Search Results for "cnv"
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Showing 45 open source projects for "cnv"
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hg38 version of the pipelines for whole exome sequencing: exome_test38.sh wole transcription sequencing: rna_test38.sh somatic calling: somatic38.sh SV detect: svdetect38.sh, meerkat38.sh cnv: svdetectcnv38.sh, contra38.sh, cnvkit38.sh *** Mutect2 instead of haptotypecaller is used to call variants in DNA-seq.
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GENET-CNV
Integrated DNA copy number variation and gene expression analysis
The Boolean implication networks outperformed Bayesian networks, Pearson’s correlation networks, and other Boolean networks in constructing genome-scale co-expression networks evaluated with comprehensive biological pathways and Gene Ontology in MSigDB. References: Guo NL, Wan YW. Pathway-based identification of a smoking associated 6-gene signature predictive of lung cancer risk and survival. Artificial Intelligence in Medicine 2012 Jun;55(2):97-105. Ye Q, Singh S, Qian PR, Guo... -
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A program for CNV detection with whole-genome low-coverage sequencing data. md5 of Increment_Ratio_of_Coverage_V2.0.tar.gz: c8dda5fbd5b43527538f5c410a303a74
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CAI[N]
Chromosomal Aberration Identifier [Numerical]
CAI[N] is a novel computational tool for CNV-karyotyping based on low coverage whole genome sequencing that uses in silico-generated normal karyotypes as a reference to calculate numerical chromosomal aberrations in fixed genomic windows in experimental samples. -
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contra.sh is a shell script to run contra-cnv mode. In addition to the original outputs of SVDetect, the script also outputs and bed.graph and an adjusted bed.graph with baseline adjusted to the average Log2Ratio of a certain chromosome or all chromosomes, and a sorted density file.
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svdetectcnv.sh
shell script to run SVDetect with baseline adjustment
svdetectcnv.sh is a shell script to run SVDetect CNV mode. In addition to the original outputs of SVDetect, the script also outputs an adjusted bed.graph with baseline adjusted to the average Log2Ratio of a certain chromosome or all chromosomes, and a sorted density file. **Update*** New version uses the splitted bam produced by exome_test.sh and allows for multithreading to split bam. -
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ParseCNV CNV call association software takes CNV calls as input and creates SNP based statistics for CNV occurrence in population study cases and controls then calls CNVRs based on neighboring SNPs of similar significance.
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CELLX
Integrates expression, CNV, mutation, compound, and meta data.
CELLX is an informatics infrastructure to manage multi-dimensional genomics datasets containing expression, copy number variation, mutation, and compound sensitivity information. A browser based web page enables an accessible way to visualize, analyze, and download the database data in a pre-formatted table suitable for offline computation. CELLX is presently focused on supporting oncology precision medicine through the evaluation of preconceived hypotheses as well as unbiased, data... -
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GENSENG
GENSENG is a software detecting CNVs from NGS data
GENSENG is a software detecting CNVs(Copy Number Variations) from NGS(Next Generation Sequencing) data. We have uploaded the data preparation codes. Please download it from Files folder. -
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XCAVATOR
A tool for the detection of CNV/CNA from whole-genome sequencing data.
XCAVATOR is a novel software package for the identification of genomic regions involved in copy number variants/alterations (CNVs/CNAs) from short and long reads whole-genome sequencing experiments. XCAVATOR has been published on BMC Genomics (https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-4137-0). -
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Increment_Ratio_of_Coverage
Method for CNV detection
A program for CNV detection with whole-genome low-coverage sequencing data. -
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karkinos
Tumor genotyper for Exome sequence that detects SNV,CNV, aTumor purity
karkinos is tumor genotyper which detects single nucleotide variation (SNV), integer copy number variation (CNV) and calculates tumor cellularity from tumor-normal paired sequencing data. Accurate CNV calling is achieved using continuous wavelet analysis and multi-state HMM, while SNV call is adjusted by tumor cellularity and filtered by heuristic filtering algorithm and Fisher Test. Also, Noise calls in low depth region are removed using EM algorithm. -
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ASGENSENG
A software to detect allele specific CNV from both WGS and WES data.
Please go to Files tab and download both the software and the InHouseScripts for data preparation. The tutorial.pptx provides the tutorial of using this software. -
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Copy Number Analysis for Targeted Resequencing (CONTRA) is a tool for copy number variation (CNV) detection for targeted resequencing data such as those from whole-exome capture data.
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SCNVSim
SCNVSim, a tool to simulate somatic CNV and Strucuture Variants
SCNVSim is a Bioinformaitcs tool developed in Java programming language for the simulation of somatic copy number variations and structure variations in cancer genome studies. The tool is capable of simulating features related to tumor samples including tumor purity, aneuploidy and heterogeneity other than common types of SV and CNV. SCNVSim generates the genomes of a cancer cell population with detailed information of copy number status, loss of heterogeneity, and structure variation break points, which are essential for developing and evaluating somatic CNV and SV detection methods in cancer genomics studies. -
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CNVision
CNV prediction from Illumina genotyping data
CNVision is a Perl script that runs Illumina genotyping data (all chips from 300k to latest Omni) through PennCNV, QuantiSNPv2.3 and GNOSIS (an in-built algorithm). It merges the results and assesses the quality of the raw data. CNVision can also identify de novo CNVs in family-based data using a highly accurate algorithm that considers the possibility of CNVs in either parent based on the raw genotyping data. The script is optimized to work in a UNIX-based environment; it should work in... -
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oasis-genomics
Oasis Genomics cancer omics integration portal
OASIS is an application that enables complex analytical queries across somatic mutations; copy number changes (CNV); and gene expression data. OASIS has been built on top of the BIoMart frameworks and has been extended to incorporate unique tools and visualizations to facilitate analysis of complex cancer "Omics" datasets. -
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Copy Number Explorer
Interactive Copy Number Analysis for Cancer Genomics
...However, current tools focus on individual gene queries rather than chromosomal and region-based queries more relevant to some researchers. Copy Number Explorer creates interactive CNV frequency, GISTIC-style and breakage frequency plots from public (or your own) data. The program is written in R and Perl and can be deployed online using ShinyApps.io . Copy Number Explorer is available under the GNU public license (GPL-3). Check the Wiki for details on how to run your own Copy Number Explorer instance. -
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CNV Explorer
Interactive Copy Number Analysis for Cancer Genomics
CNV Explorer for Gene discovery: https://arraycgh.shinyapps.io/CNV_Explorer/ CNV Explorer for survival analysis: https://arraycgh.shinyapps.io/CNV_Explorer_Survival/ CNV_Explorer is a data mining tool for cancer researchers interested in the structural and copy number changes that happen in cancer genomes. Huge volumes of genomics data from nearly every cancer type are now freely available and several online databases have begun to collate and store this information. ... -
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diggit
R package for DIGGIT algorithm
DIGGIT identify genetic variants associated with drivers of specific physiopathologic states. I computes the statistical association between the presence of genetic variants (CNV or SNP) and the activity of proteins driving physiologic or pathologic phenotype. It requires large gene expression and genetic variants datasets and depends on context-specific regulatory networks including transcriptional interactomes (usually reverse engineered by the ARACNe algorithm) and post-translational interactomes (usually generated by the MINDy algorithm). ... -
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ADTEx
Aberration detection in tumour exome
Aberration Detection in Tumour Exome (ADTEx) is a tool for copy number variation (CNV) detection for whole-exome data from paired tumour/matched normal samples. -
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cnvCapSeq
detecting & genotyping CNV in long-range targeted resequencing.
cvnCapSeq is a set of Java-based command-line tools for detecting and genotyping copy number variation (CNV) in targeted resequencing experiments of large contiguous genomic regions. -
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SubPatCNV
Approximate association pattern mining algorithm for CNVs.
...SubPatCNV is the implementation of a variation of approximate association pattern mining algorithm under a spatial constraint on the positional CNV probe features. The implementation scales to high-density array data with hundreds of thousands features.
