HuntsmanCancerInstitute / USeqLinks
180+ Java applications for analyzing next generation sequencing data from ChIPSeq, RNASeq, BisSeq, DNASeq, variant annotation/ filtering, alignment/VCF QC, capture array design, IGV/ DAS2/IGB/UCSC file manipulation, etc. Both GUI and cmd line interfaces.
☆18Updated last month
Alternatives and similar repositories for USeq
Users that are interested in USeq are comparing it to the libraries listed below
Sorting:
- CAVA (Clinical Annotation of VAriants)☆14Updated 6 years ago
- Automated human exome/genome variants detection from FASTQ files☆22Updated 3 years ago
- Gene Fusion Visualiser☆51Updated 2 years ago
- novoBreak: local assembly for breakpoint detection in cancer genomes☆26Updated 7 years ago
- Detection of Circular RNA and Fusions from RNA-Seq☆32Updated 6 years ago
- Structural Variation and fusion detection using targeted sequencing data from circulating cell free DNA☆29Updated last year
- 📊Evaluating, filtering, comparing, and visualising VCF☆28Updated 2 years ago
- Remove primer sequence from BAM alignments by soft-clipping☆31Updated 5 years ago
- A Framework to call Structural Variants from NGS based datasets☆22Updated 7 years ago
- for visual evaluation of read support for structural variation☆54Updated last year
- Plot CNV data with a genome viewer in R☆15Updated 8 years ago
- SiNVICT: Ultra-Sensitive Detection of Single Nucleotide Variants and Indels in Circulating Tumour DNA☆27Updated 4 years ago
- Copy Number Variation Detection In Next-generation sequencing Gene panels was designed for small (single-exon) copy number variation (CNV…☆21Updated 5 years ago
- A set of tools to annotate VCF files with expression and readcount data☆29Updated 5 months ago
- ONCOCNV - a package to detect copy number changes in Targeted Deep Sequencing and Exome-seq data☆25Updated 2 years ago
- Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer☆49Updated this week
- A program for summarising CpG methylation patterns☆20Updated 8 years ago
- Long read to rMATS☆32Updated 2 years ago
- Full-spectrum copy number variation detection by high-throughput DNA sequencing☆37Updated 3 years ago
- ☆46Updated 5 years ago
- Filters for false-positive mutation calls in NGS☆31Updated 6 years ago
- VisCap is an open flexible, software program targeted to clinical laboratories for inference and visualization of germline copy number va…☆23Updated 5 years ago
- Method for Identifying Novel Transcripts and Isoforms using Equivalence classes, in cancer and rare disease.☆35Updated last year
- A tool for evaluating RNA seq mapping☆22Updated 6 years ago
- alternative splicing analysis pipeline☆19Updated 4 years ago
- 10x Genomics Linked-Read Alignment, Variant Calling, Phasing, and Structural Variant Calling☆32Updated 5 years ago
- Python program designed to reconstruct immunoglobulin gene rearrangements and oncogenic translocations from WGS, WES and capture NGS in l…☆20Updated 2 years ago
- A method to identify structural variation from sequencing data in target regions☆32Updated 4 years ago
- Support code for NGS copy number algorithms. Takes a file of locations and a [cr|b]am file and generates a count of coverage of each alle…☆45Updated 2 years ago
- Code associated with 2019 manuscript entitled "Transcript expression-aware annotation improves rare variant discovery and interpretation…☆33Updated 3 years ago