Tag: Occupancy

DANPOS 2.2.2 – Dynamic Analysis of Nucleosome Position and Occupancy by Sequencing

DANPOS 2.2.2

:: DESCRIPTION

DANPOS is designed for genome-wide comparative analysis of nucleosome maps. It detect single-nucleotide-resolution change in positions(location), enrichment (occupancy), and fuzziness (phasing, positioning) of each nucleosome unit.

::DEVELOPER

Wei Li’s Computational Epigenomics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 DANPOS

:: MORE INFORMATION

Citation:

Genome Res. 2013 Feb;23(2):341-51. doi: 10.1101/gr.142067.112. Epub 2012 Nov 28.
DANPOS: dynamic analysis of nucleosome position and occupancy by sequencing.
Chen K, Xi Y, Pan X, Li Z, Kaestner K, Tyler J, Dent S, He X, Li W.

TOBIAS 0.10.1 – Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal

TOBIAS 0.10.1

:: DESCRIPTION

TOBIAS is a framework of tools for investigating transcription factor binding from ATAC-seq signal

::DEVELOPER

the Loosolab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

TOBIAS

:: MORE INFORMATION

Citation:

Beyond accessibility: ATAC-seq footprinting unravels kinetics of transcription factor binding during zygotic genome activation
Mette Bentsen, et al.
doi: https://doi.org/10.1101/869560

Ribomap v1.2 – Isoform-level Ribosome Occupancy Estimation Guided by Transcript Abudance

Ribomap v1.2

:: DESCRIPTION

Ribomap is a package that generates isoform-level ribosome profiles from ribosome profiling data.

::DEVELOPER

Kingsford Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOs
  • Sailfish/Salmon

:: DOWNLOAD

Ribomap

:: MORE INFORMATION

Citation

Isoform-level ribosome occupancy estimation guided by transcript abundance with Ribomap.
Wang H, McManus J, Kingsford C.
Bioinformatics. 2016 Jun 15;32(12):1880-2. doi: 10.1093/bioinformatics/btw085