cancerit / cgpPindelView external linksLinks
Cancer Genome Project Insertion/Deletion detection pipeline based around Pindel
☆28May 14, 2025Updated 9 months ago
Alternatives and similar repositories for cgpPindel
Users that are interested in cgpPindel are comparing it to the libraries listed below
Sorting:
- SNV expectation maximisation based mutation calling algorithm aimed at detecting somatic mutations in paired (tumour/normal) cancer sampl…☆63Apr 24, 2025Updated 9 months ago
- Somatic copy number analysis using WGS paired end wholegenome sequencing☆71Nov 20, 2020Updated 5 years ago
- A tool for diagnosing SMA in exome, genome or targeted sequencing data☆13Apr 30, 2025Updated 9 months ago
- Roslin is a reproducible and reusable workflow for Cancer Genomic Sequencing Analysis☆16Nov 13, 2024Updated last year
- Breakpoints via assembly - Identifies breaks and attempts to assemble rearrangements in whole genome sequencing data.☆57Jul 19, 2024Updated last year
- Battenberg R package for subclonal copynumber estimation☆95Dec 8, 2025Updated 2 months ago
- Tumor Heterogeneity Analysis (THetA) and THetA2 are algorithms that estimate the tumor purity and clonal/subclonal copy number aberration…☆76Aug 20, 2021Updated 4 years ago
- Annotates variants in MAF with OncoKB annotation.☆141Jan 8, 2026Updated last month
- Ximmer is a system for CNV calling on exome and targeted genomic sequencing☆19Jan 28, 2026Updated 2 weeks ago
- Single-cell analytic toolbox that offers modular workflows for multi-level cellular annotation and user-friendly analysis reports☆11May 25, 2023Updated 2 years ago
- Algorithm to implement Fraction and Copy number Estimate from Tumor/normal Sequencing.☆158Jan 29, 2026Updated 2 weeks ago
- A CNN model to identify MEIs in WGS☆12Mar 4, 2025Updated 11 months ago
- Fast, accurate and simple to use command line tool for variant detection in NGS data.☆12Sep 3, 2019Updated 6 years ago
- GeneDMRs is an R package to detect the differentially methylated regions based on genes, gene body, CpG islands and gene body interacted …☆10Nov 18, 2023Updated 2 years ago
- sort genomic data☆36Nov 7, 2025Updated 3 months ago
- Battenberg algorithm and associated implementation script☆53Oct 21, 2020Updated 5 years ago
- normalize, left-align, trim, validate and clean VCF files☆20Jul 22, 2015Updated 10 years ago
- An ultra fast and accurate paired-end adapter trimmer that needs no a priori adapter sequences.☆22Jan 19, 2021Updated 5 years ago
- Relevant papers for CNV and SV approaches☆94Nov 5, 2024Updated last year
- Identifying large scale inversions between two genomes by mapping genome 1's unique kmers onto genome 2.☆10Jun 6, 2025Updated 8 months ago
- EXPERIMENTAL implementation of side graph☆10Apr 16, 2015Updated 10 years ago
- Convert VCF (Variant Call Format) into TCGA MAF (Mutation Annotation Format)☆15Jul 15, 2016Updated 9 years ago
- Everything but the kitchen sink☆12Feb 6, 2025Updated last year
- RNA-Seq workflow for Kids-First DRC☆11Sep 22, 2025Updated 4 months ago
- SUPBUB is a tool that, in linear time, finds out superbubbles(special graph-structures) in a directed graph.☆12Sep 19, 2019Updated 6 years ago
- Alignment and variant-calling pipeline for Illumina HIV sequences.☆11May 19, 2020Updated 5 years ago
- ☆10Nov 3, 2025Updated 3 months ago
- Add functional variant annotation to MAF file☆11Nov 20, 2024Updated last year
- Functions to extract information from Oxford Nanopore sequencing data and alignments☆11Dec 4, 2025Updated 2 months ago
- Build components for CloudMan, Galaxy on the Cloud, or Galaxy Server☆20Jun 27, 2017Updated 8 years ago
- SARS-CoV-2 variant calling and consensus assembly pipeline☆26Sep 18, 2023Updated 2 years ago
- don't get DUP'ed or DEL'ed by your putative SVs.☆107Dec 14, 2020Updated 5 years ago
- Parallel Recipes : parallel workflow execution made easy☆13Sep 1, 2015Updated 10 years ago
- ☆12Feb 19, 2017Updated 8 years ago
- ☆12Nov 21, 2023Updated 2 years ago
- Hemang Parikh☆11Jan 12, 2016Updated 10 years ago
- fork of dorado that supports S/BLOW5☆12Jan 8, 2026Updated last month
- gvcf aggregation tool☆12Feb 7, 2018Updated 8 years ago
- A command line tool (in Kotlin/JVM) for intuitively visualizing BAM alignments. (Currently unmaintained)☆11Jan 7, 2024Updated 2 years ago