ShixiangWang / Variants2Neoantigen
A neoantigen calling pipeline begins from variants record file (MAF) (Not maintain now)
☆29Updated 5 years ago
Alternatives and similar repositories for Variants2Neoantigen:
Users that are interested in Variants2Neoantigen are comparing it to the libraries listed below
- Filtering of PDX samples for mouse derived reads☆27Updated 2 years ago
- An R package to plot maps of clone distributions in somatic evolution☆17Updated last year
- R package to calculate the Aneuploidy Score from Chromosome Arm-level SCNAs/Aneuploidies (CAAs) as outlined and expanded by Shukla et al.…☆16Updated 4 years ago
- ☆40Updated 7 years ago
- Code accompanying Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes☆43Updated 4 years ago
- Main repository for Drews et al. (Nature, 2022)☆39Updated last year
- Package for calculation of Homologous Recombination Deficiency☆13Updated 4 years ago
- Clonality Inference in Multiple Tumor Samples using Phylogeny☆14Updated 9 years ago
- Conveniently perform ASCAT copy-number analysis from Tumor-Normal or Tumor only BAM files in R☆11Updated 3 years ago
- ☆29Updated 6 years ago
- Combined mutation recurrence and functional impact to identify coding and non-coding cancer drivers☆15Updated 6 years ago
- knowledge-based genotyping of cancer hotspots from the tumor BAM files☆21Updated 3 years ago
- QBRC Neoantigen calling pipeline with CSiN calculation embedded☆24Updated 3 years ago
- CNApp represents the first web tool to perform a comprehensive and integrative analysis of copy number alterations (CNAs) in a user-frien…☆20Updated 5 years ago
- TIGS (Tumor Immunogenicity Score) project https://doi.org/10.7554/eLife.49020☆31Updated 3 years ago
- A pan-cancer genome-wide analysis reveals tumour dependencies by induction of nonsense-mediated decay☆14Updated 4 years ago
- A tool kit for dissecting cancer evolution from multi-region derived tumor biopsies via somatic mutations☆36Updated 3 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 4 years ago
- Model-based subclonal deconvolution from bulk sequencing.☆33Updated 3 months ago
- GCAP (Gene-level Circular Amplicon Prediction) firstly implements extrachromosomal DNA detection from whole-exome-sequencing (WES) data a…☆18Updated 3 months ago
- cDriver R package for finding candidate driver genes in cancers☆18Updated 7 years ago
- MAnorm2 for Normalizing and Comparing ChIP-seq Samples☆32Updated 2 years ago
- MutSig2CV from Lawrence et al. 2014☆31Updated 4 years ago
- Immune Cell Gene Signatures for Profiling the Microenvironment of Solid Tumours☆26Updated 4 years ago
- Dichotomous of innate immune landscape☆17Updated 5 years ago
- MicrOSAtellite Instability Classifier☆15Updated 7 years ago
- a computational pipeline for the quantification of the Tumor Immune contexture from human RNA-seq data☆18Updated 3 years ago
- Machine learning algorithm to predict biological pathway relationships based on functional genomics networks☆20Updated 6 years ago
- Collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using R.☆16Updated 3 years ago