Package: icetea 1.31.0

Vivek Bhardwaj

icetea: Integrating Cap Enrichment with Transcript Expression Analysis

icetea (Integrating Cap Enrichment with Transcript Expression Analysis) provides functions for end-to-end analysis of multiple 5'-profiling methods such as CAGE, RAMPAGE and MAPCap, beginning from raw reads to detection of transcription start sites using replicates. It also allows performing differential TSS detection between group of samples, therefore, integrating the mRNA cap enrichment information with transcript expression analysis.

Authors:Vivek Bhardwaj [aut, cre]

icetea_1.31.0.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
icetea/json (API)

# Install 'icetea' in R:

install.packages('icetea', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/vivekbhr/icetea/issues

On BioConductor:icetea-1.31.0(bioc 3.24)icetea-1.30.0(bioc 3.23)

immunooncology transcription geneexpression sequencing rnaseq transcriptomics differentialexpression cage expression rna-seq

5.08 score 2 stars 10 scripts 540 downloads 2 mentions 18 exports 98 dependencies

Last updated from:0b56cf4442. Checks:8 WARNING, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	237
linux-devel	WARNING	550
source / vignettes	OK	322
linux-release	WARNING	501
macos-release	WARNING	512
macos-oldrel	WARNING	481
windows-devel	WARNING	436
windows-release	WARNING	413
windows-oldrel	WARNING	416
wasm-release	OK	715

Exports:annotateTSS demultiplexFASTQ detectDiffTSS detectTSS exampleCSobject exportTSS filterDuplicates fitDiffTSS getGeneCounts getNormFactors mapCaps newCapSet plotReadStats plotTSSprecision sampleInfo sampleInfo<-splitBAM_byIndex splitBAM_byRepindex

Dependencies:abind AnnotationDbi askpass BH Biobase BiocBaseUtils BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob BSgenome cachem cigarillo cli codetools cpp11 crayon csaw curl DBI DelayedArray deldir DESeq2 edgeR farver fastmap formatR futile.logger futile.options generics GenomicAlignments GenomicFeatures GenomicRanges ggplot2 glue gtable httr hwriter interp IRanges isoband jpeg jsonlite KEGGREST labeling lambda.r lattice latticeExtra lifecycle limma locfit MASS Matrix MatrixGenerics matrixStats memoise metapod mime openssl pkgconfig png pwalign R6 RColorBrewer Rcpp RcppArmadillo RcppEigen RCurl restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors S7 scales Seqinfo ShortRead snow SparseArray statmod SummarizedExperiment sys TxDb.Dmelanogaster.UCSC.dm6.ensGene VariantAnnotation vctrs viridisLite withr XML XVector yaml

Analysing transcript 5'-profiling data using icetea

Rendered frommapcap_analysis.Rmdusingknitr::rmarkdown

Last update: 2025-07-23
Started: 2018-02-19

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Match BAM headers bw files and get active chromosome list (from restrict) (written by Aaron Lun, 12 Dec 2014, copied and modified here)	activeChrs
Annotate the provided Transcription Start Sites	annotateTSS
Check capset validity	check_capSet
Demultiplex and tag fastq files using sample barcodes	demultiplexFASTQ demultiplexFASTQ,CapSet-method
Detect differentially expressed Transcription Start Sites between two conditions (test)	detectDiffTSS detectDiffTSS,DESeqDataSet-method detectDiffTSS,DGEGLM-method
Detection of Trancription start sites based on local enrichment	detectTSS detectTSS,CapSet-method
Make DESeq2 or edgeR QC plots	diffQCplots
Create example CapSet object	exampleCSobject
Export the detected TSS from CapSet object as .bed files	exportTSS exportTSS,CapSet-method
Filter PCR-duplicates from mapped files using internal UMIs	filterDuplicates filterDuplicates,CapSet-method
Filter PCR-duplicates from BAM file using internal UMIs	filterDups
Detect differentially expressed Transcription Start Sites between two conditions (fit model)	fitDiffTSS fitDiffTSS,CapSet-method
Get data to create new ShortReadQ object after barcode trimming	get_newfastq
Get flags to read from bam	getBamFlags
Get chromosome bins from BAM files	getChromBins
Get chromosome sliding windows from BAM files	getChromWindows
Get gene-level counts from TSS data	getGeneCounts getGeneCounts,CapSet-method
Get platform-specific multicore params	getMCparams
Calculate normalization factors from CapSet object	getNormFactors getNormFactors,CapSet-method
Assign feature ranks on a VariantAnnotation output	getranks
Map the data from 5' profiling techniques	mapCaps mapCaps,CapSet-method
Create a new CapSet object	CapSet CapSet-class newCapSet
Count the number of reads in a given GRanges	numReadsInBed
Plotprecision background script	plotPrecision
Plot read statistics from the CapSet object	plotReadStats plotReadStats,CapSet-method
Compare the precision of TSS detection between multiple samples	plotTSSprecision plotTSSprecision,GRanges,CapSet-method plotTSSprecision,GRanges,character-method
preprocess reads to count only 3' overlaps	readsTo3p
preprocess reads to count only 5' overlaps	readsTo5p
preprocess reads to count only center overlaps	readsToCenter
Retrieve and replace sample information of a CapSet object	sampleInfo sampleInfo,CapSet-method sampleInfo<- sampleInfo<-,CapSet-method
Split paired-end fastq by barcodes	split_fastq
Split the composite BAM file using internal indexes (MAPCap)	splitBAM_byIndex
Split the composite BAM file using replicate indexes (MAPCap data)	splitBAM_byRepindex
Get features with the best rank for each TSS	splitranks
Perform stranded Bin counts	strandBinCounts