Files in vivekbhr/icetea
Integrating Cap Enrichment with Transcript Expression Analysis

.BBSoptions
.Rbuildignore
.travis.yml
DESCRIPTION
LICENSE
NAMESPACE
R/AllClasses.R R/AllGenerics.R R/annotateTSS.R R/demultiplexFASTQ.R R/detectDiffTSS.R R/detectTSS.R R/exampleCSobject.R R/filterDuplicates.R R/getGeneCounts.R R/mapCaps.R R/methods.R R/plotting_functions.R R/splitBAM_byIndex.R R/splitBAM_byRepindex.R R/utils.R README.md
appveyor.yml
docs/LICENSE-text.html
docs/articles/index.html
docs/articles/mapcap_analysis.html
docs/articles/mapcap_analysis_files/figure-html/annotateTSS-1.png
docs/articles/mapcap_analysis_files/figure-html/plotPrecision-1.png
docs/articles/mapcap_analysis_files/figure-html/plotstats-1.png
docs/articles/mapcap_analysis_files/figure-html/plotstats2-1.png
docs/authors.html
docs/docsearch.json
docs/index.html
docs/jquery.sticky-kit.min.js
docs/link.svg
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/ResizeReads.html
docs/reference/TSS_detection_precision.png
docs/reference/activeChrs.html
docs/reference/annotateTSS-1.png
docs/reference/annotateTSS.html
docs/reference/calcNormFactors.html
docs/reference/check_capSet.html
docs/reference/demult_fastq/embryo1_R1.fastq.gz
docs/reference/demult_fastq/embryo1_R2.fastq.gz
docs/reference/demult_fastq/embryo2_R1.fastq.gz
docs/reference/demult_fastq/embryo2_R2.fastq.gz
docs/reference/demult_fastq/embryo3_R1.fastq.gz
docs/reference/demult_fastq/embryo3_R2.fastq.gz
docs/reference/demult_fastq/embryo4_R1.fastq.gz
docs/reference/demult_fastq/embryo4_R2.fastq.gz
docs/reference/demultiplexFASTQ.html
docs/reference/detectDiffTSS.html
docs/reference/detectTSS.html
docs/reference/exampleCSobject.html
docs/reference/exportTSS.html
docs/reference/filterDuplicates.html
docs/reference/filterDups.html
docs/reference/filtered_bam/embryo1.filtered.bam
docs/reference/filtered_bam/embryo1.filtered.bam.bai
docs/reference/filtered_bam/embryo2.filtered.bam
docs/reference/filtered_bam/embryo2.filtered.bam.bai
docs/reference/filtered_bam/embryo3.filtered.bam
docs/reference/filtered_bam/embryo3.filtered.bam.bai
docs/reference/filtered_bam/embryo4.filtered.bam
docs/reference/filtered_bam/embryo4.filtered.bam.bai
docs/reference/fitDiffTSS.html
docs/reference/getBamFlags.html
docs/reference/getChromBins.html
docs/reference/getChromWindows.html
docs/reference/getGeneCounts.html
docs/reference/getMCparams.html
docs/reference/getNormFactors.html
docs/reference/get_newfastq.html
docs/reference/getranks.html
docs/reference/index.html
docs/reference/localFilter.html
docs/reference/mapCaps.html
docs/reference/newCapSet.html
docs/reference/numReadsInBed.html
docs/reference/plotPrecision.html
docs/reference/plotReadStats-1.png
docs/reference/plotReadStats.html
docs/reference/plotTSSprecision-1.png
docs/reference/plotTSSprecision.html
docs/reference/sampleInfo.html
docs/reference/splitBAM_byIndex.html
docs/reference/splitBAM_byRepindex.html
docs/reference/split_fastq.html
docs/reference/splitranks.html
docs/reference/strandBinCounts.html
docs/reference/testSplit_RR.bam
docs/reference/testSplit_RR.bam.bai
docs/reference/testSplit_YY.bam
docs/reference/testSplit_YY.bam.bai
docs/reference/testTSS.Rdata
docs/reference/testTSS_merged.bed
docs/reference/test_filt1.bam
docs/reference/test_filt1.bam.bai
docs/reference/test_filt2.bam
docs/reference/test_filt2.bam.bai
docs/reference/test_numbers.pdf
icetea_front.png
inst/NEWS
inst/extdata/bam/embryo1.bam
inst/extdata/bam/embryo1.bam.bai
inst/extdata/bam/embryo2.bam
inst/extdata/bam/embryo2.bam.bai
inst/extdata/bam/embryo3.bam
inst/extdata/bam/embryo3.bam.bai
inst/extdata/bam/embryo4.bam
inst/extdata/bam/embryo4.bam.bai
inst/extdata/demult_fastq/embryo1_R1.fastq.gz
inst/extdata/demult_fastq/embryo1_R2.fastq.gz
inst/extdata/demult_fastq/embryo2_R1.fastq.gz
inst/extdata/demult_fastq/embryo2_R2.fastq.gz
inst/extdata/demult_fastq/embryo3_R1.fastq.gz
inst/extdata/demult_fastq/embryo3_R2.fastq.gz
inst/extdata/demult_fastq/embryo4_R1.fastq.gz
inst/extdata/demult_fastq/embryo4_R2.fastq.gz
inst/extdata/filtered_bam/embryo1.filtered.bam
inst/extdata/filtered_bam/embryo1.filtered.bam.bai
inst/extdata/filtered_bam/embryo2.filtered.bam
inst/extdata/filtered_bam/embryo2.filtered.bam.bai
inst/extdata/filtered_bam/embryo3.filtered.bam
inst/extdata/filtered_bam/embryo3.filtered.bam.bai
inst/extdata/filtered_bam/embryo4.filtered.bam
inst/extdata/filtered_bam/embryo4.filtered.bam.bai
inst/extdata/mapcap_test_R1.fastq.gz
inst/extdata/mapcap_test_R2.fastq.gz
inst/extdata/testTSS_grl.rds
inst/extdata/testTSS_merged.bed
man/ResizeReads.Rd man/activeChrs.Rd man/annotateTSS.Rd man/check_capSet.Rd man/demultiplexFASTQ.Rd man/detectDiffTSS.Rd man/detectTSS.Rd man/diffQCplots.Rd man/exampleCSobject.Rd man/exportTSS.Rd man/filterDuplicates.Rd man/filterDups.Rd man/fitDiffTSS.Rd man/getBamFlags.Rd man/getChromBins.Rd man/getChromWindows.Rd man/getGeneCounts.Rd man/getMCparams.Rd man/getNormFactors.Rd man/get_newfastq.Rd man/getranks.Rd man/mapCaps.Rd man/newCapSet.Rd man/numReadsInBed.Rd man/plotPrecision.Rd man/plotReadStats.Rd man/plotTSSprecision.Rd man/sampleInfo.Rd man/splitBAM_byIndex.Rd man/splitBAM_byRepindex.Rd man/split_fastq.Rd man/splitranks.Rd man/strandBinCounts.Rd tests/testthat.R tests/testthat/test_CapSet.R tests/testthat/test_annotateTSS.R tests/testthat/test_demult.R tests/testthat/test_filterDups.R tests/testthat/test_tssDetect.R vignettes/mapcap_analysis.Rmd
vignettes/references.bib
vivekbhr/icetea documentation built on May 26, 2019, 5:35 a.m.