4dn-dcic / pairixLinks
1D/2D indexing and querying on bgzipped text file with a pair of genomic coordinates
☆89Updated 7 months ago
Alternatives and similar repositories for pairix
Users that are interested in pairix are comparing it to the libraries listed below
Sorting:
- TAD calling, phase imputation, 3D modeling and more for diploid single-cell Hi-C (Dip-C) and general Hi-C☆111Updated 4 years ago
- Extract 3D contacts (.pairs) from sequencing alignments☆115Updated last week
- Genomic Association Tester☆31Updated 2 years ago
- Software to compute reproducibility and quality scores for Hi-C data☆50Updated 6 years ago
- TADtool is an interactive tool for the identification of meaningful parameters in TAD-calling algorithms for Hi-C data.☆48Updated 2 years ago
- A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains☆44Updated 3 years ago
- 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
- SingleCell Nanopore sequencing data analysis☆60Updated 3 months ago
- ☆71Updated 2 years ago
- dcHiC: Differential compartment analysis for Hi-C datasets☆72Updated last year
- Allele-specific alignment sorting☆58Updated 2 years ago
- JAFFA is a multi-step pipeline that takes either raw RNA-Seq reads, or pre-assembled transcripts, then searches for gene fusions☆98Updated 2 months ago
- Snakemake-based workflow for detecting structural variants in genomic data☆80Updated 6 months ago
- RepEnrich2 is an updated method to estimate repetitive element enrichment using high-throughput sequencing data.☆40Updated 3 years ago
- ☆29Updated last year
- code associated with crane-nature-2015, 10.1038/nature14450☆36Updated 10 years ago
- trackplot is a tool for visualizing various next-generation sequencing (NGS) data, including DNA-seq, RNA-seq, single-cell RNA-seq and fu…☆97Updated 3 months ago
- Lightweight converter between hic and cool contact matrices.☆74Updated last year
- Genome-wide contact analysis using sklearn☆68Updated last year
- perl cworld module and collection of utility/analysis scripts for C data (3C, 4C, 5C, Hi-C)☆67Updated 6 years ago
- A versatile tool to perform pile-up analysis on Hi-C data in .cool format.☆80Updated 10 months ago
- A set of pipelines for Hi-C and ChIP-Seq analysis.☆47Updated last year
- SPP - R package for analysis of ChIP-seq and other functional sequencing data☆43Updated 4 years ago
- HiC for copy Number variation and Translocation detection☆39Updated 4 years ago
- IDR☆31Updated 2 years ago
- EM based transcript abundance from nanopore reads mapped to a transcriptome with minimap2☆63Updated 10 months ago
- ENCODE long read RNA-seq pipeline☆50Updated 2 years ago
- A pipeline for analyzing DNA methylation data from bisulfite sequencing.☆70Updated 2 years ago
- BISulfite-seq CUI Toolkit☆66Updated 7 months ago
- BAMscale is a one-step tool for either 1) quantifying and normalizing the coverage of peaks or 2) generated scaled BigWig files for easy …☆70Updated 8 months ago