Man pages for icetea
Integrating Cap Enrichment with Transcript Expression Analysis

activeChrsMatch BAM headers bw files and get active chromosome list...
annotateTSSAnnotate the provided Transcription Start Sites
check_capSetCheck capset validity
demultiplexFASTQDemultiplex and tag fastq files using sample barcodes
detectDiffTSSDetect differentially expressed Transcription Start Sites...
detectTSSDetection of Trancription start sites based on local...
diffQCplotsMake DESeq2 or edgeR QC plots
exampleCSobjectCreate example CapSet object
exportTSSExport the detected TSS from CapSet object as .bed files
filterDuplicatesFilter PCR-duplicates from mapped files using internal UMIs
filterDupsFilter PCR-duplicates from BAM file using internal UMIs
fitDiffTSSDetect differentially expressed Transcription Start Sites...
getBamFlagsGet flags to read from bam
getChromBinsGet chromosome bins from BAM files
getChromWindowsGet chromosome sliding windows from BAM files
getGeneCountsGet gene-level counts from TSS data
getMCparamsGet platform-specific multicore params
get_newfastqGet data to create new ShortReadQ object after barcode...
getNormFactorsCalculate normalization factors from CapSet object
getranksAssign feature ranks on a VariantAnnotation output
mapCapsMap the data from 5' profiling techniques
newCapSetCreate a new CapSet object
numReadsInBedCount the number of reads in a given GRanges
plotPrecisionPlotprecision background script
plotReadStatsPlot read statistics from the CapSet object
plotTSSprecisionCompare the precision of TSS detection between multiple...
readsTo3ppreprocess reads to count only 3' overlaps
readsTo5ppreprocess reads to count only 5' overlaps
readsToCenterpreprocess reads to count only center overlaps
sampleInfoRetrieve and replace sample information of a CapSet object
splitBAM_byIndexSplit the composite BAM file using internal indexes (MAPCap)
splitBAM_byRepindexSplit the composite BAM file using replicate indexes (MAPCap...
split_fastqSplit paired-end fastq by barcodes
splitranksGet features with the best rank for each TSS
strandBinCountsPerform stranded Bin counts
icetea documentation built on Nov. 8, 2020, 6:57 p.m.