Topic: "somatic-variants"
luntergroup/octopus
Bayesian haplotype-based mutation calling
Language: C++ - Size: 137 MB - Last synced at: 5 months ago - Pushed at: over 1 year ago - Stars: 304 - Forks: 38
bioinform/somaticseq
An ensemble approach to accurately detect somatic mutations using SomaticSeq
Language: Python - Size: 65.7 MB - Last synced at: 5 days ago - Pushed at: 9 days ago - Stars: 196 - Forks: 52
bioinform/neusomatic
NeuSomatic: Deep convolutional neural networks for accurate somatic mutation detection
Language: Python - Size: 68.4 MB - Last synced at: 5 months ago - Pushed at: over 3 years ago - Stars: 168 - Forks: 51
google/deepsomatic
DeepSomatic is an analysis pipeline that uses a deep neural network to call somatic variants from tumor-normal and tumor-only sequencing data.
Size: 50.8 KB - Last synced at: 6 days ago - Pushed at: 24 days ago - Stars: 167 - Forks: 18
AlexandrovLab/SigProfilerExtractor
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.
Language: Python - Size: 166 MB - Last synced at: 23 days ago - Pushed at: about 1 month ago - Stars: 157 - Forks: 55
ShixiangWang/sigminer
🌲 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/index.html
Language: R - Size: 51 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 134 - Forks: 18
SciLifeLab/Sarek Fork of nf-core/sarek 📦
Detect germline or somatic variants from normal or tumour/normal whole-genome or targeted sequencing
Language: Nextflow - Size: 43.8 MB - Last synced at: about 1 month ago - Pushed at: about 5 years ago - Stars: 133 - Forks: 7
AlexandrovLab/SigProfilerMatrixGenerator
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.
Language: Python - Size: 1 GB - Last synced at: 9 days ago - Pushed at: 9 days ago - Stars: 105 - Forks: 39
PoisonAlien/TCGAmutations
R data package for pre-compiled somatic mutations from TCGA cohorts and CCLE
Language: R - Size: 449 MB - Last synced at: 20 days ago - Pushed at: 7 months ago - Stars: 92 - Forks: 24
HKU-BAL/ClairS
ClairS - a deep-learning method for long-read somatic small variant calling
Language: Python - Size: 12.7 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 83 - Forks: 8
GooglingTheCancerGenome/sv-callers
Snakemake-based workflow for detecting structural variants in genomic data
Language: Python - Size: 210 MB - Last synced at: 13 days ago - Pushed at: 2 months ago - Stars: 80 - Forks: 35
HKU-BAL/ClairS-TO
ClairS-TO - a deep-learning method for tumor-only somatic variant calling
Language: Python - Size: 9.89 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 59 - Forks: 4
KChen-lab/Monopogen
SNV calling from single cell sequencing
Language: Python - Size: 96.1 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 58 - Forks: 13
KarchinLab/2020plus
Classifies genes as an oncogene, tumor suppressor gene, or as a non-driver gene by using Random Forests
Language: Python - Size: 29.7 MB - Last synced at: 24 days ago - Pushed at: 9 months ago - Stars: 49 - Forks: 17
AlexandrovLab/SigProfilerPlotting
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.
Language: Python - Size: 89.7 MB - Last synced at: 23 days ago - Pushed at: about 1 month ago - Stars: 47 - Forks: 15
cancerit/dockstore-cgpwgs
Dockstore implementation of CGP core WGS analysis
Language: Shell - Size: 3.74 MB - Last synced at: over 1 year ago - Pushed at: almost 5 years ago - Stars: 25 - Forks: 14
biowdl/germline-DNA
A BioWDL variantcalling pipeline for germline DNA data. Starting with FASTQ files to produce VCF files. Category:Multi-Sample
Language: wdl - Size: 8.93 MB - Last synced at: over 1 year ago - Pushed at: almost 2 years ago - Stars: 22 - Forks: 7
tjbencomo/ngs-pipeline
Pipeline for Somatic Variant Calling with WES and WGS data
Language: Python - Size: 12.3 MB - Last synced at: 6 months ago - Pushed at: 12 months ago - Stars: 20 - Forks: 4
AlexandrovLab/SigProfilerMatrixGeneratorR
R wrapper for utilizing the SigProfilerMatrixGenerator framework
Language: R - Size: 1.42 MB - Last synced at: about 1 year ago - Pushed at: over 2 years ago - Stars: 20 - Forks: 4
AlexandrovLab/SigProfilerSimulator
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.
Language: Python - Size: 8.43 MB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 19 - Forks: 5
AlexandrovLab/SigProfilerTopography
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.
Language: Python - Size: 5.06 MB - Last synced at: 23 days ago - Pushed at: 2 months ago - Stars: 19 - Forks: 1
carjed/helmsman
highly-efficient & lightweight mutation signature matrix aggregation
Language: Python - Size: 14.2 MB - Last synced at: over 1 year ago - Pushed at: over 3 years ago - Stars: 19 - Forks: 5
OpenOmics/genome-seek
Clinical Whole Genome and Exome Sequencing Pipeline
Language: Python - Size: 849 KB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 18 - Forks: 11
Sydney-Informatics-Hub/Bioinformatics
A suite of bioinformatics data processing and analysis pipelines, software, and training resources for common methods.
Size: 173 KB - Last synced at: about 1 month ago - Pushed at: about 2 months ago - Stars: 17 - Forks: 1
akiomiyao/tif
Transposon Insertion Finder - Detection of new TE insertions in NGS data
Language: Perl - Size: 229 MB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 16 - Forks: 4
AlexandrovLab/SigProfilerExtractorR
An R wrapper for SigProfilerExtractor that 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.
Language: R - Size: 676 KB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 15 - Forks: 2
polyactis/Accucopy
Accucopy is a computational method that infers Allele-specific Copy Number alterations from low-coverage low-purity tumor sequencing Data.
Language: C++ - Size: 1.04 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 14 - Forks: 4
tobiasrausch/nRex
nRex: Germline and somatic single-nucleotide, short indel and structural variant calling
Language: Shell - Size: 1.87 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 12 - Forks: 2
AlexandrovLab/SigProfilerPlottingR
An R wrapper for running the SigProfilerPlotting framework
Language: R - Size: 871 KB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 10 - Forks: 1
akiomiyao/tef
Transposable Element Finder - Detection of active transposable elements from NGS data
Language: Perl - Size: 649 KB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 9 - Forks: 0
INMEGEN/Pipelines_Inmegen
Flujos de trabajos desarrollados y automatizados en el Intituto Nacional de Medicina Genómica para el procesamiento de datos genómicos y transcriptómicos.
Language: Nextflow - Size: 7.37 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 9 - Forks: 0
PoisonAlien/varscan_accessories
accessory scripts for processing varscan somatic/copynumber outputs.
Language: Python - Size: 9.77 KB - Last synced at: 6 days ago - Pushed at: over 7 years ago - Stars: 9 - Forks: 10
KarchinLab/probabilistic2020
Simulates somatic mutations, and calls statistically significant oncogenes and tumor suppressor genes based on a randomization-based test
Language: Python - Size: 5.47 MB - Last synced at: 24 days ago - Pushed at: almost 2 years ago - Stars: 8 - Forks: 5
renatopuga/somatico
GATK 4 Mutect2 Somático
Language: Shell - Size: 5.28 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 7 - Forks: 29
Sentieon/sentieon-google-genomics
Run Sentieon pipelines on Google Cloud Platform
Language: Shell - Size: 127 KB - Last synced at: 14 days ago - Pushed at: 14 days ago - Stars: 6 - Forks: 7
baezortega/somatypus
A Platypus-based variant calling pipeline for cancer data
Language: Python - Size: 2.61 MB - Last synced at: over 1 year ago - Pushed at: almost 3 years ago - Stars: 6 - Forks: 6
ratschlab/secedo
Clustering tumor cells based on SNVs from single-cell sequencing data
Language: C++ - Size: 9.21 MB - Last synced at: almost 2 years ago - Pushed at: almost 3 years ago - Stars: 6 - Forks: 0
rptashkin/facets2n
Algorithm to implement Fraction and Allelic Copy number Estimate from Tumor/normal Sequencing using unmatched normal sample(s) for log ratio calculations
Language: R - Size: 240 MB - Last synced at: 25 days ago - Pushed at: almost 3 years ago - Stars: 6 - Forks: 4
DKFZ-ODCF/IndelCallingWorkflow
A Platypus-based workflow for indel calling
Language: Python - Size: 616 KB - Last synced at: 3 months ago - Pushed at: 9 months ago - Stars: 5 - Forks: 5
daormar/geno-debasher
Geno-DeBasher package for detection of germline and somatic variants
Language: Shell - Size: 3.36 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 5 - Forks: 1
caravagnalab/TINC
Tumour-in-Normal Contamination assessment with evolutionary theory.
Language: R - Size: 12.9 MB - Last synced at: 12 months ago - Pushed at: about 1 year ago - Stars: 4 - Forks: 0
nickveltmaat/SNVcaller
Pipeline to call SNV's with 4 tools (VarDict, LoFreq, Mutect2 & SiNVICT)
Language: Python - Size: 193 KB - Last synced at: about 2 months ago - Pushed at: over 2 years ago - Stars: 3 - Forks: 1
jvandinter/MitoCallPipeline
A pipeline for mitochondrial mutation calling
Language: HTML - Size: 18.2 MB - Last synced at: almost 2 years ago - Pushed at: almost 5 years ago - Stars: 3 - Forks: 0
morinlab/tools-morinlab
Galaxy Tool Shed repositories maintained and developed by the Morin Lab.
Language: Python - Size: 54.3 MB - Last synced at: about 2 years ago - Pushed at: over 7 years ago - Stars: 3 - Forks: 6
EmilieT/mutcraft
R tools to mine & craft somatic mutations from cancer genomes
Language: R - Size: 443 KB - Last synced at: 12 months ago - Pushed at: almost 8 years ago - Stars: 3 - Forks: 2
caravagn/mtree
Mutation tree from binary bulk sequencing data
Language: R - Size: 1.89 MB - Last synced at: about 2 years ago - Pushed at: over 4 years ago - Stars: 2 - Forks: 0
ghga-de/nf-snvcalling
a Nextflow SNV calling and annotation pipeline based on DKFZ-ODCF/SNVCallingWorkflow
Language: Python - Size: 16.7 MB - Last synced at: 14 days ago - Pushed at: 5 months ago - Stars: 1 - Forks: 0
ghga-de/nf-platypusindelcalling
This page is reserved for NextFlow based Indell Calling Workflow (with Platypus) from DKFZ
Language: Python - Size: 119 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 1 - Forks: 0
ghga-de/nf-aceseq
a Nextflow ACE-Seq calling and annotation pipeline based on DKFZ-ODCF/ACEseqWorkflow
Language: R - Size: 49.6 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 1 - Forks: 0
Test-Blu/GVF2VCF_Convertor_TestBlu
Super fast conversion of GVF file format to VCF file format
Language: Python - Size: 62.9 MB - Last synced at: 4 months ago - Pushed at: about 2 years ago - Stars: 1 - Forks: 1
CCBR/CCBR_GATK4_Exome_Seq_Pipeline Fork of mtandon09/CCBR_GATK4_Exome_Seq_Pipeline
Containerized GATK4 Whole Exome-sequencing Pipeline
Language: Python - Size: 10.2 MB - Last synced at: about 2 years ago - Pushed at: about 3 years ago - Stars: 1 - Forks: 0
Vedbar/DNA-seq_Somatic_Variants
Somatic Variants
Size: 128 KB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 0 - Forks: 0
clbenoit/SomaVarDB
R Shiny app for somatic genomic variants interpretation. The tool suite to deal with the underlying local structured database is provided here : https://github.com/clbenoit/SomaVarDBTools
Language: R - Size: 36.8 MB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 0 - Forks: 0
sebastian-gregoricchio/SPACCa
Snakemake Pipeline for the Analyses of ChIP-seq data in Cancer samples
Language: Python - Size: 4.63 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0
sbresnahan/TexasCancerGenomics
Analysis of paired tumor-normal whole exome sequencing data generated in a pilot open-access study of participants in Texas.
Language: HTML - Size: 331 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0
auroramaurizio/WES_ESOCA
WES Analysis scripts for "Immune determinants of response to neoadjuvant chemo-radiation in esophageal adenocarcinoma" publication
Language: Python - Size: 69.3 KB - Last synced at: 9 months ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0
akkusalper/somatic.variant.analysis.pipeline
an example open source somatic variant analysis pipeline. vLoD algorithm is also integrated.
Language: Shell - Size: 10.7 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0
MBeyens/pyAmpli
pyAmpli: an amplicon-based variant filter pipeline for targeted enriched resequencing data
Language: Python - Size: 78.1 KB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0
theLongLab/PRESM
Personalized reference editor for somatic mutation discovery
Language: Java - Size: 506 KB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0
AAlhendi1707/PhylogicNDT_Docker
PhylogicNDT dockcer for clonal evolution analysis
Language: Shell - Size: 95.7 KB - Last synced at: almost 2 years ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0
danieldanciu/secedo-experiments
Experiments for evaluating SECEDO, clustering tumor cells based on single cell sequencing data
Language: Jupyter Notebook - Size: 207 KB - Last synced at: about 2 years ago - Pushed at: about 3 years ago - Stars: 0 - Forks: 0
ammodramus/ebsom
Empirical Bayes somatic variant calling
Language: Python - Size: 447 KB - Last synced at: about 2 years ago - Pushed at: over 5 years ago - Stars: 0 - Forks: 0
pd321/dnaseq
Snakemake based workflow for analysis of dnaseq data for calling germline/somatic mutations
Language: Python - Size: 13 MB - Last synced at: over 1 year ago - Pushed at: over 5 years ago - Stars: 0 - Forks: 2
Matthew-Mosior/Variant-to-bam-readcount
A Haskell script for creating input files for bam-readcount from ensembl-vep output and variant-calling format (vcf) files.
Language: Haskell - Size: 3.41 MB - Last synced at: about 1 year ago - Pushed at: over 5 years ago - Stars: 0 - Forks: 1
Matthew-Mosior/Basic-Variant-Tools
Command-line toolkit for genomic datasets.
Language: Haskell - Size: 81.1 KB - Last synced at: about 1 year ago - Pushed at: over 5 years ago - Stars: 0 - Forks: 0
Matthew-Mosior/Basic-Variant-Filter
A Haskell script that performs basic filtration, using a filtration string, on somatic variant data.
Language: Haskell - Size: 9.07 MB - Last synced at: about 1 year ago - Pushed at: over 5 years ago - Stars: 0 - Forks: 0
Matthew-Mosior/Basic-Variant-Selector
A Haskell script for selecting variants from a variant calling format (vcf) file based on variants present in a mgibed file.
Language: Haskell - Size: 1.83 MB - Last synced at: about 1 year ago - Pushed at: almost 6 years ago - Stars: 0 - Forks: 0
Matthew-Mosior/Move-Annotate-Merge
A Haskell script that prepares .tsv files generated from sequencing data analysis for manual review.
Language: Haskell - Size: 1.83 MB - Last synced at: about 1 year ago - Pushed at: about 6 years ago - Stars: 0 - Forks: 1
jongtaek-kim/Bioinformatics-Pipeline-from-Sarek Fork of nf-core/sarek
Detect germline or somatic variants from normal or tumour/normal whole-genome, whole exome, or targeted sequencing with high performance computing.
Language: Nextflow - Size: 44.2 MB - Last synced at: over 1 year ago - Pushed at: over 6 years ago - Stars: 0 - Forks: 2
nestornotabilis/Genetic-Mechanisms-in-Duodenal-Polyposis
A collection of scripts documenting the parameter settings used to apply variant discovery to the exploration of Duodenal Polyposis.
Language: Perl - Size: 27.3 KB - Last synced at: over 1 year ago - Pushed at: about 8 years ago - Stars: 0 - Forks: 0
