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…
☆105Updated last month
Alternatives and similar repositories for TADbit
Users that are interested in TADbit are comparing it to the libraries listed below
Sorting:
- Lightweight converter between hic and cool contact matrices.☆74Updated last year
- Fit-Hi-C is a tool for assigning statistical confidence estimates to chromosomal contact maps produced by genome-wide genome architecture…☆89Updated 3 years ago
- Suite of motif tools, including a motif prediction pipeline for ChIP-seq experiments. See full GimmeMotifs documentation for detailed in…☆120Updated last week
- nucleosome calling using ATAC-seq☆107Updated 4 years ago
- A 3D genome data processing tutorial for ISMB/ECCB 2017☆50Updated 8 years ago
- CADD scripts release for offline scoring. For more information about CADD, please visit our website☆86Updated 4 months ago
- ☆72Updated 2 years ago
- Integrate DNA-seq and RNA-seq data to identify mutations that are associated with regulatory effects on gene expression.☆130Updated last year
- HiC uniform processing pipeline☆61Updated last year
- A tool for bigWig files.☆119Updated 7 years ago
- A modular Hi-C mapping pipeline☆99Updated 10 months ago
- Tool for the detection and quantification of alternative splicing events from RNA-Seq data.☆110Updated 2 months ago
- Extract 3D contacts (.pairs) from sequencing alignments☆116Updated last month
- TAD calling, phase imputation, 3D modeling and more for diploid single-cell Hi-C (Dip-C) and general Hi-C☆112Updated 4 years ago
- An R package to Identify, Annoatate and Visialize Isoform Switches with Functional Consequences (from RNA-seq data)☆117Updated 8 months ago
- A set of pipelines for Hi-C and ChIP-Seq analysis.☆48Updated last year
- Tools for working with BUS files☆101Updated 4 months ago
- Workflows for processing RNA data for germline short variant discovery with GATK v4 and related tools☆80Updated 4 years ago
- A quickstart tool for AmpliconArchitect. Performs all preliminary steps (alignment, CNV calling, seed interval detection) required prior …☆71Updated last week
- Analysis Workflow for Assay for Transposase-Accessible Chromatin using sequencing (ATAC-Seq)☆74Updated 2 years ago
- Create a *de novo* alternative splicing database, validate splicing events, and quantify percent spliced-in (Psi) from RNA seq data☆67Updated 5 years ago
- Publication quality NGS track plotting☆114Updated 3 years ago
- CoMut is a Python library for visualizing genomic and phenotypic information via comutation plots☆95Updated last year
- ☆88Updated 3 months ago
- CrossMap is a python program to lift over genome coordinates from one genome version to another.☆86Updated 3 months ago
- Estimation of Promoter Activity from RNA-Seq data☆56Updated 2 months ago
- REDItools are python scripts to investigate RNA editing at genomic scale.☆68Updated 2 months ago
- optimization of ribosome P-site positioning in ribosome profiling data☆54Updated 7 months ago
- A toolset for profiling alternative splicing events in RNA-Seq data.☆82Updated 8 months ago
- DaPars(Dynamic analysis of Alternative PolyAdenylation from RNA-seq)☆51Updated 2 years ago