raphael-group / calderLinks
CALDER (Cancer Analysis of Longitudinal Data through Evolutionary Reconstruction) reconstructs evolutionary trees from longitudinal bulk DNA sequencing data
☆15Updated 2 years ago
Alternatives and similar repositories for calder
Users that are interested in calder are comparing it to the libraries listed below
Sorting:
- Inferring selection in cancer sequencing data using ABC and population based simulations☆11Updated 4 years ago
- Model-based tumour subclonal deconvolution using population genetics☆33Updated last week
- Bayesian mixture models for estimating and clustering cancer cell fractions☆24Updated 2 years ago
- A framework to infer mutational signatures in cancer over time☆56Updated 6 years ago
- Implementation of FACETS for Terra☆12Updated 2 years ago
- Clonal and subclonal Copy Number Alteration quality check integrating somatic mutation☆24Updated last month
- ☆12Updated last year
- Dirichlet Process based methods for subclonal reconstruction of tumours☆30Updated 8 months ago
- DriverPower☆26Updated 10 months ago
- knowledge-based genotyping of cancer hotspots from the tumor BAM files☆21Updated 3 years ago
- This repository contains the code to run the ASCETS arm-level copy number events caller for targeted sequencing data. ASCETS produces arm…☆18Updated last year
- GeneDMRs is an R package to detect the differentially methylated regions based on genes, gene body, CpG islands and gene body interacted …☆10Updated 2 years ago
- Visualization tool for temporal clonal evolution.☆18Updated 5 years ago
- Differential ATAC-seq toolkit☆27Updated last year
- 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 (…☆14Updated 8 years ago
- Code accompanying The Evolutionary history of 2,658 cancers☆46Updated 4 years ago
- Pipeline to call neoantigens from intron retention events derived from RNA-Seq data.☆28Updated 4 years ago
- Python function for TMB snake plots☆16Updated 5 years ago
- Multi-sample cancer phylogeny reconstruction☆36Updated 8 years ago
- A Package For Predicting The Disruptiveness Of Single Nucleotide Polymorphisms On Transcription Factor Binding Sites.☆31Updated last year
- Subclonal Hierarchy Inference from Somatic Mutations☆21Updated 9 months ago
- cDriver R package for finding candidate driver genes in cancers☆18Updated 7 years ago
- A tool kit for dissecting cancer evolution from multi-region derived tumor biopsies via somatic mutations☆35Updated 3 years ago
- Pipeline for the identification of cancer-related mutations from RNA-seq data☆14Updated 4 years ago
- SQUID detects both fusion-gene and non-fusion-gene structural variations from RNA-seq data☆42Updated 3 years ago
- A computational method for inferring the cancer cell fraction of tumour structural variation from whole-genome sequencing data.☆41Updated 3 months ago
- Workflow for Sequenza, cellularity and ploidy☆25Updated 3 months ago
- Code accompanying "The evolutionary history of 2,658 cancers", Nature 578, 122–128 (2020)☆17Updated 5 years ago
- Testing a neutral evolution model on cancer sequencing data☆10Updated 4 years ago
- Pairtree is a method for reconstructing cancer evolutionary history in individual patients, and analyzing intratumor genetic heterogeneit…☆41Updated last year