ENCODE-DCC / caperLinks
Cromwell/WDL wrapper for Python
☆58Updated 2 years ago
Alternatives and similar repositories for caper
Users that are interested in caper are comparing it to the libraries listed below
Sorting:
- An R package to Identify, Annoatate and Visialize Isoform Switches with Functional Consequences (from RNA-seq data)☆121Updated last month
- Somatic copy number analysis using WGS paired end wholegenome sequencing☆72Updated 5 years ago
- HMMRATAC peak caller for ATAC-seq data☆98Updated last year
- Copy number calling and variant classification using targeted short read sequencing☆141Updated 4 months ago
- A toolset for profiling alternative splicing events in RNA-Seq data.☆84Updated 11 months ago
- Mutation detection using GATK4 best practices and latest RNA editing filters resources. Works with both Hg38 and Hg19☆77Updated this week
- Ultraperformant reimplementation of SICER☆58Updated last month
- phasing and Allele Specific Expression from RNA-seq☆117Updated last year
- TPMCalculator quantifies mRNA abundance directly from the alignments by parsing BAM files☆135Updated last year
- Microsatellite instability (MSI) detection for tumor only data.☆112Updated last year
- Publication quality NGS track plotting☆117Updated 3 months ago
- Tools for working with BUS files☆102Updated 7 months ago
- Tool for the detection and quantification of alternative splicing events from RNA-Seq data.☆111Updated 5 months ago
- A (mostly) universal methylation extractor for BS-seq experiments.☆176Updated last year
- A toolkit for QC and visualization of ATAC-seq results.☆72Updated last year
- Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer☆100Updated 4 years ago
- nucleosome calling using ATAC-seq☆109Updated 5 years ago
- fast and accurate alignment of BS-Seq reads using bwa-mem and a 3-letter genome☆157Updated 5 months ago
- deconstructSigs☆144Updated 2 years ago
- Battenberg R package for subclonal copynumber estimation☆94Updated last month
- Relevant papers for CNV and SV approaches☆94Updated last year
- Integrate DNA-seq and RNA-seq data to identify mutations that are associated with regulatory effects on gene expression.☆136Updated last year
- A R package and executable for the preprocessing, statistical analysis, and downstream testing and visualization of differentially methyl…☆49Updated 2 years ago
- Workflows for converting between sequence data formats☆40Updated 4 years ago
- BISulfite-seq CUI Toolkit☆70Updated 3 months ago
- JAFFA is a multi-step pipeline that takes either raw RNA-Seq reads, or pre-assembled transcripts, then searches for gene fusions☆105Updated last month
- mgatk: mitochondrial genome analysis toolkit☆109Updated last year
- Command-line tool for the visualization of splicing events across multiple samples☆136Updated 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
- ☆72Updated 2 years ago