Search Results for "gene"
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Showing 90 open source projects for "gene"
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AngClust
AngClust: Angle-based feature clustering for time series
... * The clustering outcome of our algorithm (AngClust) is better than the currently most popular STEM algorithm. * AngClust can be used to analyze any short time series gene expression profiles. -
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GOBU
Gene Browsing Utility
Gene Ontology Browsing Utility (hereinafter, GOBU, pronounced as "go-boo") is a browsing and manipulating tool for Post-Pipeline genetic data, especially useful for data with GO annotations. With help of GOBU, we expect biologists and their cooperating technicians can pay less effort on common programming stuff. At the same time, GOBU provides an Extendable Architecture which guarantees the possibility of 1. -
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BRIG is a cross-platform (Windows/Mac/Unix) application that can display circular comparisons between a large number of genomes, with a focus on handling genome assembly data. Please cite the BRIG paper if BRIG is used to generate figures for publications: NF Alikhan, NK Petty, NL Ben Zakour, SA Beatson (2011) BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons, BMC Genomics, 12:402. PMID: 21824423
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The RDP Classifier is a naive Bayesian classifier that can rapidly and accurately provides taxonomic assignments for bacterial and archaeal 16S rRNA sequences, fungal LSU and fungal ITS sequences, with confidence estimates for each assignment. More information and tutorials on how to install, use and retrain RDP Clasifier can be found on at https://github.com/rdpstaff/classifier and John Quensen's blog (https://john-quensen.com/). Citation: 1. Wang Q, Garrity GM, Tiedje JM, Cole JR....
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BD-Func
Bidirectional Functional Enrichment of Gene Expression Data
BD-Func is an algorithm to predict activation or inhibition of pathways based upon gene expression patterns. If you use BD-Func, please cite: Warden C, Kanaya N, Chen S, and Yuan Y-C. (2013) BD-Func: A Streamlined Algorithm for Predicting Activation and Inhibition of Pathways. peerJ, 1:e159 -
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Cylindrical Alignment App
Arranges alignments in a rotating cylinder
The Cylindrical Alignment App is the successor to Cylindrical BLAST Viewer. Similarly, it arranges search or other comparisons, against their "axis". Searches can be made by Basic Local Alignment Search Tool, ClustalW, or Gene Machine to name a few. This version does not require downloading or installing Java3D, and has more modern GUI features. -
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COHCAP
City of Hope CpG Island Analysis Pipeline
COHCAP (City of Hope CpG Island Analysis Pipeline, pronounced "co-cap") is an algorithm to analyze single-nucleotide resolution methylation data (Illumina 450k methylation array, targeted BS-Seq, etc.). Please note: 1) The SourceForge version of COHCAP is no longer being updated. Please see the GitHub version: https://github.com/cwarden45/COHCAP This was the source repository for the Bioconductor version, with some changes after the decision to only provide the code through... -
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Lirex
A Package for Identification of Long Inverted Repeats in Genomes
Long inverted repeats (LIRs) are evolutionarily and functionally important structures in genomes because of their involvement in RNA interference, DNA recombination, and gene duplication. Identification of LIRs is highly complicated when mismatches and indels between the repeats are permitted. Long inverted repeat explorer (Lirex) was developed and introduced here. Written in Java, Lirex provides a user-friendly interface and allows users to specify LIR searching criteria, such as length of the region, as well as pattern and size of the repeats. ... -
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DACO-algorithm
A novel transcription factor complex prediction algorithm.
Eukaryotic gene expression is controlled through molecular logic circuits that combine regulatory signals of many different factors. Complexation of transcription factors and other regulatory proteins is a prevailing and highly conserved mechanism of signal integration within critical regulatory pathways and enable to infer controlled genes as well as the exerted regulatory mechanism. -
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The source code has been migrated and is now hosted on Github: https://github.com/jenetics/jenetics Jenetics is an advanced Genetic Algorithm, Evolutionary Algorithm and Genetic Programming library, respectively, written in modern day Java. It is designed with a clear separation of the several algorithm concepts, e. g. Gene, Chromosome, Genotype, Phenotype, Population and fitness Function. Jenetics allows you to minimize or maximize the given fitness function without tweaking it. In contrast to other GA implementations, the library uses the concept of an evolution stream (EvolutionStream) for executing the evolution steps. Since the EvolutionStream implements the Java Stream interface, it works smoothly with the rest of the Java Stream API. ...
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OptFlux is an open-source and modular software aimed at being the reference computational application in the field. It is the first tool to incorporate strain optimization tasks, i.e., the identification of Metabolic Engineering targets.
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Taxoblast
Taxoblast is a pipeline to identify contamination in genomic sequence
Raw genomic sequences are frequently contaminated with sequences of other organism. Their identification is essential for the interpretation of genomic data. In this context it is essential to distinguish between horizontal gene transfers and contamination. The genomic context of sequences can help distinguish the two scenarios. Taxoblast splits genomic scaffolds into sub-sequences of defined length and for each of them determines the closest related taxon. It then summarizes this information for the entire scaffold, taking into account the taxonomic ontology. ... -
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GNAT
GNAT recognizes gene names in text and maps them to NCBI Entrez Gene
GNAT is a BioNLP/text mining tool to recognize and identify gene/protein names in natural language text. It will detect mentions of genes in text, such as PubMed/Medline abstracts, and disambiguate them to remove false positives and map them to the correct entry in the NCBI Entrez Gene database by gene ID. March 2017: We started to upload GNAT output on Medline. See files/results/medline/. -
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MOIRAI
Simple Scientific Workflow System for CAGE Analysis
Cap analysis of gene expression (CAGE) is a sequencing based technology to capture the 5’ ends of RNAs in a biological sample. After mapping, a CAGE peak on the genome indicates the position of an active transcriptional start site (TSS) and the number of reads correspond to its expression level. CAGE is prominently used in both the FANTOM and ENCODE project. -
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Mauve computes and interactively visualizes genome sequence comparisons. Using FastA or GenBank sequence data, Mauve constructs multiple genome alignments that identify large-scale rearrangement, gene gain, gene loss, indels, and nucleotide substutit
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SILA
Automated bacterial and archaeal genome annotation system
SILA is a system for automated annotation of bacterial and archaeal genomes. It provides accurate gene prediction using a combination of tools (Prodigal and HGF) and a web site for task management and visualization of annotation. This project is in alpha stage. Please use the online service available at: http://www.bioinfo.ufpr.br/SILA/login.jsp Documentation (portuguese only): http://hdl.handle.net/1884/34801 -
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STON
Translator of SBGN PD and AF maps into Neo4j graph database.
STON, Sbgn TO Neo4j, is a Java-based framework that imports and translates metabolic, signalling and gene regulatory pathways presented in SBGN (Systems Biology Graphical Notation, http://www.sbgn.org) Process Description (PD) and Activity Flow (AF) languages to a graph-oriented format compatible with Neo4j (http://neo4j.com/). STON1.2 allows also to link common processes between two different PD maps. This framework uses two sets of libraries: LibSBGN and Neo4j libraries. ... -
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Analyze My Genes
Compare gene analysis results from 23andme with the human genome
This program compares personal gene analysis results from 23andme with extracted databases from the human genome project. An typical example of an extracted database is a dataset which contains all alternative alleles which occur less than 1% of the time. -
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GSA-SNP is a gene set analysis software that can process SNP data as well as gene and haplotype data.
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PromKappa 2.0 (DNA patterns in Java)
PromKappa 2.0 (Java source code and bin)
A Java adaptation of DNA patterns based on the article "Eukaryotic genomes may exhibit up to 10 generic classes of gene promoters". by Ilie Guta (Java source code for DNA patterns) -
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came
Identification of chromatin accessibility from NOMe-seq
Chromatin accessibility plays a key role in epigenetic regulation of gene activation and silencing. Open chromatin regions allow regulatory elements such as transcription factors and polymerases to bind for gene expression while closed chromatin regions prevent the activity of transcriptional machinery. Recently, nucleosome occupancy and methylome sequencing (NOMe-seq) has been developed for simultaneously profiling of chromatin accessibility and DNA methylation on single molecules. ... -
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PLEASE NOTE: THIS PROJECT PAGE WILL NO LONGER BE UPDATED - PLEASE USE THE GITHUB PAGE (https://github.com/gantzgraf/MutationMapper) TO FIND THE LATEST RELEASE (https://github.com/gantzgraf/MutationMapper/releases/latest). Predict functional consequences of mutations identified from sanger sequencing.
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A Tool for Retrieval, Visualization and Analysis of biological Pathways. Import a Gene or Protein Set from any Excel file. Automatically find signaling Pathways from KEGG. Integrate your Data in Seconds with a live interactive Force-directed Layout.
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oasis-genomics
Oasis Genomics cancer omics integration portal
OASIS is an application that enables complex analytical queries across somatic mutations; copy number changes (CNV); and gene expression data. OASIS has been built on top of the BIoMart frameworks and has been extended to incorporate unique tools and visualizations to facilitate analysis of complex cancer "Omics" datasets. -
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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.