Search Results for "cnv"
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Showing 38 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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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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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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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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Magnolya
De novo CNV detection by co-assembly
Magnolya enables copy number variation (CNV) detections without using a reference genome. Magnolya directly compares two next-generation sequencing datasets. -
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Ymap - Yeast Mapping Analysis Pipeline
Pipeline for large-scale genome changes analysis of genome datasets.
...A copy of the history was successfully scrubbed and then hosted at github. -------- Eukaryotic pathogens have complicated and dynamic genomes. To facilitate analysis of copy number variations (CNV), single nucleotide polymorphisms (SNPs), and loss of heterozygosity (LOH) events in Candida albicans, the most common human fungal pathogen, we developed a pipeline for analyzing diverse genome-scale datasets from microarray, deep sequencing, and restriction site associated DNA sequence experiments for clinical and laboratory strains. ... -
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MERAP
Medical Resequencing Analysis Pipeline
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cnvOffSeq
detecting & genotyping intergenic CNVs using off-target exome data
cnvOffSeq is a set of Java-based command-line tools for detecting and genotyping intergenic copy number variation (CNV) using off-target data from whole-exome sequencing experiments.