Files in icetea
Integrating Cap Enrichment with Transcript Expression Analysis
README.md
icetea documentation built on Nov. 8, 2020, 6:57 p.m.
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
