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The Top 23 Copy Number Variation Open Source Projects

Open source projects categorized as Copy Number Variation
Categories > Copy Number Variation
Pcgr ⭐ 234
Personal Cancer Genome Reporter (PCGR)
most recent commit 6 months ago
Scevan ⭐ 65
R package that automatically classifies the cells in the scRNA data by segregating non-malignant cells of tumor microenviroment from the malignant cells. It also infers the copy number profile of malignant cells, identifies subclonal structures and analyses the specific and shared alterations of each subpopulation.
most recent commit 3 months ago
Clincnv ⭐ 65
Detection of copy number changes in Germline/Trio/Somatic contexts in NGS data
most recent commit 5 months ago
Titancna ⭐ 59
Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer
most recent commit 3 years ago
Classifycnv ⭐ 43
ClassifyCNV: a tool for clinical annotation of copy-number variants
most recent commit a year ago
Doabsolute ⭐ 31
📦 Automate Absolute Copy Number Calling using 'ABSOLUTE' package
most recent commit 5 months ago
Cnv ⭐ 29
Copy Number Variation
most recent commit 10 months ago
Witty.er ⭐ 26
What is true, thank you, ernestly. A large variant benchmarking tool analogous to hap.py for small variants.
most recent commit 7 months ago
Aceseqworkflow ⭐ 22
Allele-specific copy number estimation with whole genome sequencing
most recent commit a year ago
Scicone ⭐ 20
Single-cell copy number calling and event history reconstruction.
most recent commit 4 months ago
Viscap ⭐ 18
VisCap is an open flexible, software program targeted to clinical laboratories for inference and visualization of germline copy number variants (CNVs) from targeted next-generation sequencing data. For algorithmic details, see Pugh TJ et al. Genet Med. 2016 Jul;18(7):712-9.
most recent commit 4 years ago
Neural Ensemble Method For Cancer Prediction ⭐ 15
A Snapshot Neural Ensemble Method for Cancer Type Prediction Based on Copy Number Variations
most recent commit 4 years ago
Postre ⭐ 13
POSTRE: Prediction Of STRuctural variant Effects
most recent commit a year ago
Genome Seek ⭐ 12
Clinical Whole Genome Sequencing Pipeline
most recent commit 5 months ago
Cnaqc ⭐ 12
CNAqc - Copy Number Alteration (CNA) Quality Check package
most recent commit 6 months ago
Scatrex ⭐ 11
Map single-cell transcriptomes to copy number evolutionary trees.
total releases 6most recent commit a year ago
Npore ⭐ 10
nPoRe: n-Polymer Realigner for improved pileup-based variant calling
most recent commit 2 years ago
Deepsvp ⭐ 10
Prioritizing Copy Number Variants (CNV) using Phenotype and Gene Functional Similarity
most recent commit 2 years ago
Orthnet ⭐ 9
CLfinder-OrthNet, a pipeline to encode orthologs from multiple genomes and their evolutionary history into networks (OrthNets) based on co-linearity between them. OrthNets enable detection of all orthologous gene groups that share the same evolutionary history, using a search based on network topology
most recent commit 2 years ago
Plethora ⭐ 8
Copy number estimation of highly duplicated sequences
most recent commit 7 years ago
Sequenza ⭐ 8
Workflow for Sequenza, cellularity and ploidy
most recent commit 7 months ago
Copynumberplots ⭐ 6
R package to create plots representing copy number data using karyoploteR
most recent commit 7 months ago
Facets2n ⭐ 5
Algorithm to implement Fraction and Allelic Copy number Estimate from Tumor/normal Sequencing using unmatched normal sample(s) for log ratio calculations
most recent commit 2 years ago
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