cancerit / cgpPindelLinks
Cancer Genome Project Insertion/Deletion detection pipeline based around Pindel
☆28Updated 3 months ago
Alternatives and similar repositories for cgpPindel
Users that are interested in cgpPindel are comparing it to the libraries listed below
Sorting:
- SV clustering☆29Updated 4 years ago
- SNV expectation maximisation based mutation calling algorithm aimed at detecting somatic mutations in paired (tumour/normal) cancer sampl…☆63Updated 4 months ago
- ☆35Updated 4 years ago
- SQUID detects both fusion-gene and non-fusion-gene structural variations from RNA-seq data☆42Updated 3 years ago
- Simultaneous detection of SNPs and Indels using a 16-genotype probabilistic model☆27Updated last year
- Keep Me Around: Intron Retention Detection☆29Updated 6 years ago
- An automated RNA-seq pipeline using Nextflow☆37Updated 11 months ago
- Using k-mers to call HLA alleles in RNA sequencing data☆23Updated 7 years ago
- MIP based joint inference of copy number and rearrangement state in cancer whole genome sequence data.☆58Updated 5 months 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 3 years ago
- a Shiny/R application to view and annotate copy number variations☆28Updated 2 years ago
- Pipeline for identifying viral integration and fusion mRNA reads from NGS data. Manuscript is currently in preparation.☆28Updated 4 years ago
- gnomAD browser pre-ASHG 2018☆33Updated 4 years ago
- utilities for working with IGV: opening files remotely in either desktop IGV or a web viewer (igv.js), creating screenshots, etc.☆49Updated 6 years ago
- Differential ATAC-seq toolkit☆27Updated last year
- A set of tools to annotate VCF files with expression and readcount data☆29Updated 5 months ago
- See the main fork of this repository here >>>☆38Updated 3 months ago
- novoBreak: local assembly for breakpoint detection in cancer genomes☆26Updated 7 years ago
- picking up low allelic-fraction, somatic variants from tumor samples☆14Updated 7 years ago
- Decrypting somatic mutation patterns to reveal the evolution of cancer☆56Updated 4 years ago
- DriverPower☆26Updated 7 months ago
- R API for browsing, analyzing, and manipulating reference-aligned genome graphs in a GenomicRanges framework☆41Updated this week
- Opossum is a tool to pre-process RNA-seq reads prior to variant calling.☆28Updated 7 years ago
- CLAMMS is a scalable tool for detecting common and rare copy number variants from whole-exome sequencing data.☆29Updated 4 years ago
- Filters for false-positive mutation calls in NGS☆32Updated 6 years ago
- Run Picard on BAM files and collate 90 metrics into one file.☆40Updated 7 years ago
- ☆11Updated 7 years ago
- Fast fusion detection using kallisto☆80Updated 2 months ago
- ☆25Updated 7 years 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