Search Results for "maf"

DNA and RNA nucleotide sequences are an ubiquitous element of all biological cells and are serving on one hand as a comprehensive library of capabilities for the cells and on the other as an impressive regulatory system to control cellular function. The presented multi-alignment framework (MAF) should give researchers a simple sequence alignment platform as a functional template, flexible enough to adjust all steps but also comprehensive enough to join many different tools and custom parameter combinations if in-depth analysis is necessary or advised in e.g. low read rate situations. The platform enables researcher to apply multiple sequence aligners and further pre- and postprocessing tools in flexible combinations to analyze the subtle to remarkable differences between different sequence alignment and processing algorithms applied to the same data basis. ...

vcf2maf is a Perl-based tool developed by the Memorial Sloan Kettering Cancer Center to convert Variant Call Format (VCF) files into Mutation Annotation Format (MAF) files. This conversion standardizes variant annotations, facilitating downstream analyses in cancer genomics. ​

...It can also be used as a filter to extract and convert searches or alignments to common formats. Inputs: - 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.

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 about VARSCAN is corrected. Mutlithreading for dbsnp annotation, Haplotypecaller, Varscan and bamreadcount more efficient. ...

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.

...***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.

...For data exploration and dimensionality reduction, it includes multivariate methods common in the ToF-SIMS community: PCA (Principal Component Analysis), MCR (Multivariate Curve Resolution), MAF (Maximum Autocorrelation Factors), and MNF (Minimum Noise Fraction). It also interoperates with Bioconductor’s imaging stack (e.g. EBImage) so users can apply segmentation and image analysis operations on mass images.

...Formats which can be generated 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

...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. Reference: http://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0830-7

...General pipeline: 1-iterative De Novo assembly, with different k-mer values, trying to assemble a build that matches 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.

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 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.