Files in icetea

Integrating Cap Enrichment with Transcript Expression Analysis

README.md

NAMESPACE

DESCRIPTION

LICENSE

build/vignette.rds

R/annotateTSS.R R/splitBAM_byRepindex.R R/mapCaps.R R/AllGenerics.R R/detectTSS.R R/utils.R R/plotting_functions.R R/demultiplexFASTQ.R R/filterDuplicates.R R/splitBAM_byIndex.R R/AllClasses.R R/detectDiffTSS.R R/methods.R R/exampleCSobject.R R/getGeneCounts.R

vignettes/references.bib

vignettes/mapcap_analysis.Rmd man/readsToCenter.Rd man/readsTo5p.Rd man/filterDups.Rd man/demultiplexFASTQ.Rd man/exampleCSobject.Rd man/numReadsInBed.Rd man/detectDiffTSS.Rd man/newCapSet.Rd man/split_fastq.Rd man/diffQCplots.Rd man/getGeneCounts.Rd man/sampleInfo.Rd man/readsTo3p.Rd man/getChromBins.Rd man/strandBinCounts.Rd man/getBamFlags.Rd man/exportTSS.Rd man/getranks.Rd man/mapCaps.Rd man/getMCparams.Rd man/splitBAM_byIndex.Rd man/filterDuplicates.Rd man/splitranks.Rd man/get_newfastq.Rd man/plotReadStats.Rd man/plotTSSprecision.Rd man/getChromWindows.Rd man/plotPrecision.Rd man/check_capSet.Rd man/fitDiffTSS.Rd man/annotateTSS.Rd man/getNormFactors.Rd man/activeChrs.Rd man/detectTSS.Rd man/splitBAM_byRepindex.Rd tests/testthat.R tests/testthat/test_annotateTSS.R tests/testthat/test_CapSet.R tests/testthat/test_filterDups.R tests/testthat/test_demult.R tests/testthat/test_tssDetect.R

inst/NEWS

inst/CITATION

inst/doc/mapcap_analysis.R inst/doc/mapcap_analysis.Rmd

inst/doc/mapcap_analysis.html

inst/extdata/mapcap_test_R1.fastq.gz

inst/extdata/testTSS_grl.rds

inst/extdata/testTSS_merged.bed

inst/extdata/mapcap_test_R2.fastq.gz

inst/extdata/bam/embryo2.bam.bai

inst/extdata/bam/embryo3.bam.bai

inst/extdata/bam/embryo4.bam

inst/extdata/bam/embryo1.bam

inst/extdata/bam/embryo2.bam

inst/extdata/bam/embryo3.bam

inst/extdata/bam/embryo4.bam.bai

inst/extdata/bam/embryo1.bam.bai

inst/extdata/filtered_bam/embryo1.filtered.bam.bai

inst/extdata/filtered_bam/embryo4.filtered.bam

inst/extdata/filtered_bam/embryo1.filtered.bam

inst/extdata/filtered_bam/embryo3.filtered.bam

inst/extdata/filtered_bam/embryo2.filtered.bam

inst/extdata/filtered_bam/embryo2.filtered.bam.bai

inst/extdata/filtered_bam/embryo3.filtered.bam.bai

inst/extdata/filtered_bam/embryo4.filtered.bam.bai

inst/extdata/demult_fastq/embryo1_R2.fastq.gz

inst/extdata/demult_fastq/embryo1_R1.fastq.gz

inst/extdata/demult_fastq/embryo2_R2.fastq.gz

inst/extdata/demult_fastq/embryo4_R1.fastq.gz

inst/extdata/demult_fastq/embryo3_R1.fastq.gz

inst/extdata/demult_fastq/embryo4_R2.fastq.gz

inst/extdata/demult_fastq/embryo3_R2.fastq.gz

inst/extdata/demult_fastq/embryo2_R1.fastq.gz

icetea documentation built on Nov. 8, 2020, 6:57 p.m.