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 tumour subclonal deconvolution using population genetics☆33Updated 2 weeks 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
- Bayesian mixture models for estimating and clustering cancer cell fractions☆24Updated 2 years ago
- ☆12Updated last year
- Clonal and subclonal Copy Number Alteration quality check integrating somatic mutation☆22Updated 3 months 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
- DriverPower☆26Updated 8 months ago
- A framework to infer mutational signatures in cancer over time☆55Updated 6 years ago
- Inferring selection in cancer sequencing data using ABC and population based simulations☆11Updated 4 years ago
- Implementation of FACETS for Terra☆12Updated 2 years ago
- Code accompanying The Evolutionary history of 2,658 cancers☆46Updated 4 years ago
- Combined mutation recurrence and functional impact to identify coding and non-coding cancer drivers☆15Updated 6 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
- mutSignatures R package - updated (dev) version - 2.1.4☆14Updated 2 years 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
- A neoantigen calling pipeline begins from variants record file (MAF) (Not maintain now)☆29Updated 6 years ago
- A Package For Predicting The Disruptiveness Of Single Nucleotide Polymorphisms On Transcription Factor Binding Sites.☆29Updated last year
- Explore the cancer relevance of your gene list☆52Updated 6 months ago
- Differential ATAC-seq toolkit☆27Updated 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 last year
- Testing a neutral evolution model on cancer sequencing data☆10Updated 4 years ago
- Codes and Data for FFPEsig manuscript☆17Updated last year
- Detecting somatic mutations and predicting tumor-specific neo-antigens☆29Updated 4 years ago
- Pairtree is a method for reconstructing cancer evolutionary history in individual patients, and analyzing intratumor genetic heterogeneit…☆38Updated last year
- A computational method for inferring the cancer cell fraction of tumour structural variation from whole-genome sequencing data.☆41Updated 3 weeks ago
- ☆12Updated 5 years ago
- RNA-seq data comprehensive data analysis toolbox☆19Updated 2 years ago