raphael-group / calderLinks
CALDER (Cancer Analysis of Longitudinal Data through Evolutionary Reconstruction) reconstructs evolutionary trees from longitudinal bulk DNA sequencing data
☆15Updated last year
Alternatives and similar repositories for calder
Users that are interested in calder are comparing it to the libraries listed below
Sorting:
- Model-based subclonal deconvolution from bulk sequencing.☆33Updated last week
- Inferring selection in cancer sequencing data using ABC and population based simulations☆11Updated 4 years ago
- Bayesian mixture models for estimating and clustering cancer cell fractions☆24Updated 2 years ago
- ☆12Updated last year
- CNAqc - Copy Number Alteration (CNA) Quality Check package☆22Updated 3 months ago
- DriverPower☆26Updated 7 months ago
- knowledge-based genotyping of cancer hotspots from the tumor BAM files☆21Updated 3 years ago
- Python function for TMB snake plots☆16Updated 5 years ago
- ☆12Updated 2 weeks ago
- Dirichlet Process based methods for subclonal reconstruction of tumours☆29Updated 5 months ago
- Pipeline to call neoantigens from intron retention events derived from RNA-Seq data.☆28Updated 4 years ago
- A framework to infer mutational signatures in cancer over time☆55Updated 6 years ago
- Singularity port of HLA typing based on an input exome BAM file and is currently infers infers alleles for the three major MHC class I (…☆13Updated 8 years ago
- Detecting somatic mutations and predicting tumor-specific neo-antigens☆29Updated 4 years ago
- ☆22Updated 6 months ago
- Multi-sample cancer phylogeny reconstruction☆35Updated 7 years ago
- Implementation of FACETS for Terra☆12Updated 2 years ago
- A tool kit for dissecting cancer evolution from multi-region derived tumor biopsies via somatic mutations☆36Updated 3 years ago
- Git repo for CONIPHER tree building☆22Updated 5 months ago
- Codes and Data for FFPEsig manuscript☆17Updated last year
- Subclonal Hierarchy Inference from Somatic Mutations☆21Updated 6 months ago
- SQUID detects both fusion-gene and non-fusion-gene structural variations from RNA-seq data☆43Updated 3 years ago
- A Package For Predicting The Disruptiveness Of Single Nucleotide Polymorphisms On Transcription Factor Binding Sites.☆29Updated last year
- Integrative pipeline for profiling DNA copy number and inferring tumor phylogeny☆20Updated 5 years ago
- Code accompanying The Evolutionary history of 2,658 cancers☆46Updated 4 years ago
- This repository contains the code to run the ASCETS arm-level copy number events caller for targeted sequencing data. ASCETS produces arm…☆16Updated last year
- Differential ATAC-seq toolkit☆27Updated last year
- ☆12Updated last year
- DRAGEN Tumor/Normal workflow post-processing☆22Updated last year
- 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