Tag: TSS

TSRchitect 1.20.0 – Promoter Identification from large-scale TSS Profiling data

TSRchitect 1.20.0

:: DESCRIPTION

TSRchitect allows the user to efficiently identify the putative promoter (the transcription start region, or TSR) from a variety of TSS profiling data types, including both single-end (e.g. CAGE) as well as paired-end (RAMPAGE, PEAT, STRIPE-seq).

::DEVELOPER

The Brendel Group @ Indiana University

:: REQUIREMENTS

  • Linux
  • R
  • Bioconductor

:: DOWNLOAD

TSRchitect

:: MORE INFORMATION

Citation

Raborn RT, Brendel VP.
Using RAMPAGE to Identify and Annotate Promoters in Insect Genomes.
Methods Mol Biol. 2019;1858:99-116. doi: 10.1007/978-1-4939-8775-7_9. PMID: 30414114.

TSSr – Comprehensive Analyses of Transcription Start Sit (TSS) data

TSSr

:: DESCRIPTION

TSSr is an R package that provides rich functions for mapping transcription start sites (TSSs) and characterizations of structures and activities of core promoters based on various types of sequencing data generated by high-throughput techniques that sequence the very 5’end of RNA transcripts (TSS sequencing), such as cap analysis of gene expression (CAGE),nAnT-iCAGE, NanoCAGE, transcript leader sequencing (TL-seq), transcript isoform sequencing (TIF-seq), TSS-seq, RAMPAGE, single-cell tagged reverse transcription (STRT), global nuclear run-on cap (GRO-cap) and STRIPE-seq.

::DEVELOPER

Zhenguo Lin’s lab at Saint Louis University.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOS
  • R

:: DOWNLOAD

TSSr

:: MORE INFORMATION

Citation:

Lu Z, Berry K, Hu Z, Zhan Y, Ahn TH, Lin Z.
TSSr: an R package for comprehensive analyses of TSS sequencing data.
NAR Genom Bioinform. 2021 Nov 12;3(4):lqab108. doi: 10.1093/nargab/lqab108. PMID: 34805991; PMCID: PMC8598296.