Search Results for "genes" - Page 7
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Showing 268 open source projects for "genes"
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Rent Manager is award-winning property management software built for residential, commercial, and short-term-stay portfolios of any size. The program’s fully customizable features include a double-entry accounting system, maintenance management/scheduling, marketing integration, mobile applications, more than 450 insightful reports, and an API that integrates with the best PropTech providers on the market.
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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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CollapseFPKM
This code is a solution to collapsing duplicate FPKMs for a gene
This code is a solution to collapsing duplicate FPKMs for a gene. Problem/Issue: In the cufflinks output files *_genes.expr (which reports the gene-level coordinates and expression values), sometimes I get more than one row for the same gene? It's like in some cases the FPKM values from the transcripts corresponding to the same gene do not get summed, although the transcripts are assigned to the same gene. Reasons and Solution: The multiple FPKM problem occurs when genes have... -
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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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pmutualinformation
Computes pairwise genes mutual information using GEPs
pmutualinformation (parallel mutual information) computes the pairwise Mutual Information for all pairs of genes from a potentially massive and heterogeneous dataset containing GEPs. GEPs can be part of different experiments collected from public repositories. pmutualinformation runs on MIMD systems and has been implemented in C using the MPI standard. -
Collaborate is customizable case management software for non-profits and social services agencies with teams of 5+ staff.
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DOTS-Finder
Driver Oncogenes and Tumor Suppressors Finder
A key challenge in the analysis of cancer genomes is the identification of driver genes from the vast number of mutations present in a cohort of patients. DOTS-Finder, is a new tool which allows the detection of driver genes through the sequential application of functional and frequentist approaches, and is specifically tailored to the analysis of few tumor samples. We have identified driver genes in the genomic data of 34 tumor types derived from existing exploratory projects... -
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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.
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netClass is an R package for network-based feature (gene) selection for biomarkers discovery via integrating biological information. This package adapts the following 5 algorithms for classifying and predicting gene expression data using prior knowledge: 1) average gene expression of pathway (aep); 2) pathway activities classification (PAC); 3) Hub network classification (hubc); 4) filter via top ranked genes (FrSVM); 5) network smoothed t-statistic (stSVM).
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SeqSelector
Tools to select sequences for capture enrichment of next-gen libraries
The SeqSelector toolset is a suite of user-friendly, platform independent python scripts to facilitate selection of sequences for targeted enrichment of next-generation libraries through hybridization-based sequence capture. The scripts require no knowledge of programming, and can be applied to genome sequences of model or non-model species. We suggest a workflow in which genes of interest are first identified from previous studies and publicly available datasets of functional gene annotation... -
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VIGOR3
Annotation of Viral Genomes
VIGOR is a tool for annotating coding genes in viral genomes. It was developed by Jeffrey Hoover and Shiliang Wang for The JCVI Genomic Sequencing Center for Infectious Diseases (GSCID). http://www.biomedcentral.com/content/pdf/1471-2105-11-451.pdf contact: Jeff Hoover 301-540-7858 jefhv@aol.com -
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Java Biomorph Simulator
Simulates biomorph evolution in real-time
This program is an evolution simulator that simulates computer generated organisms called biomorphs. Each biomorph is a recursively drawn tree and contains 9 genes. The genes control the attributes of the biomorph, such as its speed and shape. In this program biomorphs compete against each other, creating offspring as they live. Each offspring is a mutated version of its parent. When a biomorph creates an offspring, its energy is halved. -
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The automated Prokaryotic Annotation Pipeline was developed to generate on demand ORF prediction and functional annotation for prokaryotic genomes. A round of non-coding RNA prediction is done using various tools such as tRNA-scanSE and BLAST. Gene finding is done using a self-training, iterated glimmer3 analysis. The predicted genes are then analyzed for overlaps, and homology based evidence is gathered using a system of hidden markov model search and BLAST. Roles and gene symbols are assigned...
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Maximum Gene Support Tree Approach
Maximum Gene-Support Tree Approach to Infer-ring a Spec
GeneSupport implements a genome-scale algorithm: Maximum Gene-Support Tree to estimate species tree from gene trees based on multilocus sequences. It provides a new option for multiple genes to infer species tree. It is incorporated into popular phylogentic program: PHYLIP package with the same usage and user interface. It is suitable for phylogenetic methods including not only Baysian, but also maximum parsimony, maximum likelihood, neighbour-joining and so on. These methods are used... -
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Ontologizer is an Open Source tool with the purpose of identifing enriched Gene Ontology terms in lists of names of genes or gene products.
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This is the tool for the project of "Classifying substrates transported bye membrane transporters proteins using neighboring genes".
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CQ-calculate
Find Y chromosome genes with CQ-calculate
Software to find Y chromosome genes using separate male and female next-generation sequence data. -
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Models & Algorithms: Metabolites & Genes
Models & algorithms for gene cum metabolite analysis
The aim is to provide a set of models and tools that would enable scientists to efficiently & effectively (a) map the genes associated with a disorder, disease, etc., to “molecular interaction and reaction networks” maps, (b) conduct comparative analysis across volunteers and anatomic structures, and more. -
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Multi-Pipeline Gene Expression Analysis
Helps users to determine the optimal gene expression analysis pipeline
.... Summarization (mas5, rma, farms, DFW) 4. Gene Selection (SAM, ANOVA) Then executes K-means clustering on the significant genes, and evaluates the pipelines using the cumulative distribution funciton of the GO term co-clustering p-values. From this, the optimal microarray data workflow is chosen. Input files are CEL files along with a CLM file, which is a tab delimited text file containing one scan, sample and class per line. -
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plasmiddesigner
Software for drawing plasmid map
Plasmid designer (PlaNer) is a software developed to easily create plasmid maps and extract the figure of it. Features, that is 'genes' (i.e. sequences of interest) or 'sites' (e.g. restriction sites), can be added, removed or deleted at any time. For every Feature, a different colour can be determined for appropriate visualization. The list of the features can be saved at any time and an existing one can be loaded to continue configuring a previously saved plasmid map. PlaNer uses the easy... -
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Genomic Binding Sites Analyser (BiSA)
Genomic Region Archiving and Binding Sites Analysis (BiSA)
...; regions that are not overlapping; average region sizes. BiSA can also annotate binding regions of interest with nearby genes. The results of overlap analysis can be imported into the Knowledge Base, allowing them to go into downstream analysis and independent annotation. A Venn diagram tool is also integrated into the software to allow users to visualize overlap results. -
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OrthoRBH
Rapidly identify orthologous cDNA sequences in related species
OrthoRBH is a tool/pipeline designed to identify families of protein coding transcripts/genes in related species using a reciprocal blast method. It can search through databases of full-length cDNAs, ESTs or mRNA-seq data. Optional assembly of candidate sequences allows assembly of contigs. It is suited to handling a mixture of EST and mRNA-seq sequence data. It performs batch blast searches, so it is ideal for large multi-gene families. After collecting candidate sequences, it performs... -
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Introminer
Extracts intronic information from annotated genomic sequence
Created by Julie Shay and Claudio Slamovits. Introminer reads a sequence file with genomic data that contains sequence and intron positions in genbank format. It extracts positional and sequence data as well as the intronic sequences and other important parameters to study gene architecture and intron evolution at a genome-wide scale. -
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GenSim
A free chicken genetics simulator
Gensim is a free Mendelian genetics simulator based on the expression of genes in chickens. -
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babybiomorphs
Biomorphs simulation with Baby X
Biomorphs are a way of explaining evolution invented by Richard Dawkins. The shapes are controlled by a small set of genes, which give colour, segment length, size, and degree of recursion. By changing a gene by a small amount, a small difference is made in neighbours. Many fascinating shapes can be found, and you can often home in on a desired shape by selecting relatives that are closer to your goal. The program uses the Baby X toolkit. -
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srst
Short Read Sequence Typing
Update - SRST2 Now Available ------ 25 Sep, 2013 This project has now been replaced by SRST2 - Short Read Sequence Typing for Bacterial Pathogens, available at http://katholt.github.io/srst2/ The new SRST2 program does gene typing as well as MLST (e.g. typing resistance genes, virulence genes, etc). SRST2 is faster and more accurate than the old SRST, using bowtie2 to achieve local alignments (no need for flanking sequences) and a brand new scoring system. -
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PseudoDomain
Accurate identification of pseudogenes without genome annotations
Pseudogenes are dysfunctional DNA sequences that share sequence similarities with functional genes. Accurate identification of pseudogenes is important to understand biological and evolutionary histories of genomes and genes. PseudoDomain is a processed pseudogene identification tool with high sensitivity and low false positive rate. It can identify pseudogenes in species that do not have accurate genome annotations. In addition, it can accurately predict the number and positions of frameshifts...