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/usr/lib/R/site-library/ShortRead/CITATION
/usr/lib/R/site-library/ShortRead/DESCRIPTION
/usr/lib/R/site-library/ShortRead/INDEX
/usr/lib/R/site-library/ShortRead/Meta/Rd.rds
/usr/lib/R/site-library/ShortRead/Meta/features.rds
/usr/lib/R/site-library/ShortRead/Meta/hsearch.rds
/usr/lib/R/site-library/ShortRead/Meta/links.rds
/usr/lib/R/site-library/ShortRead/Meta/nsInfo.rds
/usr/lib/R/site-library/ShortRead/Meta/package.rds
/usr/lib/R/site-library/ShortRead/Meta/vignette.rds
/usr/lib/R/site-library/ShortRead/NAMESPACE
/usr/lib/R/site-library/ShortRead/NEWS
/usr/lib/R/site-library/ShortRead/R/ShortRead
/usr/lib/R/site-library/ShortRead/R/ShortRead.rdb
/usr/lib/R/site-library/ShortRead/R/ShortRead.rdx
/usr/lib/R/site-library/ShortRead/doc/Overview.R
/usr/lib/R/site-library/ShortRead/doc/Overview.Rnw
/usr/lib/R/site-library/ShortRead/doc/Overview.pdf
/usr/lib/R/site-library/ShortRead/doc/index.html
/usr/lib/R/site-library/ShortRead/extdata/Data/C1-36Firecrest/Bustard/GERALD/s_1_sequence.txt
/usr/lib/R/site-library/ShortRead/extdata/Data/C1-36Firecrest/Bustard/GERALD/s_2_export.txt
/usr/lib/R/site-library/ShortRead/extdata/Data/C1-36Firecrest/Bustard/GERALD/s_5_0001_realign.txt
/usr/lib/R/site-library/ShortRead/extdata/Data/C1-36Firecrest/Bustard/s_1_0001_prb.txt
/usr/lib/R/site-library/ShortRead/extdata/Data/C1-36Firecrest/Bustard/s_1_0001_seq.txt
/usr/lib/R/site-library/ShortRead/extdata/Data/C1-36Firecrest/Bustard/s_1_1_0001_qseq.txt
/usr/lib/R/site-library/ShortRead/extdata/Data/C1-36Firecrest/s_1_0001_int.txt
/usr/lib/R/site-library/ShortRead/extdata/Data/C1-36Firecrest/s_1_0001_nse.txt
/usr/lib/R/site-library/ShortRead/extdata/E-MTAB-1147/ERR127302_1_subset.fastq.gz
/usr/lib/R/site-library/ShortRead/extdata/E-MTAB-1147/ERR127302_2_subset.fastq.gz
/usr/lib/R/site-library/ShortRead/extdata/bowtie/s_1_aligned_bowtie.txt
/usr/lib/R/site-library/ShortRead/extdata/maq/out.aln.1.txt
/usr/lib/R/site-library/ShortRead/extdata/maq/out.aln.2.txt
/usr/lib/R/site-library/ShortRead/help/AnIndex
/usr/lib/R/site-library/ShortRead/help/ShortRead.rdb
/usr/lib/R/site-library/ShortRead/help/ShortRead.rdx
/usr/lib/R/site-library/ShortRead/help/aliases.rds
/usr/lib/R/site-library/ShortRead/help/paths.rds
/usr/lib/R/site-library/ShortRead/html/00Index.html
/usr/lib/R/site-library/ShortRead/html/R.css
/usr/lib/R/site-library/ShortRead/libs/ShortRead.so
/usr/lib/R/site-library/ShortRead/script/qa-test.R
/usr/lib/R/site-library/ShortRead/template/0000-Header.html
/usr/lib/R/site-library/ShortRead/template/1000-Overview.html
/usr/lib/R/site-library/ShortRead/template/1100-Overview-SolexaRealign.html
/usr/lib/R/site-library/ShortRead/template/2000-RunSummary.html
/usr/lib/R/site-library/ShortRead/template/3000-ReadDistribution.html
/usr/lib/R/site-library/ShortRead/template/4000-CycleSpecific.html
/usr/lib/R/site-library/ShortRead/template/5000-PerTile.html
/usr/lib/R/site-library/ShortRead/template/6000-Alignment.html
/usr/lib/R/site-library/ShortRead/template/7000-MultipleAlignment.html
/usr/lib/R/site-library/ShortRead/template/8000-DepthOfCoverage.html
/usr/lib/R/site-library/ShortRead/template/9000-AdapterContamination.html
/usr/lib/R/site-library/ShortRead/template/9999-Footer.html
/usr/lib/R/site-library/ShortRead/template/QA.css
/usr/lib/R/site-library/ShortRead/template/QAAdapterContamination.html
/usr/lib/R/site-library/ShortRead/template/QAFiltered.html
/usr/lib/R/site-library/ShortRead/template/QAFlagged.html
/usr/lib/R/site-library/ShortRead/template/QAFooter.html
/usr/lib/R/site-library/ShortRead/template/QAFrequentSequence.html
/usr/lib/R/site-library/ShortRead/template/QAHeader.html
/usr/lib/R/site-library/ShortRead/template/QANucleotideByCycle.html
/usr/lib/R/site-library/ShortRead/template/QANucleotideUse.html
/usr/lib/R/site-library/ShortRead/template/QAQualityByCycle.html
/usr/lib/R/site-library/ShortRead/template/QAQualityUse.html
/usr/lib/R/site-library/ShortRead/template/QAReadQuality.html
/usr/lib/R/site-library/ShortRead/template/QASequenceUse.html
/usr/lib/R/site-library/ShortRead/template/QASources.html
/usr/lib/R/site-library/ShortRead/template/image/bioclogo-small.gif
/usr/lib/R/site-library/ShortRead/template/qa_solexa.Rnw
/usr/lib/R/site-library/ShortRead/unitTests/cases/PE_export.txt.gz
/usr/lib/R/site-library/ShortRead/unitTests/cases/s_1_0001_int_head.txt.p
/usr/lib/R/site-library/ShortRead/unitTests/cases/s_1_0001_nse_head.txt.p
/usr/lib/R/site-library/ShortRead/unitTests/cases/s_1_0001_pos_head.txt
/usr/lib/R/site-library/ShortRead/unitTests/cases/s_1_results_head.txt
/usr/lib/R/site-library/ShortRead/unitTests/cases/s_1_sequence.8_lines_illegal_nucleotide.txt
/usr/lib/R/site-library/ShortRead/unitTests/cases/s_1_sequence.8_lines_read_mismatch.txt
/usr/lib/R/site-library/ShortRead/unitTests/cases/s_1_sequence.8_lines_read_quality_mismatch.txt
/usr/lib/R/site-library/ShortRead/unitTests/cases/s_1_sequence.9_lines.txt
/usr/lib/R/site-library/ShortRead/unitTests/cases/s_1_sequence.txt
/usr/lib/R/site-library/ShortRead/unitTests/cases/s_2_0001_realign_3col_head.txt
/usr/lib/R/site-library/ShortRead/unitTests/cases/s_2_0001_realign_head.txt
/usr/lib/R/site-library/ShortRead/unitTests/cases/s_2_export_run_as_factor.txt
/usr/lib/R/site-library/ShortRead/unitTests/cases/s_2_export_toIUPAC.txt
/usr/lib/R/site-library/ShortRead/unitTests/cases/sanger.fastq
/usr/lib/R/site-library/ShortRead/unitTests/cases/soap.txt
/usr/lib/R/site-library/ShortRead/unitTests/cases/solexa.fastq
/usr/lib/R/site-library/ShortRead/unitTests/test_AlignedRead.R
/usr/lib/R/site-library/ShortRead/unitTests/test_AllClasses.R
/usr/lib/R/site-library/ShortRead/unitTests/test_FastqFile.R
/usr/lib/R/site-library/ShortRead/unitTests/test_Intensity.R
/usr/lib/R/site-library/ShortRead/unitTests/test_SRError.R
/usr/lib/R/site-library/ShortRead/unitTests/test_SRFilter.R
/usr/lib/R/site-library/ShortRead/unitTests/test_SRFilterResult.R
/usr/lib/R/site-library/ShortRead/unitTests/test_SRList.R
/usr/lib/R/site-library/ShortRead/unitTests/test_SRVector.R
/usr/lib/R/site-library/ShortRead/unitTests/test_ShortRead.R
/usr/lib/R/site-library/ShortRead/unitTests/test_ShortReadQ.R
/usr/lib/R/site-library/ShortRead/unitTests/test_SolexaIntensity.R
/usr/lib/R/site-library/ShortRead/unitTests/test_append.R
/usr/lib/R/site-library/ShortRead/unitTests/test_coverage.R
/usr/lib/R/site-library/ShortRead/unitTests/test_filterFastq.R
/usr/lib/R/site-library/ShortRead/unitTests/test_functions.R
/usr/lib/R/site-library/ShortRead/unitTests/test_qa.R
/usr/lib/R/site-library/ShortRead/unitTests/test_readPrb.R
/usr/lib/R/site-library/ShortRead/unitTests/test_readQseq.R
/usr/lib/R/site-library/ShortRead/unitTests/test_readXStringColumns.R
/usr/lib/R/site-library/ShortRead/unitTests/test_renew.R
/usr/lib/R/site-library/ShortRead/unitTests/test_trimEnds.R
/usr/lib/R/site-library/ShortRead/unitTests/test_trimTails.R
/usr/lib/R/site-library/ShortRead/unitTests/test_writeFastq.R
/usr/share/doc/r-bioc-shortread/changelog.Debian.gz
/usr/share/doc/r-bioc-shortread/copyright