Search Results for "sv"
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Showing 50 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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Roundcube installer for Linux Void
Script to install and configure Roundcube and his dependencies
# Mail Server Installer for Void Linux with Avahi, Roundcube DB Population, and PAM for Dovecot # Installs and configures Apache (apache package), MariaDB, Roundcube 1.6.11, Dovecot 2.4.1, PHP 8.4, Postfix, Avahi # Uses Maildir format, generates self-signed certificates, sets up Roundcube in /srv/www/apache/ # Configures Avahi first for .local domain, autodetects FQDN and .local, updates /etc/hosts, creates and activates services # Configures Apache to execute PHP files (not display source code), uses mpm_prefork # Populates Roundcube MySQL database with initial schema # Uses PAM for Dovecot authentication with system users # Excludes php-fileinfo installation # Uses /etc/sv/mysqld for MariaDB service, lets runit manage supervise directory # Prompts for IP only; Run as sudo ./roundcube_installer_void.sh # Updated for Dovecot 2.4.1: Replaces mail_location with mail_driver and mail_path -
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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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Memu
8080/6800/6502/Z80/8086 emulator, arcade emulator, CP/M emulator
Memu is a multiple machine emulator. Some CPUs are emulated: 8080, 6800, Z80, 8086. Some arcade machines which based on 8080 CPU are emulated. CP/M 1.3, 1.4, 2.0 runnable. Altair BASIC 3.0 runnable. PC emulation is under construction. -
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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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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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Bitcoin-sv-windows
Unofficial compiled windows 10 binaries
A DIY compilation with vcpkg and Visual Studio 2017 purely for RegTest and development purposes. I would have put it in a .zip archive but was causing corruption on retrieval for some reason... -
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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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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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Tkinter Data Dict Form Error
Tkinter data dictionary form
...%s=Entry(self.form,text="",''insertbackground="yellow",''width=%d+1)\n' % (pstr,field,width) pstr = '%sself.%s.place(relx=%f, rely=%f,' 'anchor=W)\n' % (pstr,field,(self.anchor+0.02),self.ypos) eval('%sself.%sV=StringVar()\n''self.%s["textvariable"] = self.%sV' % (pstr,field,field,field)) self.ypos = self.ypos + self.incr idx = idx + 1 self.update_display() -
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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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varcgnlww2d-sv
Nonlinear Gravity Water Waves 2D (SV)
Variational finite element code for 2D nonlinear gravity water waves with Stormer-Verlet time integration. -
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GRASPER
Repetitive structural variation caller using short paired-end reads
WE HAVE MOVED TO A GIT REPO. Please go to https://github.com/COL-IU/GRASPER GRASPER (Genome Rearrangement Analysis using Short Paired-End Reads) is a de novo structural variation (SV) calling software that is capable of detecting repetitive SVs. It constructs A-Bruijn graphs to capture approximate repeats within a reference genome then SVs are detected on the graphs. GRASPER requires a reference genome sequence in a FASTA formatted file along with a Illumina paired-end sequencing data of a sample genome. -
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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.
