msCentipede 1.0 – Hierarchical Multiscale model for inferring Transcription Factor Binding from Chromatin Accessibility data

msCentipede 1.0

:: DESCRIPTION

msCentipede is an algorithm for accurately inferring transcription factor binding sites using chromatin accessibility data (Dnase-seq, ATAC-seq)

::DEVELOPER

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux / MacOS
Python

:: DOWNLOAD

:: MORE INFORMATION

Citation

msCentipede: Modeling Heterogeneity across Genomic Sites and Replicates Improves Accuracy in the Inference of Transcription Factor Binding.
Raj A, Shim H, Gilad Y, Pritchard JK, Stephens M.
PLoS One. 2015 Sep 25;10(9):e0138030. doi: 10.1371/journal.pone.0138030.

MEDEA – Motif Enrichment of Differential Elements of Accessibility

MEDEA

:: DESCRIPTION

MEDEA identifies lineage-specifying transcription factors (TFs) from chromatin accessibility assays.

::DEVELOPER

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

:: MORE INFORMATION

Citation

Mariani L, Weinand K, Gisselbrecht SS, Bulyk ML.
MEDEA: analysis of transcription factor binding motifs in accessible chromatin.
Genome Res. 2020 May;30(5):736-748. doi: 10.1101/gr.260877.120. Epub 2020 May 18. PMID: 32424069; PMCID: PMC7263192.