Search Results for "genomics" - Page 3
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Showing 106 open source projects for "genomics"
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SplitMEM
Graphical pan-genome analysis with suffix skips
With the rise of improved sequencing technologies, genomics is expanding from a single reference per species paradigm into a more comprehensive pan-genome approach with multiple individuals represented and analyzed together. Here we introduce a novel O(n log n) time and space algorithm called splitMEM, that directly constructs the compressed de Bruijn graph for a pan-genome of total length n. -
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GenomeView is a genome browser and annotation editor that displays reference sequence, annotation, multiple alignments, short read alignments and graphs. Most major data formats are supported. Local and internet files can be loaded. This project has moved to GitHub: https://github.com/GenomeView/genomeview
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RAREVATOR
Tool for the detection of variants in rare reference allele loci
RAREVATOR (RAre REference VAriant annotaTOR) is a tool for the identification and annotation of germline and somatic variants in rare reference allele loci from second generation sequencing data. RAREVATOR has been published on BMC Genomics. Magi A, D'Aurizio R, Palombo F, Cifola I, Tattini L, Semeraro R, Pippucci T, Giusti B, Romeo G, Abbate R, Gensini GF. Characterization and identification of hidden rare variants in the human genome. BMC Genomics. 2015 Apr 24;16:340. doi: 10.1186/s12864-015-1481-9. -
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fitGCP
Fitting genome coverage distributions with mixture models
Genome coverage, the number of sequencing reads mapped to a position in a genome, is an insightful indicator of irregularities within sequencing experiments. While the average genome coverage is frequently used within algorithms in computational genomics, the complete information available in coverage profiles (i.e. histograms over all coverages) is currently not exploited to its full extent. Thus, biases such as fragmented or erroneous reference genomes often remain unaccounted for. Making this information accessible can improve the quality of sequencing experiments and quantitative analyses. ... -
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CNV Explorer
Interactive Copy Number Analysis for Cancer Genomics
CNV Explorer for Gene discovery: https://arraycgh.shinyapps.io/CNV_Explorer/ CNV Explorer for survival analysis: https://arraycgh.shinyapps.io/CNV_Explorer_Survival/ CNV_Explorer is a data mining tool for cancer researchers interested in the structural and copy number changes that happen in cancer genomes. Huge volumes of genomics data from nearly every cancer type are now freely available and several online databases have begun to collate and store this information. However, current tools focus on individual gene queries rather than chromosomal and region-based queries more relevant to some researchers. CNV_Explorer creates interactive CNV frequency, GISTIC-style and breakage frequency plots from public (or your own) data. ... -
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CCH
A genetics tool that identifies genomic regions of shared ancestry
...The associated publication regarding CCH may be accessed here: http://www.biomedcentral.com/1471-2164/16/163 If you use CCH please cite: Levine AP, Connor TM, Oygar DD, Neild GH, Segal AW, Maxwell PH, Gale DP. Combinatorial Conflicting Homozygosity (CCH) analysis enables the rapid identification of shared genomic regions in the presence of multiple phenocopies. BMC Genomics. 2015 Dec;16(1):1360. doi: 10.1186/s12864-015-1360-4. Epub 2015 Mar 10. -
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CG-Pipeline
A computational genomics pipeline for prokaryotic sequencing projects
This project has moved to Github! However, please see the Sourceforge wiki for any help. https://github.com/lskatz/cg-pipeline http://cg-pipeline.sourceforge.net/wiki/index.php/Main_Page -
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sirfast
Mapper for Complete Genomics
sirFAST is a sensitive read map for the Complete Genomics (CG) technology based on the seed-and-extend paradigm that can quickly map CG reads to a reference genome. -
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Bayesian Estimated Core Genome
A pipeline for estimating the core genome of a set of genome sequences
...van Tonder AJ, Mistry S, et al.Defining the estimated core genome of bacterial populations using a Bayesian decision model. (under review) 3. Krzywinski M, Schein J et al. Circos: an information aesthetic for comparative genomics. Genome Res 2009, 19:1639-1645. -
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...MGEScan-non-LTR is a software for the identification of non-LTR retrotransposons in genomic sequences, following a computational approach inspired by a generalized hidden Markov model (GHMM). References: 1. M. Rho et al., "De novo identification of LTR retrotransposons in eukaryotic genomes", BMC Genomics (2007) 8:90. 2. M. Rho and H. Tang, "MGEScan-non-LTR: computational identification and classification of autonomous non-LTR retrotransposons in eukaryotic genomes", Nucleic Acids Research (2009) 37:21.
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TAMrS
Transcriptome assembly made (really) simple
TAMrS aims to make transcriptome assembly 'really easy'. In short, the software will allow the user to --USING A SINGLE COMMAND-- input paired end or single end Illumina data, and get out an assembly and estimates of gene expression. The program only operates on Linux. executing 'make' downloads the required software (using curl and wget) and ensures that the everything is in the right place. -
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EXCAVATOR-tool
Tool for detecting CNVs from whole-exome sequencing data
ATTENTION!!!!!ATTENTION!!!!!ATTENTION!!!!!ATTENTION!!!!! We recently published on BMC Genomics a novel software package, named XCAVATOR, for the identification of CNVs/CNAs from short and long reads whole-genome sequencing experiments (https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-4137-0). XCAVATOR is freely available at http://sourceforge.net/projects/xcavator/. EXCAVATOR is a novel software package for the detection of copy number variants (CNVs) from whole-exome sequencing data. ... -
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The Complete Genomics Analysis Tools is an open source project to provide tools to simplify analysis of genomics data produced by Complete Genomics.
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Bioinformatic tools for analyzing an orfeome using translated ORFs and compares each ORF to the provided Orfeome/Proteome. Our script uses NCBI BLAST run locally and MySQL as the main engines in a new and interisting way. It is designed specifically for Poxvirus genomes, and provides the VACV-COP nomenclature and Cowpox Ortholog groups per each ORF. The BLAST stats are generated when compared to the Proteome you provide. It can be easily adapted for other genomes.
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ConoSorter
A Large-scale Cone Snail Transcriptome/Proteome Analysis Program
ConoSorter is a high-throughput standalone program that implements regular expressions and profile Hidden Markov Models (pHMMs) for large-scale identification and classification of precursor conopeptides into gene superfamilies and classes based on the ER signal, pro-, and mature conopeptide regions generated from raw next-generation transcriptomic or proteomic data. ConoSorter also generates a set of relevant additional information (frequency of protein sequences, length, number of... -
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locusvu
Tool for genomics;automates data retrieval from db;enables workflows
...Thus, LocusVu provides a basic framework that can be used by users and developers alike in simplifying existing workflows and creating newer ones to support data analysis in genomics. -
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ReferenceFree
Scripts for reference free genomic analysis
These are Python scripts plus C/C++ programs for automating the reference free genomic analysis described in: Kua C-S, Ruan J, Harting J, Ye C-X, Helmus MR, et al. (2012) Reference-Free Comparative Genomics of 174 Chloroplasts. PLoS One 7(11). http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0048995 Analytical concept conceived by CHCannon and CSKua. Original script written in Mathematica by CHCannon. -
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siMacro is simple GUI tool for cell based genome wide siRNA screen data processing. It calculates statistical parameters such as Z score and robust Z score.
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TreeLiker
TreeLiker is a collection of fast algorithms for working with complex
...In experiments with real-life data, the algorithms were shown to be able to construct complete non-redundant sets of patterns for chemical datasets involving several thousands of molecules as well as for comparably large datasets from genomics or proteomics. The included relational learning algorithms are tailored towards so-called tree-like features for which some otherwise very hard sub-problems (NP-hard) become tractable. -
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locsmoc
piecewise polynomial curves for genomic signals
Locsmoc produces piecewise polynomial models for one-dimensional signals of the type encountered in genomics. The project wiki contains an overview of the tool and usage examples. -
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Software for making Clusters of Orthologous Groups (featuring the new EdgeSearch algorithm). Latest ref: Kristensen DM, Kannan L, Coleman MK, Wolf YI, Sorokin A, Koonin EV, Mushegian A. Bioinformatics 2010.
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Intrepid Bioinformatics' Integrative Genomics Viewer (IGV) modifications designed to integrate Intrepid's repository with the Broad Institute's IGV visualization tool.
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The Katsura tool overlays microarray gene expression data, proteomics, and similar biological data onto metabolic pathways. [Pathogen Functional Genomics Resource Center (PFGRC) @ J. Craig Venter Institute (JCVI)]
