Search Results for "genes" - Page 4
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Showing 160 open source projects for "genes"
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LowMACA
Low frequency Mutation Analysis via Consensus Alignment
The remarkable efforts recently carried out to fully understand the mutational landscape of various kinds of cancer have revealed that the mutational processes can be extremely variable depending on the tumor type and the clinical features of patients. Thanks to these efforts, we have reached a clear picture of the most commonly mutated genes in various types of cancer. However, we are still far from a complete picture of rarely mutated genes, which can be an important target for personalized... -
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Relative Metabolic Differences
RMetD scripts
The scripts for Relative Metabolic Differences (RMetD) method which is RAVEN compatible and developed in Matlab. This script is mainly used for compare the difference of two cells based on the differentially expressed genes between them and use genome-scale metabolic model as platforms. -
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GOBIG is a toolbox that can be used for detecting genetic variations. The project is intended to handle big data. What's more important is that it be used to detect clusters of SNP variants. It is the intention to use the toolbox with common and rare variants. To use it, for example, to find the genetic map of genes causing complex diseases.
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MESPA is a python based pipeline that builds gene models from fragmented genome assemblies. The identification of genomic regions underlying phenotypic differences is central to many questions in evolutionary biology. These studies involve the generation of a high-quality genome and annotation, which consumes a considerable amount of resources in terms of time, money, and personnel. However, most of the causal variation is found in or near genes, so having good gene models is essential. We...
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CoGA
R package for differential co-expression analysis
... interfaces for network visualization, ranking of genes according to their "importance" in the network, and the standard single gene differential expression analysis. -
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QueTAL-effectors
suite to compare TAL effector sequences
The suite QueTAL was developed to offer tailored tools for comparison of TAL effector genes. The program DisTAL considers each repeat as a unit, transforms a TAL effector sequence into a sequence of coded repeats and makes pair-wise alignments between these coded sequences to construct trees. The program FuncTAL is aimed at finding TAL effetors with similar DNA-binding capabilities. It calculates correlations between positional weight matrices obtained from the RVD sequence, and builds trees... -
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Gene Studio is a free tool for modelling of DNA manipulation. It will allow to work with vectors, to design primers, to clone molecules and provide user friendly intewrface.
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Auto Primer3
Automatically design primers to genes/coordinates using primer3.
PLEASE NOTE: THIS PROJECT PAGE WILL NO LONGER BE UPDATED - PLEASE USE THE GITHUB PAGE (https://github.com/gantzgraf/autoprimer3) TO FIND THE LATEST RELEASE (https://github.com/gantzgraf/autoprimer3/releases/latest). AutoPrimer3 retrieves gene information, DNA sequences and SNP information from the UCSC genome browser and uses primer3 to automatically design primers to genes or genomic coordinate targets. Primers may be designed using information from any of the UCSC hosted genomes... -
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GESPA
Accurately predicts disease association of single nucleotide mutations
GESPA (GEnomic Single nucleotide Polymorphism Analyzer) is a bioinformatics tool for classifying Nonsynonymous Single Nucleotide Polymorphisms (nsSNPs). GESPA predicts if a nsSNP is pathogenic using reports from literature and various algorithms to assess conservation in orthologous and paralogous protein alignments. Using reports from literature, GESPA is also able to predict the phenotype of a nsSNP with high accuracy. The software can be used clinically to determine if observed nsSNPs are... -
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Exreco
EXperimental REplicator COllider
... time), and defining the environment of these replicators. If it is all done you can let it run observing what kind of genes prevail over time. The tool typically runs the same world (experiment scenario) over and over again to have a statistical understanding of the various replicator strategies. -
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TransGeneScan
TransGeneScan is a gene finding tool for metatranscriptomic sequences
.../), and can predict a sense transcript containing one or multiple genes (in an operon) or an antisense transcript. -
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PRADA
PRADA : Pipeline for RNA-Sequencing Data Analysis
... from RNAseq data: preprocess: Generates aligned and recalibrated BAM files. expression: Generates gene expression (RPKM) and quality metrics. fusion: Identifies candidate gene fusions. guess-ft: Supervised search for fusion transcripts. guess-if: Supervised search for intragenic fusions. homology: Calculates homology between given two genes. frame: Predicts functional consequence of fusion transcript -
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CCH
A genetics tool that identifies genomic regions of shared ancestry
Combinatorial Conflicting Homozygosity (CCH) uses dense Single Nucleotide Polymorphism (SNP) genotypes to identify regions of the genome inherited from a common ancestor among any or all subsets of a group. Analysis is rapid and can identify loci containing genes for dominant traits. CCH is robust to the presence of phenocopies and can detect undisclosed shared common ancestry. The associated publication regarding CCH may be accessed here: http://www.biomedcentral.com/1471-2164/16/163... -
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SEM_bestShortestPath
A SEM-based method for disease module detection
SEM_bestShortestPath is a Structural Equation Modeling (SEM)-based methodology to evaluate the most important shortest paths between differentially expressed genes in biological interaction networks, with absolutely no need of user-defined parameters or heuristic rules, enabling a free-of-bias discovery and overcoming common issues affecting recent network-based algorithms. SEM-bsp is based on Structural Equation Modeling techniques to detect significantly perturbed sub-networks (disease... -
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Toolkit to examine the topology of a phylogenetic tree, place amino acid substitutions on specific branches, polarize them and compare amino acid sequences of homologous proteins to answer a wide range of questions about protein evolution.
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miRStat
identification of common sets of microRNAs for groups of genes
miRStat enables identification of regulatory microRNA targeting several genes in a custom gene group. This Python application is based on the TargetScan 6.2 microRNA target prediction data. Conserved and Nonconserved site context+ scores files are required (unzip and place to directory with program). Available at http://targetscan.org/cgi-bin/targetscan/data_download.cgi?db=vert_61 -
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HomSI
Homozygous Stretch Identifier from next-generation sequencing data
In consanguineous families, as a result of inheriting the same genomic segments through both parents, the individuals have stretches of their genomes that are homozygous. This situation leads to the prevalence of recessive diseases among the members of these families. Homozygosity mapping is based on this observation and several recessive disease genes have been discovered with the help of this technique in consanguineous families. The researchers typically use SNP arrays to determine... -
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SimplyTheBlast
Blast query sequences on a set of fasta formatted genomes
SimplyTheBlast: a small perl tool to build genes presence/absence matrices over a set of Fasta formatted genomes. This code requires: Bio::SeqIO; Bio::Perl; Bio::Tools::Run::StandAloneBlast; Bio::Seq; Bio::Tools::Blast; Bio::DB::GenBank; Bio::DB::WebDBSeqI; and BLAST 2.2.28 (blastall and formatcmd) installed and reachable from your command line Usage: perl SimplyTheBlast-Align.pl <fasta formatted seeds file> <path to genomes folder> <Alignment length threshold in %> <Alignment... -
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rseqflow
RNA-Seq analysis pipeline for QC, Expression, DifferentialExpression
RseqFlow is an RNA-Seq analysis pipeline which offers an express implementation of analysis steps for RNA sequencing datasets. It can perform pre and post mapping quality control (QC) for sequencing data, calculate expression levels for uniquely mapped reads, identify differentially expressed genes, and convert file formats for ease of visualization. A detailed description of the pipeline] is given here: https://sourceforge.net/p/rseqflow/wiki/PipelineDescription RseqFlow offers two run mode... -
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adLIMS
adLIMS: a Laboratory Information Management System with ADempiere
Many biological laboratories dealing with genomic samples are facing the problem of sample tracking, both for pure laboratory management and efficiency, and for internal policies, such as Good Laboratory Practices (GLP). Our laboratory exploits PCR techniques and next-generation sequencing (NGS) methods, to perform high-throughput integration site monitoring in different clinical trials and scientific projects, based on the delivery of therapeutic genes by viral vectors integrating... -
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Deem
Analyze time-course data with significance tests, clustering, modeling
Use statistical methods to analyze time-course data (gene expression microarray and RNA-seq data in particular, but not limited to). Apply significance tests to filter out only significant genes or time series. Cluster time series into similar groups. Generate network models, including linear or non-linear models. Variable selection and optimization routines included. Written in Scala and R. The application is a cross-platform desktop app with a simple GUI and is fully functional... -
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..." to ensure that the java virtual machine has enough space to run. You can find sample test files under code/Test. Test files for clustering part are under code/Test/InputFile which contains two chameleon datasets from: http://glaros.dtc.umn.edu/gkhome/cluto/cluto/download Also, you can find sample test files for self-learning and co-training under its corresponding folders. Mainly genes/miRNAs expressions downloaded from : http://0-www.ncbi.nlm.nih.gov.elis.tmu.edu.tw/
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GIIRA
RNA-Seq driven gene finding incorporating ambiguous reads
GIIRA is a gene prediction method that identifies potential coding regions exclusively based on the mapping of reads from an RNA-Seq experiment. It was foremost designed for prokaryotic gene prediction and is able to resolve genes within the expressed region of an operon. However, it is also applicable to eukaryotes and predicts exon intron structures as well as alternative isoforms. -
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Allele Builder
python-based tool for multi-allele gene analysis
Allele Builder aims at analysis of multi-allele and multi-locus genes as well as microbiome study. In contrast to the other software enabling 454 data prcessing the Allele Builder allows the usage of long amplicons with two-tailed reads. Allele Builder effectively eliminates chimeric reads coming from artificial recombination between two PCR amplicons. -
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... http://rdp.cme.msu.edu/tutorials/framebot/RDPtutorial_FRAMEBOT.html. Updates: FrameBot now uses a kmer pre-filtering heuristic for no-metric-search. This pre-filtering may increase the speed by one to two orders of magnitude. CITATION: Wang, Q., Quensen, J. F., Fish, J. A., Lee, T. K., Sun, Y., Tiedje, J. M., and Cole, J. R. 2013. Ecological patterns of nifH genes in four terrestrial climatic zones explored with targeted metagenomics using FrameBot, a new informatics tool. mBio 4:e00592-13.