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

vivekbhr/icetea documentation built on June 8, 2020, 4:45 a.m.