Search Results for "genes" - Page 3
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Showing 194 open source projects for "genes"
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Panacea
PAN And Core-gEnome Analysis
A tool to calculate the Pan-Genome of a set of annotated genomes -
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VacSol
An in slico pipeline to predict potential therapeutic targets
... to identify putative therapeutic targets against the infectious agents. In current study we have developed an in silico, multi-threaded, configurable and scalable pipeline employing subtractive-reverse vaccinology analysis technique and named it VacSol (https://sourceforge.net/projects/vacsol/). The principle objective of the VacSol development is to screen out genes/proteins from microbial genome/proteome that could be employed as potential therapeutic targets -
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CoreAlyze
Use core genes to assess the coverage and fragmentation of a gene set
CoreAlyze analyzes the coverage and completeness of a curated set of widely-conserved, mostly single copy in one or more input test genomes. The characteristics of this subset provide insight into the coverage and fragmentation of the input gene set as a whole. CoreAlyze places its findings in context with other gene sets, adding to the robustness of the results. CoreAlyze also provides phylogenetic and biological information about input genomes. -
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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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FUNN-MG is a tool for functional analysis and visual networks involving genes and metabolic functions previously annotated. ## PREREQUISITES FUNN-MG does not require installation, however depends on the following items: # A network connection. # JRE version >=6. # R version 3.4.1 ## EXECUTION AND PARAMETERS FUNN-MG requests as input file the results obtained from the kaas tool (Moriya et al., 2007). For more information about execution access the README file...
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wgssat_nbfgr
WGSSAT: SSR Annotation Pipeline
WGSSAT provides a Graphical User Interface pipeline to mine and characterize SSR from Whole genome data. This pipeline integrates prediction of genes, ncRNA, repeats and SSR from whole genome assembly and mapping of these predicted SSR on to the genome (classified according to genes, ncRNA, repeats, exonic and intronic region) along with primer designing and mining of cross-species amplification markers. The mining of SSRs from whole genome provides valuable information on the abundance of SSRs... -
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BPGA
A tool for ultra-fast pan-genome analysis of microbes.
BPGA is a fast pan-genome analysis tool for microbial genomes. Along with regular pan genome profiles, BPGA also provides detailed statistics and sequences with their downstream analysis like KEGG/COG assignments and phylogeny based on core as well as pan genome. In addition, it also studies genes with extreme/atypical GC contents as that of the genomic GC content, sub-grouping of large datasets etc. -
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IGSA
Individual Gene Sets Analysis
IGSA (Individual Gene Sets Analysis) is an application software based on Java and R that leverages a powerful analytical capacity. It can be used for gene sets enrichment and samples clustering. In gene sets enrichment, IGSA takes account of the heterogeneity of genes expression in samples and the homogeneity at the functional level, trying to pick out more particular and more significant gene sets. In sample clustering, IGSA clusters the samples based on the significant pathways rather than... -
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Crosshub
Multi-way analysis of The Cancer Genome Atlas (TCGA) project datasets
Crosshub enables multi-way analysis of RNA-Seq, miRNA-Seq and methylome data of The Cancer Genome Atlas (TCGA) project: 1. differential expression analysis (genes, alternative transcripts and miRNA) 2. regulatory miRNA prediction (TargetScan, DIANA microT, mirSVR, PicTar, miRTarBase + co-expression) 3. regulatory TF prediction (ENCODE ChIP-Seq + co-expression) 4. methylation profiling analysis 5. RNA-Seq vs. clinical (TNM, stage, follow-up) correlation analysis Generates Excel summaries... -
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SnowyOwl
RNA-Seq based gene prediction pipeline for fungal genomes
... predictor Augustus with varied input parameters, and selectivity by choosing the models with best homology to known proteins and best agreement to the RNA-Seq data. SnowyOwl has successfully predicted genes in 26 novel fungal genomes. The pipeline can be installed locally for high throughput and control over configuration. It can also be run on a remote server through a convenient web interface for occasional use. -
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HPOSim
Analysis phenotypic similarity between genes and between diseases
This package implements multiple similarity measures for HPO terms, genes and diseases. It is aiming at phenotype analysis for gene sets and disease sets. Functions for HPO enrichment analysis is also provided. -
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SimilarityViewer
Identify co-occuring genes in cyanobacteria
The SimilarityViewer allows the identification of genes co-occurring in subsets of 77 cyanobacterial organisms. The software is available as a MATLAB script and as stand-alone applications for Mac, Linux, and Windows computers. To install this program download the zip file appropriate for your system, unzip it, and follow the instructions in the README file. SimilarityViewer and the included data are licensed under the Apache License Version 2.0. If you use the SimilarityViewer... -
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HGPEC
A tool for gene and phenotype prioritization and evidence collection
Finding gene-disease and disease-disease associations are important issues in the biomedical area and many prioritization methods have been proposed for this goal. Among these, approaches based on heterogeneous network of genes and phenotypes were considered state-of-the-art ones, which can use for diseases with/without known molecular basis. Here, we develop a Cytoscape plugin, namely HGPEC, based on a ran-dom walk with restart algorithm on a heterogeneous network of genes and phenotypes... -
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ConsPred
ConsPred is a pipeline combining several gene/CDS annotation tools
ConsPred is a prokaryotic genome annotation framework that performs various intrinsic gene predictions, homology searches, predictions of non-coding genes, and complex features and integrates all evidence into a consensus annotation. ConsPred achieves high-quality and comprehensive annotations based on rules and priorities, similar to decision making in manual curation. Parameters controlling the annotation process are configurable by the user and the framework can be easily extended... -
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MPIGeneNet
Parallel tool to construct gene co-expression networks
MPIGeneNet is a parallel tool to construct gene co-expression networks using Pearson’s correlation and Random Matrix Theory (RMT). This tool takes as input a matrix with the expression values (a float value) for different genes observed from several samples. It is a parallelization of RMTGenNet tool (https://github.com/spficklin/RMTGeneNet). MPIGeneNet integrates the whole procedure of creating the in one program, which makes the tool easier to work with (the users only have to launch... -
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ETHA
Hybrid Illumina/PacBio assembly of Plasmodium falciparum var genes
ETHA is a software package for hybrid assembly of Plasmodium falciparum var genes from Illumina and PacBio sequencing data -
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Integrated Merging of Orthogonal [Genetic] Datasets to identify novel genes involved in processes starting with known genes. For UNIX-like systems (C code + TCSH scripts), command-line based.
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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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metawatt
Binner for assembled metagenomes
The Metawatt binner is a graphical binning tool that makes use of multivariate statistics of tetranucleotide frequencies and differential coverage based binning. It also performs taxonomic assessment of binning quality (via diamond BLASTx). Created bins can be edited and exported as fasta. The Metawatt is implemented in Java SWING and minimally depends on Diamond, HMMer3.1, BBMap, Prodigal and the Batik library for the export of SVG graphics. Citation: Strous M, Kraft B, Bisdorf R,... -
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... be used for downstream analysis including assembly to identify genes that are differentially abundant between groups of metagenomes (e.g., healthy vs diseased). Please refer to our RECOMB paper for more details: Wontack Han, Mingjie Wang and Yuzhen Ye. A concurrent subtractive assembly approach for identification of disease associated sub-metagenomes. Proceeding of RECOMB 2017.
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MITP
MITP - conserve & novel miRNA identification & target prediction tool
miRNA is a widely known small non-coding RNA which can mediate gene regulation of most important biological processes in plants and animals. Therefore, identification conserve and novel miRNA and their target genes in model and new sequenced species are inevitable. MITP is designed to identify miRNA easily and faster based on sequence mapping result from any mapping software which producing SAM format output result, blast result (default output result) or blat result (default output result... -
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PExFInS
Post-GWAS Explorer for Functional Indels and SNPs
The generation of Post-GWAS Explorer for Functional Indels and SNPs (PExFInS) was originated from the observation that high proportion of cis-acting expression quantiative trait loci (cis-eQTLs) emerged in GWAS SNPs and the underexplored status of indel cis-eQTLs for GWAS. We believe that the integration of cis-eQTLs, especially indel cis-eQTLs, with candidate disease-associated variants generated from GWAS could facilitate the identification of causal genes or disease mechanisms. On the other... -
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WIMSi
Bioinformatics Tools for the Anaysis of DNA Methylation Data
... assumptions about what patterns should exist in the data. The GENE LIST tool is designed to take advantage of the patterns found to elucidate genes likely regulated by DNA methylation. -
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The objective of this project is to provide an innovative tool for visualization of multiples genomes. Written in Java, it presents a simple and intuitive user interface to view and manipulate the relationships between groups of genes.
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PGAP
PGAP is a pipeline for pan-genome analysis.
PGAP is a pan-genomes analysis pipeline developed with Perl. It could perform five analytic functions with only one command, including cluster analysis of functional genes, pan-genome profile analysis, genetic variation analysis of functional genes, species evolution analysis and function enrichment analysis of gene clusters.