Package: TSSr 0.99.21

Zhenguo Lin

TSSr: TSS sequencing data analysis

TSSr package provides a comprehensive workflow on TSS data starts from identification of accurate TSS locations, clustering TSSs within small genomic regions corresponding to core promoters, and transcriptional activity quantifications, as well as specialized downstream analyses including core promoter shape, cluster annotation, gene differential expression, core promoter shift. TSSr can take multiple formats of files as input, such as Binary Sequence Alignment Map (BAM) files (single-ended or paired-ended), Browser Extension Data (bed) files, BigWig files, ctss files or tss tables. TSSr also generates various types of TSS or core promoter track files which can be visualized in the UCSC Genome Browser or Integrative Genomics Viewer (IGV). TSSr also exports downstream analyses result tables and plots. Multiple cores are supported on Linux or Mac platforms.

Authors:Zhaolian Lu [aut, com], Keenan Berry [aut, com], Zhenbin Hu [aut, ctb], Yu Zhan [aut, ctb], Tae-Hyuk Ahn [aut, cph], Zhenguo Lin [aut, cre, cph], National Science Foundation [fnd]

TSSr_0.99.21.tar.gz
TSSr_0.99.21.zip(r-4.7-any)TSSr_0.99.21.zip(r-4.6-any)TSSr_0.99.21.zip(r-4.5-any)
TSSr_0.99.21.tgz(r-4.6-any)TSSr_0.99.21.tgz(r-4.5-any)
TSSr_0.99.21.tar.gz(r-4.7-any)TSSr_0.99.21.tar.gz(r-4.6-any)
TSSr_0.99.21.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
TSSr/json (API)

# Install 'TSSr' in R:

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

Bug tracker:https://github.com/linlab-slu/tssr/issues

Datasets:

exampleTSSr - TSSr example data

On BioConductor:TSSr-0.99.21(bioc 3.24)

software transcription coverage geneexpression generegulation peakdetection dataimport datarepresentation transcriptomics sequencing annotation genomebrowsers normalization preprocessing visualization differentialexpression alignment clustering bioconductor bioinformatics cage core-promoter-elements genomics transcription-start-site tss-sequencing

6.65 score 11 stars 17 scripts 88 downloads 40 exports 92 dependencies

Last updated from:bba29ddb31. Checks:1 NOTE, 5 OK, 4 ERROR. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	200
linux-devel	OK	423
source / vignettes	OK	304
linux-release	OK	515
macos-release	OK	358
macos-oldrel	ERROR	374
windows-devel	ERROR	388
windows-release	ERROR	319
windows-oldrel	ERROR	354
wasm-release	OK	161

Exports:annotateCluster assignedClusters callEnhancer clusterShape clusterTSS consensusCluster consensusClusters deGene DEtables enhancers exportClustersTable exportClustersToBed exportDETable exportEnhancerTable exportShapeTable exportShiftTable exportTSStable exportTSStoBedgraph filteredClusters filterTSS getTSS librarySizes mergeSamples normalizeTSS plotCorrelation plotDE plotInterQuantile plotShape plotTSS plotTssPCA PromoterShift refTable shapeCluster shiftPromoter show tagClusters TAGtables TSSmatrix TSSr unassignedClusters

Dependencies:AnnotationDbi askpass BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocIO BiocParallel biomaRt Biostrings bit bit64 bitops blob cachem cigarillo cli codetools cpp11 crayon curl data.table DBI dbplyr digest dplyr farver fastmap filelock formatR futile.logger futile.options generics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 glue gtable hms httr httr2 IRanges isoband jsonlite KEGGREST labeling lambda.r lifecycle magrittr memoise mime openssl pillar pkgconfig png prettyunits progress purrr R6 RColorBrewer RCurl restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Vectors S7 scales Seqinfo snow stringi stringr sys tibble tidyr tidyselect txdbmaker UCSC.utils utf8 vctrs viridisLite withr XML xml2 XVector yaml

TSSr Vignette

Rendered fromvignette.Rmdusingknitr::rmarkdown

Last update: 2026-08-21
Started: 2020-06-27

Help page	Topics
Annotate clusters with GFF annotation file.	annotateCluster annotateCluster,TSSr-method
Identification of enhancers	callEnhancer callEnhancer,TSSr-method
Cluster TSSs into tag clusters	clusterTSS clusterTSS,TSSr-method
Make consensus clusters across multiple samples.	consensusCluster consensusCluster,TSSr-method
Analysis of gene differential expression.	deGene deGene,TSSr-method
TSSr example data	exampleTSSr
Export cluster tables	exportClustersTable exportClustersTable,TSSr-method
Creating bed files of clusters	exportClustersToBed exportClustersToBed,TSSr-method
Export gene differential expression results table	exportDETable exportDETable,TSSr-method
Export enhancer tables	exportEnhancerTable exportEnhancerTable,TSSr-method
Export core promoter shape score tables	exportShapeTable exportShapeTable,TSSr-method
Export core promoter shift table	exportShiftTable exportShiftTable,TSSr-method
Export TSS tables	exportTSStable exportTSStable,TSSr-method
Creating Bedgraph/BigWig tracks of TSSs	exportTSStoBedgraph exportTSStoBedgraph,TSSr-method
Filter raw TSS counts or normalized TSS	filterTSS filterTSS,TSSr-method
Precisely identify TSSs from bam files, paired end bam files, bed files, BigWig files, tss files, or tss tables.	getTSS getTSS,TSSr-method
Merge TSS samples	mergeSamples mergeSamples,TSSr-method
Normalize raw TSS counts	normalizeTSS normalizeTSS,TSSr-method
Pairwise scatter plots and correlations of TSS signal	plotCorrelation plotCorrelation,TSSr-method
Plot gene differential expressions	plotDE plotDE,TSSr-method
Plot core promoter interquantile width	plotInterQuantile plotInterQuantile,TSSr-method
Plot core promoter shape	plotShape plotShape,TSSr-method
Plot TSSs and clusters	plotTSS plotTSS,TSSr-method
Plotting principle component analysis (PCA)	plotTssPCA plotTssPCA,TSSr-method
Analysis of core promoter shape	shapeCluster shapeCluster,TSSr-method
Select genes which have core promoter shift across different experiments.	shiftPromoter shiftPromoter,TSSr-method
Display a compact summary of a TSSr object	show,TSSr-method
Access data stored in a TSSr object	assignedClusters assignedClusters,TSSr-method clusterShape clusterShape,TSSr-method consensusClusters consensusClusters,TSSr-method DEtables DEtables,TSSr-method enhancers enhancers,TSSr-method filteredClusters filteredClusters,TSSr-method librarySizes librarySizes,TSSr-method PromoterShift PromoterShift,TSSr-method refTable refTable,TSSr-method tagClusters tagClusters,TSSr-method TAGtables TAGtables,TSSr-method TSSmatrix TSSmatrix,TSSr-method TSSr-accessors unassignedClusters unassignedClusters,TSSr-method
TSSr: A package for transcription start site sequencing data analyses.	TSSr TSSr-class

Package: TSSr 0.99.21

TSSr: TSS sequencing data analysis

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