Search Results for "snp" - Page 3
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Showing 120 open source projects for "snp"
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HubSpot is an AI-powered customer platform with all the software, integrations, and resources you need to connect your marketing, sales, and customer service. HubSpot's connected platform enables you to grow your business faster by focusing on what matters most: your customers.
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HubSpot is an AI-powered customer platform with all the software, integrations, and resources you need to connect your marketing, sales, and customer service. HubSpot's connected platform enables you to grow your business faster by focusing on what matters most: your customers.
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SNP-SACK
Pipeline and set of tools for SNP calling and classification
SNP-SACK provides a complete ''de novo'' pipeline for the calling of variants in any organism and a set of tools for the classification of this variants according to their level of conservation. SNP-SACK was conceived and designed for the efficient characterisation and classification of SNPs and other markers in pseudo-diploid organisms. -
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GenomicVis
Genomic data visualisation
GenomicVis is a R package that contains a collection of function for the visualisation of genomic data typically derived from high-throughput whole genome sequencing and SNP-Chip experiments. Most of the functions provided by this package are agnostic about where the data actually comes from, that is, they required input in simple data.frame instances that are not tied to a particular file format; however, we also provide many examples of creating these simply data.frames from standard file... -
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Athus
Manage, merge, filter and convert population genetics data
This project assists you in performing population genetic analyses by taking over the ugly, boring and error-prone data manipulation steps. Starting from well specified input formats VCF, BED and FASTA and a unique configuration file describing data (f.e. from SNP-arrays or sequencing) as well as filtering one can create standard POPGEN formats like Eigenstrat, PEDMAP (PLINK), Treemix ... In addition there are several utilities for * generating VCF from SNPArray data (NCBI - GEO, Illumina... -
Desktop Central is a unified endpoint management (UEM) solution that helps in managing servers, laptops, desktops, smartphones, and tablets from a central location.
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Lep-MAP
fast and accurate linkage map construction for large SNP datasets
Lep-MAP is a novel linkage map construction software. Note there is a new version, Lep-MAP2 available in https://sourceforge.net/projects/lepmap2/ Also note a bug in Lep-MAP: genotype alleles should be given in numerical order like "1 2", not as "2 1". If you use Lep-MAP, please cite Lep-MAP: fast and accurate linkage map construction for large SNP datasets Pasi Rastas; Lars Paulin; Ilkka Hanski; Rainer Lehtonen; Petri Auvinen Bioinformatics 2013; doi: 10.1093/bioinformatics/btt563 -
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Genome-wide SNP calling for NGS data
seeders's technological scripts
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core_ope
Tools that from raw assembly to core genomic analysis
Eight PERL scripts. remap_qualifiedASM.pl strict_filter.pl - Refine the MUMmer alignment aln_extract.pl - Extract sequence from MUMmer alignment core_genome_build.pl - Build (relaxed) core genome based on sequences in MUMmer alignment core_remove_region.pl - Remove repetitive regions or other regions core_map2snp.pl - Extract SNPs from the core genome nucmer_filter.pl - A integrated script that run MUMmer to generate a mapped sequence core_snp2fas.pl - Build a SNP-only alignment based... -
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DNAA is the DNA analysis package, for analyzing next-generation post-alignment whole genome resequencing data. Specifically, DNAA is able to find structural variation, SNP and indel variants, as well as evaluating the mapping and data quality.
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Paligo is an end-to-end Component Content Management System (CCMS) solution for technical documentation, policies and procedures, knowledge management, and more.
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AWclust is easy to use non-parametric population structure analysis software written for R with a GUI interface. Just point and click and you will be on your way to discovering the important cluster information in your SNP data sets.
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GwasLD
Quick search the LD SNPs against reported GWAS Catalog.
we invented a simple desktop stand-alone program (GWAS-LD) and also web-based program to identify the previous GWAS SNPs and the reported traits in high linkage disequilibrium (LD) state with a query SNP. To make the program, we downloaded all GWAS SNPs from GWAS catalogue database (http://www.genome.gov) and investigated all proxy (in 1 Mbp) SNPs which was in high LD (r2 = 0.9) with the reported GWAS SNPs by SNAP program (http://www.broadinstitute.org/mpg/snap). -
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This package contains code for use with Short Read DNA Sequencing technologies, and includes packages for ChIP-Seq, Whole Transcriptome Shotgun Sequencing, Whole Genome Shotgun Sequencing, SNP Detection, Transcript expression and file conversion.
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SNPTools is a suite of tools that enables integrative SNP analysis in next generation sequencing data with large cohorts. It not only calls SNP in a population with high sensitivity and accuracy, but also employs a novel imputation engine to achieve highly accurate genotype calling and phasing in an efficient way.
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ALCHEMY is a genotype calling algorithm for Affymetrix and Illumina products which is not based on clustering methods. Features include explicit handling of reduced heterozygosity due to inbreeding and accurate results with small sample sizes
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estMOI
estimating Multiplicity Of Infection using short read sequence data
..., BOWTIE, SMALT or other short read aligners to generate a BAM file. 2. Single Nucleotide Polymorphysms (SNPs) are then identified using SAMTools in the VCF format. 3. The reference FASTA file is expected to be indexed using 'samtools faidx' to generate a *.fai file. estMOI generates files containing MOI estimates for each SNP combinations (file with name *.LOG) and a summary for all chromosomes (file with name *.txt). Contact: samuel.assefa @ lshtm.ac.uk -
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Snp Viewer
A program for visualising Affymetrix SNP array data
A program for visualising Affymetrix SNP array data for identification regions of homozygosity. Written to aid autozygosity mapping and aid the discovery of potential disease loci. -
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TRAMS
TRAMS stands for "Tool for Rapid Annotation of Microbial SNPs".
TRAMS annotates SNPs between microbial genomes using a tab-delimited SNP file and a reference genome (EMBL or Genbank format). -
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MCPerm: Monte Carlo SNP permutation
Monte Carlo permutation method for SNP multiple test correlation
MCPerm: A Monte Carlo permutation method for multiple test correlation in case-control association study Traditional permutation (TradPerm) test is an important non-parametric analysis method which can be treated as the gold standard for multiple testing corrections in case-control association study. However, it relies on the original single nucleotide polymorphism (SNP) genotypes and phenotypes data to perform a large number of random shuffles, and thus it is computationally intensive... -
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Bis-SNP
Bisulfite-seq/NOMe-seq SNPs & cytosine methylation caller
Bis-SNP is a package based on the Genome Analysis Toolkit (GATK) map-reduce framework for genotyping in bisulfite treated massively parallel sequencing (Bisulfite-seq, NOMe-seq and RRBS) on Illumina platform. It uses bayesian inference with either manually specified or automatically estimated methylation probabilities of different cytosine context(not only CpG, CHH, CHG in Bisulfite-seq, but also GCH et.al. in other bisulfite treated sequencing) to determine genotypes and methylation levels... -
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hrefinder
Detection of homologous recombination events from SNP data
This software detects homologous recombination events (HREs) from SNP data. Based on SNP alleles calls and locations, it breaks the genomes into locally colinear blocks, and looks for cases where SNPs do not agree with the vertical pattern of inheritance in a phylogeny. It applies a dynamic programming algorithm to model whether changes within a block are likely a result of mutations, sequencing errors, or HRE. We use information from the nearby SNPs, so that if 1-2 alleles in a series of SNPs... -
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hrefinder
Detection of homologous recombination events from SNP data
This software detects homologous recombination events (HREs) from SNP data. Based on SNP alleles calls and locations, it breaks the genomes into locally colinear blocks, and looks for cases where SNPs do not agree with the vertical pattern of inheritance in a phylogeny. It applies a dynamic programming algorithm to model whether changes within a block are likely a result of mutations, sequencing errors, or HRE. We use information from the nearby SNPs, so that if 1-2 alleles in a series of SNPs... -
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mendelFix
Correction of SNP Mendelian errors in trio data
mendelFix is a Perl script for checking Mendelian errors in genome-wide SNP data of trio designs. The program takes 12-recoded PLINK PED and MAP files as input, and calculates a series of summary statistics for Mendelian errors, sets as missing offspring genotypes that present Mendelian inconsistencies, and implements a simplistic procedure to infer missing genotypes using parent information. The program can be easily incorporated in any pipeline for family-based SNP data analysis... -
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asoovir
Annotating Sequence Ontology of Variants in Ruby
ASOoViR is a set of Ruby modules to annotate consequence terms, defined by the Sequence Ontology, of variants (SNP/SNVs, INDELs, SVs, CNAs) using Ensembl gene sets. Prior to annotation of variants an Ensembl gene set and reference coding sequences are loaded into memory from a database file, which can be downloaded or generated by the user from reference files. This allows rapid annotation of variants, making it suitable for annotation of whole genome scale calls. Annotation is performed...