Search Results for "sv"
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Showing 31 open source projects for "sv"
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Verible
Verible is a suite of SystemVerilog developer tools
The Verible project's main mission is to parse SystemVerilog (IEEE 1800-2017) (as standardized in the SV-LRM) for a wide variety of applications, including developer tools. It was born out of a need to parse un-preprocessed source files, which is suitable for single-file applications like style-linting and formatting. In doing so, it can be adapted to parse preprocessed source files, which is what real compilers and toolchains require. -
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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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...This creates a new wrapper by encapsulating the instance 4. flatteninstances : Flattens the given list of hierarchical instances- this removes hierarchy by pulling the contents in the higher leve 5. removehierarchy : Verilog Hierarchy Removal Tool to ungroup all the instances in a given module 6. comparemoduleinterfaces - Diff module ports and parameter. Tool to compare the interfaces ( ports, parameters, SV interfaces ) between two versions of a Verilog module or two similar modules 7. Verilog Testbench Generator 8. VHDL Testbench Generator 9. Verilog Remove Assignments 10. Verilog Find Instances or Nets 11. Clock And Reset Tree Analyzer( Alpha)
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Dayon! (active)
Remote assistance made easy!
Dayon! is an open source remote desktop and assistance solution. It is easy to use, secure, requires no registration and is free for personal and commercial use! -
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Sparx' EA - MDG for TRAK
MDG for Sparx' Enterprise Architect to Create TRAK arch. descriptions
Custom add-in (MDG technology) for Sparx Systems Enterprise Architect UML modelling tool (https://sparxsystems.com/products/ea/index.html) to create architecture descriptions using TRAK https://sf.net/projects/trak Provides: - the set of TRAK views that can be represented using UML and SysML . Each view display a custom toolbox palette with the objects and relationships that are needed for that TRAK view - relationships can be made directly from the objects on a view using the... -
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PhaseDel
Phasing-based somatic deletion caller from single-cell WGS data
PhaseDel is a Java-based variant caller designed for detecting somatic deletions from single-cell whole-genome sequencing (scWGS) data. It is highly specialized for discriminating genuine somatic focal deletions (several bases to kilo-bases in length) from excessive SV-like artifacts, which are inevitably occurring during single-cell whole-genome amplification. PhaseDel accurately detects such true deletions based on the linkage information between deletion breakpoints and nearby germline heterozygous SNP sites. The important features of PhaseDel are: • Accurate identification of somatic focal deletions at single-base-pair resolution in scWGS using phasing information • Estimation of the genome-wide somatic deletion rate for a given cell with the controlled FDR level • Characterization of underlying DSB repair mechanisms for identified deletion candidates A more detailed description of the tool is provided in the [[wiki]] tab. -
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vulscan
Advanced vulnerability scanning with Nmap NSE
Vulscan is a module that enhances nmap to a vulnerability scanner. The nmap option -sV enables version detection per service which is used to determine potential flaws according to the identified product. The data is looked up in an offline version of VulDB. -
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svdetect.sh is a shell script to run SVDetect to detect SV in exome-seq and Shatterproof to detect chromothripsis. ***Update*** The output files of SVDetect can be annotated by genes with multi-threading.
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MongoDB Atlas runs apps anywhereMongoDB Atlas gives you the freedom to build and run modern applications anywhere—across AWS, Azure, and Google Cloud. With global availability in over 115 regions, Atlas lets you deploy close to your users, meet compliance needs, and scale with confidence across any geography.
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inGAP-family provides an efficient and effective framework to discover, filter and visualize DNA polymorphisms and structural variants from alignment of short reads. Applying this method on polymorphism detection on real datasets shows that elimination of artificial variants greatly facilitates the precise identification of meiotic recombination points, recognizing causal mutations in mutant genomes or QTL loci. In addition, inGAP-family provides user-friendly graphical interface for...
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meerkat.sh
script of SV calling in Exome-seq
meerkat.sh is a shell script to run Meerkat for SV detection in Exome-seq. The script accepts single BAM or paired tumor-normal BAMs. -
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novoBreak
Robust detection of somatic structural breakpoints in cancer genomes
novoBreak is a tool used in cancer genomic studies to discover SV (both somatic and germline) breakpoints. It can report accurate breakpoints of Deletions (DEL), Duplications (DUP), Inversions (INV) and Translocations (TRA) (you should consider some of them are mobile elements insertions or templated insertions). For novel insertions, we may only report the breakpoints but not the inserted sequence. -
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Swedish-English Open Dictionary
Swe-Eng Kindle Dictionary Based on Folkets Lexikon
This is a transcoded and reformatted version of "The People's Dictionary" (Folkets Lexikon, see http://folkets-lexikon.csc.kth.se for more information). The project contains encoding and formatting scripts along with instructions for converting the dictionary database into a Kindle book. The dictionary is in the Kindle's native dictionary format and integrates with the Smart Lookup feature which allows you to access words definitions without leaving your book page - just press and hold to... -
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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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LAMSA
Long Approximate Matches-based Split Aligner
LAMSA (Long Approximate Matches-based Split Aligner) is a novel split alignment approach with faster speed and good ability of handling SV events. It is well-suited to align long reads (over thousands of base-pairs). -
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SVMerge is a meta structural variation (SV) calling pipeline, which makes SV predictions with a collection of SV callers which are then, merged, and computationally validated using local de novo assembly.
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MERAP
Medical Resequencing Analysis Pipeline
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Structural Variant Detection
SV detection in paired end whole genome sequencing data
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isvm: incremental svm implementation for Stephe ruiping's algorithm based on libsvm svmovoovr: implement for OVO OVR classification. pso-svm: PSO svm implementation
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The SV CMS is an CMS with an userfriendly interface. There is an tool for users, a page tool and much more.
