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Benoukraf Lab's Projects

forkedtf icon forkedtf

ForkedTF is an R-library that introduces Forked-PMW (FPMW) and Forked-Sequence Logos (F-Logos) to provide a more comprehensive depiction of the sequence affinity of a Transcription factor (TF) of interest, including its DNA sequence and DNA methylation level, along with a segregated list of partner TFs.

forkedtf-beta icon forkedtf-beta

forkedTF: Representing Transcription Factor Dimer Binding Sites Using Forked-Position Weight Matrices and Forked-Sequence Logos

gatk4-exome-analysis-pipeline icon gatk4-exome-analysis-pipeline

This WDL pipeline implements data pre-processing and initial variant calling according to the GATK Best Practices for germline SNP and Indel discovery in human exome sequencing data.

nanovar icon nanovar

Structural variant caller for low-depth long-read sequencing data

slicercoloc-z-stats icon slicercoloc-z-stats

This is an extension for computing the percentage of colocalization (Spatial overlap between different channels) of Z-stack images.

sns icon sns

Analysis pipelines for sequencing data

tfregulomer icon tfregulomer

TFregulomeR reveals transcription factors’ context-specific features and functions

tfregulomer-old icon tfregulomer-old

TFregulomeR reveals transcription factors’ context-specific features and functions

warp icon warp

WDL Analysis Research Pipelines

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