Oshlack / JAFFA
JAFFA is a multi-step pipeline that takes either raw RNA-Seq reads, or pre-assembled transcripts, then searches for gene fusions
☆93Updated 8 months ago
Alternatives and similar repositories for JAFFA:
Users that are interested in JAFFA are comparing it to the libraries listed below
- T1K is a versatile methods to genotype highly polymorphic genes (e.g. KIR, HLA) with bulk or single-cell RNA-seq, WGS or WES data.☆71Updated 2 weeks ago
- Allele-specific alignment sorting☆55Updated 2 years ago
- Robust detection of clinically relevant structural and copy number variation from whole genome sequencing data☆69Updated 8 months ago
- QDNAseq package for Bioconductor☆50Updated 9 months ago
- Snakemake-based workflow for detecting structural variants in genomic data☆80Updated 2 months ago
- Full-length transcriptome splicing and mutation analysis☆82Updated 10 months ago
- An R package to Identify, Annoatate and Visialize Isoform Switches with Functional Consequences (from RNA-seq data)☆112Updated 3 months ago
- ☆68Updated last year
- Single Cell Long Read is a suite of tools dedicated to Cell barcode / UMI assignment and analysis of highly multiplexed single cell Nanop…☆73Updated 2 years ago
- Microsatellite instability (MSI) detection for tumor only data.☆104Updated last year
- Lima - Demultiplex Barcoded PacBio Samples☆66Updated last week
- ☆58Updated 3 years ago
- Technology agnostic long read analysis pipeline for transcriptomes☆143Updated last year
- phasing and Allele Specific Expression from RNA-seq☆114Updated 9 months ago
- Battenberg R package for subclonal copynumber estimation☆86Updated last month
- Variant Calling Pipeline Using GATK4 and Nextflow☆54Updated 2 years ago
- R package designed to simplify structural variant analysis☆72Updated 3 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…☆89Updated last month
- Publication quality NGS track plotting☆111Updated 2 years ago
- Characterization of Germline variants☆98Updated 3 years ago
- Mutation detection using GATK4 best practices and latest RNA editing filters resources. Works with both Hg38 and Hg19☆74Updated 9 months ago
- fork of RSeQC python RNAseq metrics suit of tools☆48Updated 6 years ago
- MIP based joint inference of copy number and rearrangement state in cancer whole genome sequence data.☆56Updated last month
- Somatic copy number analysis using WGS paired end wholegenome sequencing☆71Updated 4 years ago
- Somatic structural variant caller for long-read data☆65Updated 2 weeks ago
- REDItools are python scripts to investigate RNA editing at genomic scale.☆64Updated 6 months ago
- nextNEOpi: a comprehensive pipeline for computational neoantigen prediction☆73Updated 2 weeks ago
- Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer☆97Updated 4 years ago
- Ribo-seq TIS Hunter, predicting translation initiation sites and ORFs using riboseq data☆38Updated 5 months ago
- optimization of ribosome P-site positioning in ribosome profiling data☆52Updated 2 months ago