Topic: somatic-variants Goto Github
Some thing interesting about somatic-variants
Some thing interesting about somatic-variants
somatic-variants,Transposable Element Finder - Detection of active transposable elements from NGS data
User: akiomiyao
somatic-variants,Transposon Insertion Finder - Detection of new TE insertions in NGS data
User: akiomiyao
somatic-variants,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.
Organization: alexandrovlab
somatic-variants,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.
Organization: alexandrovlab
somatic-variants,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.
Organization: alexandrovlab
somatic-variants,R wrapper for utilizing the SigProfilerMatrixGenerator framework
Organization: alexandrovlab
somatic-variants,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.
Organization: alexandrovlab
somatic-variants,An R wrapper for running the SigProfilerPlotting framework
Organization: alexandrovlab
somatic-variants,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.
Organization: alexandrovlab
somatic-variants,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.
Organization: alexandrovlab
somatic-variants,A Platypus-based variant calling pipeline for cancer data
User: baezortega
somatic-variants,NeuSomatic: Deep convolutional neural networks for accurate somatic mutation detection
Organization: bioinform
somatic-variants,An ensemble approach to accurately detect somatic mutations using SomaticSeq
Organization: bioinform
Home Page: http://bioinform.github.io/somaticseq/
somatic-variants,A BioWDL variantcalling pipeline for germline DNA data. Starting with FASTQ files to produce VCF files. Category:Multi-Sample
Organization: biowdl
Home Page: https://biowdl.github.io/germline-DNA/
somatic-variants,Dockstore implementation of CGP core WGS analysis
Organization: cancerit
somatic-variants,Mutation tree from binary bulk sequencing data
User: caravagn
somatic-variants,Tumour-in-Normal Contamination assessment with evolutionary theory.
Organization: caravagnalab
Home Page: https://caravagnalab.github.io/TINC
somatic-variants,highly-efficient & lightweight mutation signature matrix aggregation
User: carjed
somatic-variants,Experiments for evaluating SECEDO, clustering tumor cells based on single cell sequencing data
User: danieldanciu
somatic-variants,Geno-DeBasher package for detection of germline and somatic variants
User: daormar
Home Page: https://daormar.github.io/geno-debasher/
somatic-variants,A Platypus-based workflow for indel calling
Organization: dkfz-odcf
somatic-variants,R tools to mine & craft somatic mutations from cancer genomes
User: emiliet
somatic-variants,This page is reserved for NextFlow based Indell Calling Workflow (with Platypus) from DKFZ
Organization: ghga-de
somatic-variants,a Nextflow SNV calling and annotation pipeline based on DKFZ-ODCF/SNVCallingWorkflow
Organization: ghga-de
somatic-variants,DeepSomatic is an analysis pipeline that uses a deep neural network to call somatic variants from tumor-normal sequencing data.
Organization: google
somatic-variants,Snakemake-based workflow for detecting structural variants in genomic data
Organization: googlingthecancergenome
Home Page: https://research-software.nl/software/sv-callers
somatic-variants,ClairS - a deep-learning method for long-read somatic small variant calling
Organization: hku-bal
somatic-variants,ClairS-TO - a deep-learning method for tumor-only somatic variant calling
Organization: hku-bal
somatic-variants,Flujos de trabajos desarrollados y automatizados en el Inmegen para el procesamiento de datos genómicos y transcriptómicos.
Organization: inmegen
Home Page: https://serviciosbio.inmegen.gob.mx/
somatic-variants,A pipeline for mitochondrial mutation calling
User: jvandinter
somatic-variants,Classifies genes as an oncogene, tumor suppressor gene, or as a non-driver gene by using Random Forests
Organization: karchinlab
Home Page: http://2020plus.readthedocs.org
somatic-variants,Simulates somatic mutations, and calls statistically significant oncogenes and tumor suppressor genes based on a randomization-based test
Organization: karchinlab
Home Page: http://probabilistic2020.readthedocs.org
somatic-variants,SNV calling from single cell sequencing
Organization: kchen-lab
somatic-variants,Bayesian haplotype-based mutation calling
Organization: luntergroup
somatic-variants,Galaxy Tool Shed repositories maintained and developed by the Morin Lab.
Organization: morinlab
somatic-variants,Pipeline to call SNV's with 4 tools (VarDict, LoFreq, Mutect2 & SiNVICT)
User: nickveltmaat
somatic-variants,Clinical Whole Genome and Exome Sequencing Pipeline
Organization: openomics
Home Page: https://openomics.github.io/genome-seek/
somatic-variants,R data package for pre-compiled somatic mutations from TCGA cohorts (from Broad Firehose and TCGA MC3 Project)
User: poisonalien
somatic-variants,accessory scripts for processing varscan somatic/copynumber outputs.
User: poisonalien
somatic-variants,Accucopy is a computational method that infers Allele-Specific Copy Number alterations from low-coverage low-purity tumor sequencing data.
User: polyactis
Home Page: https://www.yfish.org/software/Accucopy
somatic-variants,Clustering tumor cells based on SNVs from single-cell sequencing data
Organization: ratschlab
somatic-variants,GATK 4 Mutect2 Somático
User: renatopuga
somatic-variants,Algorithm to implement Fraction and Allelic Copy number Estimate from Tumor/normal Sequencing using unmatched normal sample(s) for log ratio calculations
User: rptashkin
somatic-variants,Run Sentieon pipelines on Google Cloud Platform
Organization: sentieon
Home Page: https://cloud.google.com/genomics/docs/tutorials/sentieon
somatic-variants,🌲 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
User: shixiangwang
Home Page: https://shixiangwang.github.io/sigminer/
somatic-variants,A suite of bioinformatics data processing and analysis pipelines, software, and training resources for common DNA and RNA sequence analysis methods.
Organization: sydney-informatics-hub
somatic-variants,Super fast conversion of GVF file format to VCF file format
Organization: test-blu
somatic-variants,Pipeline for Somatic Variant Calling with WES and WGS data
User: tjbencomo
somatic-variants,nRex: Germline and somatic single-nucleotide, short indel and structural variant calling
User: tobiasrausch
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