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/CITATION
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/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/readsTo3p.Rd
man/readsTo5p.Rd
man/readsToCenter.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
