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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
Use with AI
Install the MCP server or CLI to instantly fetch BPNet documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/bpnet
AlleleSeq — pipeline for detecting allele-specific expression (ASE) and allele-specific binding (ASB) from RNA-seq and ChIP-seq data at heterozygous SNP positions. Constructs a personal diploid genome
2 shared topics • 2 shared operations
BaalChIP — Bioconductor R package for detecting allele-specific binding (ASB) in ChIP-seq data. Identifies allelic imbalance at heterozygous SNPs using a Bayesian statistical framework with logistic r
2 shared topics • 2 shared operations
BWA-MEM2 — accelerated Burrows-Wheeler Aligner for mapping short DNA reads to reference genomes. Use when aligning Illumina WGS, WES, targeted panel, ChIP-seq, or ATAC-seq FASTQ reads. Drop-in replace
2 shared topics • 2 shared operations
DeepConsensus — Google's gap-aware sequence transformer for improving PacBio CCS (HiFi) read accuracy post-basecalling. Use for: polishing PacBio long reads, reducing insertion/deletion errors in CCS
2 shared topics • 2 shared operations
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
2 shared topics • 2 shared operations