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TOBIAS — Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal. Python toolkit for differential transcription factor (TF) footprinting from ATAC-seq data. Corrects Tn5 insertio
Use with AI
Install the MCP server or CLI to instantly fetch TOBIAS documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/tobias
BPNet — deep learning framework for learning base-resolution regulatory sequence features from genomics assays (ChIP-seq, ATAC-seq, CUT&RUN). Uses dilated convolutional neural networks to predict TF b
2 shared topics • 2 shared operations
HMMRATAC — Hidden Markov Model-based peak caller for ATAC-seq chromatin accessibility data. Identifies nucleosome-free regions (NFR), mono-, di-, and tri-nucleosomal fragments using an HMM that models
3 shared topics
Bismark — bisulfite-seq alignment and methylation calling toolkit. Maps bisulfite-treated reads to a reference genome using Bowtie 2, HISAT2, or minimap2, performs cytosine methylation calls in CpG/CH
2 shared topics • 1 shared operation
Use when working with bsseeker2 — BSseeker2 — bisulfite sequencing aligner
2 shared topics • 1 shared operation
wigToBigWig converts Wiggle (.wig) format files — fixedStep and variableStep — to bigWig binary format for genome browsers (UCSC, IGV, WashU Epigenome Browser). Essential for ChIP-seq, ATAC-seq, RNA-s
2 shared topics • 1 shared operation