Package: icetea 1.25.0

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]

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icetea.pdf |icetea.html✨
icetea/json (API)
NEWS

# 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-1.25.0(bioc 3.21)icetea-1.24.0(bioc 3.20)

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

5.08 score 2 stars 7 scripts 224 downloads 2 mentions 18 exports 107 dependencies

Last updated 5 months agofrom:795af55fc2. Checks:1 OK, 8 WARNING. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Mar 19 2025
R-4.5-win	WARNING	Mar 19 2025
R-4.5-mac	WARNING	Mar 19 2025
R-4.5-linux	WARNING	Mar 19 2025
R-4.4-win	WARNING	Mar 19 2025
R-4.4-mac	WARNING	Mar 19 2025
R-4.4-linux	WARNING	Mar 19 2025
R-4.3-win	WARNING	Mar 19 2025
R-4.3-mac	WARNING	Mar 19 2025

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 BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob BSgenome cachem cli codetools colorspace cpp11 crayon csaw curl DBI DelayedArray deldir DESeq2 edgeR fansi farver fastmap formatR futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges ggplot2 glue gtable httr hwriter interp IRanges isoband jpeg jsonlite KEGGREST labeling lambda.r lattice latticeExtra lifecycle limma locfit magrittr MASS Matrix MatrixGenerics matrixStats memoise metapod mgcv mime munsell nlme openssl pillar pkgconfig plogr png pwalign R6 RColorBrewer Rcpp RcppArmadillo RcppEigen RCurl restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors scales ShortRead snow SparseArray statmod SummarizedExperiment sys tibble TxDb.Dmelanogaster.UCSC.dm6.ensGene UCSC.utils utf8 VariantAnnotation vctrs viridisLite withr XML XVector yaml

Analysing transcript 5'-profiling data using icetea

Vivek Bhardwaj and Thomas Manke

Rendered frommapcap_analysis.Rmdusingknitr::rmarkdownon Mar 19 2025.

Last update: 2018-05-18
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