3DGenomes / TADbitLinks
TADbit is a complete Python library to deal with all steps to analyze, model and explore 3C-based data. With TADbit the user can map FASTQ files to obtain raw interaction binned matrices (Hi-C like matrices), normalize and correct interaction matrices, identify and compare the so-called Topologically Associating Domains (TADs), build 3D models f…
☆108Updated 2 months ago
Alternatives and similar repositories for TADbit
Users that are interested in TADbit are comparing it to the libraries listed below
Sorting:
- A 3D genome data processing tutorial for ISMB/ECCB 2017☆52Updated 8 years ago
- Fit-Hi-C is a tool for assigning statistical confidence estimates to chromosomal contact maps produced by genome-wide genome architecture…☆92Updated 3 years ago
- Lightweight converter between hic and cool contact matrices.☆74Updated last year
- Extract 3D contacts (.pairs) from sequencing alignments☆124Updated this week
- A set of pipelines for Hi-C and ChIP-Seq analysis.☆48Updated last year
- ☆75Updated 2 years ago
- TAD calling, phase imputation, 3D modeling and more for diploid single-cell Hi-C (Dip-C) and general Hi-C☆116Updated 3 weeks ago
- CADD scripts release for offline scoring. For more information about CADD, please visit our website☆90Updated 3 months ago
- A modular Hi-C mapping pipeline☆101Updated last year
- Accurate and flexible loops calling tool for 3D genomic data.☆114Updated 3 years ago
- A tool for bigWig files.☆118Updated 7 years ago
- nucleosome calling using ATAC-seq☆110Updated 5 years ago
- Extract data quickly from Juicebox via straw☆69Updated 10 months ago
- Integrate DNA-seq and RNA-seq data to identify mutations that are associated with regulatory effects on gene expression.☆136Updated last year
- ☆53Updated 3 years ago
- HiC uniform processing pipeline☆62Updated 2 years ago
- ☆94Updated 7 months ago
- This package computes informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. It can also be used to…☆62Updated 5 years ago
- Analysis pipeline for the GUIDE-seq assay.☆81Updated 2 years ago
- Analysis Workflow for Assay for Transposase-Accessible Chromatin using sequencing (ATAC-Seq)☆75Updated 2 years ago
- Tools for working with BUS files☆102Updated 8 months ago
- Workflows for processing RNA data for germline short variant discovery with GATK v4 and related tools☆84Updated 4 years ago
- Microsatellite Instability (MSI) detection using high-throughput sequencing data.☆115Updated 10 months ago
- Suite of motif tools, including a motif prediction pipeline for ChIP-seq experiments. See full GimmeMotifs documentation for detailed in…☆124Updated 4 months ago
- A quickstart tool for AmpliconArchitect. Enables all steps (alignment, CNV calling, seed interval detection) prior to running AmpliconArc…☆77Updated this week
- phasing and Allele Specific Expression from RNA-seq☆117Updated last year
- Publication quality NGS track plotting☆117Updated 3 months ago
- Deep-learning Augmented RNA-seq analysis of Transcript Splicing☆115Updated last year
- Create a *de novo* alternative splicing database, validate splicing events, and quantify percent spliced-in (Psi) from RNA seq data☆67Updated 5 years ago
- optimization of ribosome P-site positioning in ribosome profiling data☆59Updated 11 months ago