yuchaojiang / Canopy
Accessing Intra-Tumor Heterogeneity and Tracking Longitudinal and Spatial Clonal Evolutionary History by Next-Generation Sequencing.
☆68Updated 3 years ago
Alternatives and similar repositories for Canopy:
Users that are interested in Canopy are comparing it to the libraries listed below
- Create mutation signatures from MAF's, and decompose them into Stratton signatures☆60Updated 5 years ago
- Tools to handle reads sequenced with unique molecular identifiers (UMIs).☆30Updated 7 years ago
- An R package for studying mutational signatures and structural variant signatures along clonal evolution in cancer.☆70Updated 11 months ago
- An archived version of the scater repository, see https://github.com/davismcc/scater for the active version.☆64Updated 7 years ago
- GREAT Analysis - Functional Enrichment on Genomic Regions☆87Updated last month
- R package for bcbio RNA-seq analysis.☆62Updated 7 months ago
- Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer☆97Updated 4 years ago
- SPP - R package for analysis of ChIP-seq and other functional sequencing data☆42Updated 3 years ago
- Glimma R package☆50Updated 7 months ago
- Disambiguation algorithm for reads aligned to human and mouse genomes using Tophat or BWA mem☆31Updated 6 years ago
- Battenberg algorithm and associated implementation script☆52Updated 4 years ago
- A collection of resources to filter 'bad' probes from the Illumina 450k and EPIC methylation arrays☆30Updated last year
- RNA-Sequencing data differential expression analysis pipeline. Performs: genome coverage (via bedtools and HTSeq), generates Circos code …☆55Updated 12 years ago
- R package for genomic feature analysis and visualization☆76Updated last week
- Transcript quantification import with automatic metadata detection☆68Updated 2 months ago
- An R package for inferring the subclonal architecture of tumors☆117Updated last year
- Tools for visualizing genomics data☆67Updated 3 years ago
- Utility functions for FACETS☆35Updated last year
- Differential Count Data Analysis Toolbox☆61Updated last year
- Reference transcriptome indices build from kallisto for popular organisms☆42Updated last year
- processes GoT amplicon data and generates a table of metrics☆29Updated 2 years ago
- a peak-calling and differential analysis tool for replicated ChIP-Seq data☆37Updated 2 years ago
- R package for Inference of differentially methylated regions (DMRs) from bisulfite sequencing☆58Updated 7 months ago
- Filtering of PDX samples for mouse derived reads☆27Updated 2 years ago
- Preprocessing of single-cell RNA-Seq (deprecated)☆62Updated 5 years ago
- ☆53Updated 2 months ago
- Snakemake based pipeline for RNA-Seq analysis☆31Updated 5 years ago
- ☆40Updated 7 years ago
- Inferring and visualizing clonal evolution in multi-sample cancer sequencing☆147Updated 4 years ago
- Scripts to import your FeatureCounts output into DEXSeq☆33Updated 6 years ago