Files in Bioconductor/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

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/count.c

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.Rmd

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/ShortRead documentation built on Nov. 2, 2024, 4:38 p.m.

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Bioconductor/ShortRead
FASTQ input and manipulation

Files in Bioconductor/ShortRead
FASTQ input and manipulation

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Bioconductor/ShortRead FASTQ input and manipulation

Files in Bioconductor/ShortRead FASTQ input and manipulation

R Package Documentation

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We want your feedback!

Bioconductor/ShortRead
FASTQ input and manipulation

Files in Bioconductor/ShortRead
FASTQ input and manipulation