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The Top 23 Somatic Variants Open Source Projects

Open source projects categorized as Somatic Variants
Categories > Somatic Variants
Octopus ⭐ 285
Bayesian haplotype-based mutation calling
most recent commit 8 months ago
Somaticseq ⭐ 185
An ensemble approach to accurately detect somatic mutations using SomaticSeq
total releases 1most recent commit 6 months ago
Sigprofilerextractor ⭐ 132
SigProfilerExtractor allows de novo extraction of mutational signatures from data generated in a matrix format. The tool identifies the number of operative mutational signatures, their activities in each sample, and the probability for each signature to cause a specific mutation type in a cancer sample. The tool makes use of SigProfilerMatrixGenerator and SigProfilerPlotting.
dependent packages 3total releases 50most recent commit 5 months agopypi SigProfilerExtractor} Downloads
Sarek ⭐ 126
Detect germline or somatic variants from normal or tumour/normal whole-genome or targeted sequencing
most recent commit 4 years ago
Neusomatic ⭐ 124
NeuSomatic: Deep convolutional neural networks for accurate somatic mutation detection
most recent commit 3 years ago
Sigminer ⭐ 119
🌲 An easy-to-use and scalable toolkit for genomic alteration signature (a.k.a. mutational signature) analysis and visualization in R https://shixiangwang.github.io/sigminer/reference/
total releases 32most recent commit 4 months ago
Sigprofilermatrixgenerator ⭐ 91
SigProfilerMatrixGenerator creates mutational matrices for all types of somatic mutations. It allows downsizing the generated mutations only to parts for the genome (e.g., exome or a custom BED file). The tool seamlessly integrates with other SigProfiler tools.
dependent packages 10total releases 102most recent commit 3 months agopypi SigProfilerMatrixGenerator} Downloads
Sv Callers ⭐ 52
Snakemake-based workflow for detecting structural variants in genomic data
most recent commit a year ago
Monopogen ⭐ 50
SNV calling from single cell sequencing
most recent commit 3 months ago
Deepsomatic ⭐ 45
DeepSomatic is an analysis pipeline that uses a deep neural network to call somatic variants from tumor-normal sequencing data.
most recent commit 6 months ago
Tcgamutations ⭐ 44
R data package for pre-compiled somatic mutations from TCGA cohorts (from Broad Firehose and TCGA MC3 Project)
most recent commit 3 years ago
Sigprofilerplotting ⭐ 43
SigProfilerPlotting provides a standard tool for displaying all types of mutational signatures as well as all types of mutational patterns in cancer genomes. The tool seamlessly integrates with other SigProfiler tools.
dependent packages 9total releases 86most recent commit 5 months agopypi sigProfilerPlotting} Downloads
Clairs ⭐ 42
ClairS - a deep-learning method for long-read somatic small variant calling
most recent commit 3 months ago
2020plus ⭐ 39
Classifies genes as an oncogene, tumor suppressor gene, or as a non-driver gene by using Random Forests
most recent commit 4 years ago
Germline Dna ⭐ 23
A BioWDL variantcalling pipeline for germline DNA data. Starting with FASTQ files to produce VCF files. Category:Multi-Sample
most recent commit a year ago
Helmsman ⭐ 19
highly-efficient & lightweight mutation signature matrix aggregation
most recent commit 3 years ago
Sigprofilersimulator ⭐ 18
SigProfilerSimulator allows realistic simulations of mutational patterns and mutational signatures in cancer genomes. The tool can be used to simulate signatures of single point mutations, double point mutations, and insertion/deletions. Further, the tool makes use of SigProfilerMatrixGenerator and SigProfilerPlotting.
most recent commit 7 months ago
Clairs To ⭐ 18
ClairS-TO - a deep-learning method for tumor-only somatic SNV calling
most recent commit 3 months ago
Sigprofilermatrixgeneratorr ⭐ 17
R wrapper for utilizing the SigProfilerMatrixGenerator framework
most recent commit a year ago
Tif ⭐ 16
Transposon Insertion Finder - Detection of new TE insertions in NGS data
most recent commit 2 years ago
Sigprofilertopography ⭐ 13
SigProfilerTopography allows evaluating the effect of chromatin organization, histone modifications, transcription factor binding, DNA replication, and DNA transcription on the activities of different mutational processes. SigProfilerTopography elucidates the unique topographical characteristics of mutational signatures.
dependent packages 1total releases 250most recent commit 3 months agopypi SigProfilerTopography} Downloads
Accucopy ⭐ 13
Accucopy is a computational method that infers Allele-specific Copy Number alterations from low-coverage low-purity tumor sequencing Data.
most recent commit 9 months ago
Ngs Pipeline ⭐ 12
Pipeline for Somatic Variant Calling with WES and WGS data
most recent commit a year ago
The 4 Most Depended On Somatic Variants Open Source Projects
The 7 Latest Releases In Somatic Variants Open Source Projects
Somaticseq ⭐ 185
An ensemble approach to accurately detect somatic mutations using SomaticSeq
total releases 1latest release May 04, 2022most recent commit 6 months ago
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