Search Results for "maf"

...: - Sequence database search: BLAST, FASTA suites. - Multiple sequence alignment: CLUSTAL, HSSP, MSF, FASTA, PIR, MAF. Outputs: - HTML, FASTA, CLUSTAL, MSF, PIR, RDB (tab-separated). Found a bug? Please open an issue on the MView issue tracker at https://github.com/desmid/mview/issues or send an email to biomview@gmail.com.

somatic.sh is a shell script to run varscan somatic for somatic variant-calling, and Annovar to annotate. It calls both SNPs and Indels. It also produces 2 MAF files compatible with MutSigCV. Now the script allows for multithreading. The script is updated according to new format.

exome_test.sh is a shell script to run GATK best practice and varscan for variant-calling in exomseq. It uses bwa for alignment, UnifiedGenotyper and varscan to call variants, and Annovar to annotate. It also employs DepthofCoverage and BAM-readcount. [Notice] MAF files compatible with MutSigCV are added. The Annovar filter dbnsfp30a is updated. Correction of an error in the title line of merge file. -ni option added. -vb option (-B in varscan) added exac03nontcga is added. An error...

A script to filter exome-seq by 1000G, ExAc, dbSNP with minimal coverage and T/N ratio. The script uses the files produced by exome_test.sh. An error is corrected. The script also produces MAF file that only includes variants detected by BOTH GATK and Varscan. A few errors are corrected.

allmut.sh is a shell script to run MutSigCV and genvisr. ***Update*** The genelist file reports those with p<0.05 only. Now the script incorporates genvisr. hg38 option is added. md (most deleterous) option is added. A script to transform TCGA MAF file is provided.

Electronic Fuel Injection based on STM32F4 running ChibiOS MOVED TO https://github.com/rusefi/rusefi June 2016 status: racing proven! electronic throttle body works in progress! hip9011 integration Vehicle speed sensor Stepper idle valve Speed Density CAN protocol support Sequential injection Spark advance table lookup Fuel table lookup based on RPM & MAF with temperature correction Wideband O2 input Idle Valve Control

... by fcGENE: plink-pedigree, plink-raw, plink-dosage, mach-inputs, minimac-inputs, impute-inputs, beagle-inputs and bimbam-inputs, HAPLOVIEW-inputs, EIGENSOFT-inputs. Further application: -obtaining templates of necessary imputation commands and commands of other imputation tool - Quality control according as MAF,HWE & CALLRATE. key words: genotype transformation, convert genotype format, imputation output, PLINK, IMPUTE, MACH, minimac, HAPLOVIEW, BEAGLE, BIMBAM,EIGENSOFT.

A reworking in C++ of KBMAG. A package and C++ library for computing automatic structures and confluent rewriting system for group and coset rewriting systems, and for computing with finite state automata

DHOEM (Densification of Haplotypes by lOEess and Maximum Likelihood) is a novel R application which performs simulation of new markers in real SNP marker data. The new markers are generated according to real local data characteristics, modeled statistically, and are interpolated locally between real markers in the data. The function allows the user to specify a desired level of marker density, with a minor allele frequency (MAF) limit, which is produced in a reasonable computation time...

... a target mitochondrial genome given. 2-searches for all mitochondrial gene features and circularization. 3-stores the best result found. 4-uses the best assembly as backbone for a reference based assembly, using MIRA and MITObim, trying to extend the mitogenome and close gaps. 5-annotates the best assembly, identifying the start and end position of each and every feature. 6-creates a folder with all the results (PNG, GENBANK, FASTA, SEQUIN, CAF, MAF and a stats logfile).

Inspired by MAF and MEF in creating extensible applications. A simple but flexible plug-in framework for .NET/Mono-based applications. Extend your application with CLI-compatible, Java, Ruby, Python, and native binaries.

A personal genealogy/family history application for Mac OS X and iPhone, modelled after a previous version of PAF for Macintosh called Family Records. This is intended to be easy to learn for newer users and to be familiar to previous users of Family Rec

Trinity is mobile agent framework for creation of wide range of mobile agent types. Main goal of project is to provide a tool for rapid development of non-complex agents. Trinity is implemented in .NET v3.5 with usage of Windows Workflow Foundation and W

MAF (Mobile Application Framework) is a cross-platform C++ framework for cellphone (mainly Brew/Symbian) application development. A SGI-STL style template library (called MTL, Micro Template Library) is also included as a part.

MAF (Mobile Agent Framework) is a research prototype which aims to facilitate the development and evaluation of mobile agent by providing a set of handy primitatives and simulation tools.