TSSr
This is the development version of TSSr; to use it, please install the devel version of Bioconductor.
TSS sequencing data analysis
Bioconductor version: Development (3.24)
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.
Author: Zhaolian Lu [aut, com]
, Keenan Berry [aut, com], Zhenbin Hu [aut, ctb], Yu Zhan [aut, ctb], Tae-Hyuk (Ted) Ahn [aut, cph], Zhenguo Lin [aut, cre, cph]
, National Science Foundation [fnd] (NSF 1951332)
Maintainer: Zhenguo Lin <zhenguo.lin at slu.edu>
citation("TSSr")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("TSSr")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("TSSr")| TSSr Vignette | HTML | R Script |
| Reference Manual |
Details
| biocViews | Alignment, Annotation, Clustering, Coverage, DataImport, DataRepresentation, DifferentialExpression, GeneExpression, GeneRegulation, GenomeBrowsers, Normalization, PeakDetection, Preprocessing, Sequencing, Software, Transcription, Transcriptomics, Visualization |
| Version | 0.99.21 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.6.0) |
| Imports | BiocGenerics(>= 0.36.1), GenomeInfoDb(>= 1.26.7), GenomicFeatures(>= 1.42.3), GenomicRanges(>= 1.42.0), IRanges(>= 2.24.1), Rsamtools(>= 2.6.0), cigarillo(>= 0.99.2), data.table (>= 1.14.0), dplyr (>= 1.0.7), ggplot2 (>= 3.3.5), grDevices (>= 4.0.3), graphics (>= 4.0.3), methods (>= 4.0.3), parallel (>= 4.0.3), rtracklayer(>= 1.50.0), stats (>= 4.0.3), stringr (>= 1.4.0), txdbmaker(>= 1.0.0), utils (>= 4.0.3) |
| System Requirements | |
| URL | https://github.com/Linlab-slu/TSSr |
| Bug Reports | https://github.com/Linlab-slu/TSSr/issues |
See More
| Suggests | BSgenome.Scerevisiae.UCSC.sacCer3, DESeq2(>= 1.30.1), Gviz(>= 1.34.1), calibrate (>= 1.7.7), ggfortify (>= 0.4.12), knitr, pkgdown, rmarkdown, testthat (>= 3.0.0), withr |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
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| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | TSSr_0.99.21.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | TSSr_0.99.21.tgz |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/TSSr |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/TSSr |
| Bioc Package Browser | https://code.bioconductor.org/browse/TSSr/ |
| Package Short Url | https://bioconductor.org/packages/TSSr/ |
| Package Downloads Report | Download Stats |