mcmero / SVclone
A computational method for inferring the cancer cell fraction of tumour structural variation from whole-genome sequencing data.
☆40Updated 4 months ago
Related projects ⓘ
Alternatives and complementary repositories for SVclone
- Dirichlet Process based methods for subclonal reconstruction of tumours☆29Updated last month
- 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…☆43Updated 2 years ago
- Model-based subclonal deconvolution from bulk sequencing.☆33Updated last year
- Flexible Bayesian inference of mutational signatures☆33Updated last year
- Pairtree is a method for reconstructing cancer evolutionary history in individual patients, and analyzing intratumor genetic heterogeneit…☆37Updated 7 months ago
- Single Cell Caller (SCcaller) - Identify single nucleotide variations (SNVs) from single cell sequencing data☆34Updated last year
- Comprehensive genome-wide visualization of absolute copy number and copy neutral variations☆28Updated 5 years ago
- Package Homepage: http://bioconductor.org/packages/devel/bioc/html/annotatr.html Bug Reports: https://support.bioconductor.org/p/new/post…☆26Updated 3 months ago
- SQUID detects both fusion-gene and non-fusion-gene structural variations from RNA-seq data☆41Updated 2 years ago
- An R package for predicting HR deficiency from mutation contexts☆27Updated last year
- deepStats: a stastitical toolbox for deeptools and genomic signals☆32Updated 3 years ago
- Main repository for Drews et al. (Nature, 2022)☆38Updated last year
- Single nucleotide variant (SNV) detection and genotyping algorithm for single-cell DNA sequencing data☆11Updated 4 years ago
- A nextflow pipeline to perform state-of-the-art genome-wide association studies.☆63Updated 5 months ago
- Method for Identifying Novel Transcripts and Isoforms using Equivalence classes, in cancer and rare disease.☆34Updated 4 months ago
- DeCiFer is an algorithm that simultaneously selects mutation multiplicities and clusters SNVs by their corresponding descendant cell frac…☆20Updated 6 months ago
- An R package for studying mutational signatures and structural variant signatures along clonal evolution in cancer.☆69Updated 5 months ago
- a set of NGS pipelines☆24Updated 2 weeks ago
- SV clustering☆26Updated 3 years ago
- Opossum is a tool to pre-process RNA-seq reads prior to variant calling.☆28Updated 6 years ago
- a peak-calling and differential analysis tool for replicated ChIP-Seq data☆37Updated 2 years ago
- DeTiN is designed to measure tumor-in-normal contamination and improve somatic variant detection sensitivity when using a contaminated ma…☆49Updated 2 years ago
- DriverPower☆26Updated 5 months ago
- Combined mutation recurrence and functional impact to identify coding and non-coding cancer drivers☆15Updated 6 years ago
- Texomer: Integrating Analysis of Cancer Genome and Transcriptome Sequencing Data☆20Updated 4 years ago
- ☆43Updated 6 years ago
- RNA editing tests☆16Updated 4 years ago
- A Package For Predicting The Disruptiveness Of Single Nucleotide Polymorphisms On Transcription Factor Binding Sites.☆28Updated 3 months ago
- RNA-seq workflow: differential transcript usage☆20Updated last year
- Identify cell types and pathways affected by genetic risk loci.☆35Updated 8 months ago