertVis.Rnw_
vignettes/ShortRead_and_HilbertVis.pdf
vignettes/hilbert.bib
vignettes/images/HilbertDisplay_GUI.pdf
vignettes/images/HilbertDisplay_GUI.png
vignettes/images/HilbertPlot_H3K4me1.pdf
vignettes/images/HilbertPlot_H3K4me1.png
vignettes/images/HilbertPlot_H3K4me3.pdf
vignettes/images/HilbertPlot_H3K4me3.png
vignettes/images/Strand_and_Dir.pdf vignettes/images/hilbert_3col.pdf
vignettes/images/hilbert_3col.png
vignettes/qa_E-MTAB-1147.Rda
vignettes/simon2.bst
Bioconductor-mirror/ShortRead documentation built on June 1, 2017, 2:21 a.m.