ENCODE-DCC / dnase_pipelineLinks
ENCODE DNase-seq pipeline essentials for running on dnanexus.
☆12Updated 6 years ago
Alternatives and similar repositories for dnase_pipeline
Users that are interested in dnase_pipeline are comparing it to the libraries listed below
Sorting:
- nucleosome calling using ATAC-seq☆109Updated 5 years ago
- A tool for bigWig files.☆118Updated 7 years ago
- DCC uses output from the STAR read mapper to systematically detect back-splice junctions in next-generation sequencing data. DCC applies …☆37Updated 3 years ago
- AQUAS TF and histone ChIP-seq pipeline☆111Updated 3 years ago
- Neoantigens prediction pipeline for multi- or single-region vcf files using ANNOVAR and netMHCpan.☆112Updated last year
- DEPRECATED. This tool has been superseded by https://github.com/griffithlab/pVACtools☆61Updated 6 years ago
- A toolset for profiling alternative splicing events in RNA-Seq data.☆83Updated 11 months ago
- STAR based ENCODE Long RNA-Seq processing pipeline☆96Updated 4 years ago
- Tools for processing UMI RNA-tag data☆131Updated 2 years ago
- ENCODE Uniform processing pipeline for ChIP-seq☆123Updated 5 years ago
- ☆72Updated 2 years ago
- Analysis of epigenetic signals captured by fragmentation patterns of cell-free DNA☆77Updated 5 years ago
- An R package for inferring the subclonal architecture of tumors☆122Updated 2 years ago
- ☆120Updated 2 years ago
- Analysis Workflow for Assay for Transposase-Accessible Chromatin using sequencing (ATAC-Seq)☆75Updated 2 years ago
- ☆57Updated 5 years ago
- xHLA: Fast and accurate HLA typing from short read sequence data☆113Updated 2 years ago
- MISO: Mixture of Isoforms model for RNA-Seq isoform quantitation☆137Updated 3 years ago
- A combined strategy to identify circular RNAs (circRNAs and ciRNAs) (Zhang et al., Complementary Sequence-Mediated Exon Circularization, …☆62Updated 6 years ago
- Documenting usage and experience with bioinformatic tools☆40Updated 10 years ago
- ☆91Updated 5 months ago
- Fast and accurate in silico inference of HLA genotypes from RNA-seq☆150Updated last year
- Deep-learning Augmented RNA-seq analysis of Transcript Splicing☆115Updated last year
- ☆49Updated 3 years ago
- fast and accurate alignment of BS-Seq reads using bwa-mem and a 3-letter genome☆157Updated 4 months ago
- Relevant papers for CNV and SV approaches☆94Updated last year
- Battenberg algorithm and associated implementation script☆53Updated 5 years ago
- This repo has been archived, these workflows are still available in the GATK repository under the scripts directory. The workflows are al…☆78Updated 5 years ago
- ☆50Updated 4 years ago
- A Nextflow-based pipeline for comprehensive analyses of long non-coding RNAs from RNA-seq datasets☆84Updated 3 years ago