sfu-compbio / citup
Clonality Inference in Multiple Tumor Samples using Phylogeny
☆13Updated 9 years ago
Alternatives and similar repositories for citup:
Users that are interested in citup are comparing it to the libraries listed below
- Main repository for Drews et al. (Nature, 2022)☆39Updated last year
- Fork of https://bitbucket.org/mcgranahanlab/lohhla☆16Updated 4 years ago
- All-FIT - Allele-Frequency-based Imputation of Tumor Purity☆17Updated 5 years ago
- ☆18Updated 6 years ago
- Comprehensive genome-wide visualization of absolute copy number and copy neutral variations☆28Updated 5 years ago
- CNApp represents the first web tool to perform a comprehensive and integrative analysis of copy number alterations (CNAs) in a user-frien…☆19Updated 5 years ago
- MAnorm2 for Normalizing and Comparing ChIP-seq Samples☆32Updated 2 years ago
- Fork from https://bitbucket.org/mcgranahanlab/lohhla/src, modified for MSKCC needs☆30Updated last year
- Pipeline to call neoantigens from intron retention events derived from RNA-Seq data.☆28Updated 3 years ago
- Code accompanying Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes☆43Updated 3 years ago
- Quantifying copy number signatures from absolute copy number profiles☆23Updated 3 weeks ago
- Filtering of PDX samples for mouse derived reads☆27Updated 2 years ago
- Combined mutation recurrence and functional impact to identify coding and non-coding cancer drivers☆15Updated 6 years ago
- Algorithm for detecting alternative splicing in a population of single cells. See details in Welch et al., Nucleic Acids Research 2016: h…☆21Updated 8 years ago
- Package for calculation of Homologous Recombination Deficiency☆13Updated 4 years ago
- ☆14Updated 2 years ago
- CNV analysis workflow code for the manuscript☆13Updated 4 years ago
- RNA editing tests☆16Updated 4 years ago
- R package to calculate the Aneuploidy Score from Chromosome Arm-level SCNAs/Aneuploidies (CAAs) as outlined and expanded by Shukla et al.…☆16Updated 3 years ago
- ☆13Updated 7 years ago
- Next-Gen Sequencing tools from the Horvath Lab☆39Updated this week
- MutSig2CV from Lawrence et al. 2014☆30Updated 4 years ago
- ☆24Updated last year
- A neoantigen calling pipeline begins from variants record file (MAF) (Not maintain now)☆29Updated 5 years ago
- Dirichlet Process based methods for subclonal reconstruction of tumours☆29Updated 3 months ago
- Filters for false-positive mutation calls in NGS☆30Updated 5 years ago
- Explore, compare, and evaluate Bioconductor packages related to genomic copy number analysis☆21Updated last year
- A flexible framework to annotate and prioritize cancer somatic mutations.☆8Updated 7 years ago
- CLIP-seq Analysis of Multi-mapped reads☆29Updated 3 years ago
- SigProfilerTopography allows evaluating the effect of chromatin organization, histone modifications, transcription factor binding, DNA re…☆19Updated last month