Search Results for "genes" - Page 2
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Showing 268 open source projects for "genes"
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... biopsy from cancers, quantitative transcriptome analysis to estimate accurate expression levels of genes or transcripts, and even single-cell sequencing of large cell populations. Operating system: Linux Programming language: C++ License: Non-Commercial Research Use Only
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CODON SOFTWARE
The dataset and codon project files are available here.
Genome annotation conceptually consists of inferring and assigning biological information to gene products. Over the years, numerous pipelines and computational tools have been developed aiming to automate this task and assist researchers in gaining knowledge about target genes of study. However, even with these technological advances, manual annotation or manual curation is necessary. To assist with this problem, we present CODON, a tool for the prediction, annotation, and manual curation... -
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Fun4Me
A package for functional annotation for metagenomes
This package includes a few programs for rapid functional annotation for metagenomic sequences, including, 1) Gene prediction by FragGeneScan; 2) Similarity search by RAPSearch2; 3) Functional annotation in GO (Gene Ontology) and EC (Enzyme Commission) based on similarity search results; 4) From EC to metabolic pathway reconstruction by MinPath. Inputs: Just sequencing reads (or assemblies) Outputs: Protein-coding genes (or gene fragments); similarity search; functional annotations (in GO... -
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Bt_proteindatabase
Specific Bacillus thuringiensis protien Blast database
A specific protein database of insecticidal genes (Cry, Vip, Sip, Mtx-like, Bin-like and other protins) from the Bacillus thuringiensis toxin nomenclature. -
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miRDiana
MATLAB package to find the miRNAs targeting a list of genes
To select miRNA target genes we developed software in MATLAB® (MathWorks®) called miRDiana that collects the union of mouse validated targets from the TargetScan, MicroCosm, mirTarBase and miRWalk 2.0 databases. Firstly, the software downloads each database and preprocesses by standardizing the miRNA and gene names. It strips the miRNA names from the species ids and converts the gene names to the official symbols of the National Center for Biotechnology Information (NCBI) database. Next... -
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gsasnp2
PubMed ID: 29562348 / DOI: 10.1093/nar/gky175
* GSA-SNP2 is a successor of GSA-SNP (Nam et al. 2010, NAR web server issue). GSA-SNP2 accepts human GWAS summary data (rs numbers, p-values) or gene-wise p-values and outputs pathway genesets ‘enriched’ with genes associated with the given phenotype. It also provides both local and global protein interaction networks in the associated pathways. * Article: SYoon, HCTNguyen, YJYoo, JKim, BBaik, SKim, JKim, SKim, DNam, "Efficient pathway enrichment and network analysis of GWAS summary data using... -
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miniABS
miniABS (mini Absolute Breast Cancer Subtyper)
miniABS (mini Absolute Breast Cancer Subtyper) is an absolute, single-sample subtype classifier for breast cancer using Random Forest model of pairwise gene expression ratios (PGER) among 11 functional genes. With a systematic gene selection and reduction step, we aimed to minimize the size of gene set without losing a functional interpretability of the classifier. We validated the model performance using a large, heterogeneous cohort that consists of multiple public datasets across four... -
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TARGT pipeline
Targeted Analysis of sequence Reads for GenoTyping of HLA/MHC genes
The 'TARGT' pipeline for Targeted Analysis of sequencing Reads for GenoTyping can be used for genotyping of MHC/HLA genes (or other genomic regions) from ancient and modern shotgun sequence data with moderate to low sequence coverage. The pipeline consists of a main bash script that calls the different steps of the pipeline and can either be called directly or submitted to a cluster queue system, as well as additional sub-scripts and files, that are required to perform the different steps... -
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Tree2GD
A method for inferring gene duplication events from gene trees
Tree2GD is a method for gene duplication inference based on gene-tree/species-tree reconciliation. For each gene-family tree, the LCA was assigned for each gene clade, determined by taxon groups of the species carrying the genes in the clade. We then examined the species corresponding to all genes in a clade before and two sister clades after a putative duplication. -
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GranthamDist
Perl scripts for calculating amino acid sequence divergence
This package contains two perl scripts and corresponding distance matrixes to calculate amino acid sequence divergence among alleles in a pairwise manner or among all alleles of an individual. The scripts were specifically written to calculate divergence between alleles of MHC/HLA immune genes. Written by Tobias Lenz, last updated May 2020. Please cite the following reference when using this script in your research: Pierini & Lenz (2018) Divergent allele advantage at human MHC genes: signatures... -
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gcdm
Gene Circuit Dynamical Model
This program implements gene circuit dynamical model of segmentation genes in Drosophila embryo. The code was originally based on the code FlyCode: http://flyex.uchicago.edu/newlab/download/fly9.4_ser.tar.gz -
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MSIGNET
A Bayesian approach for disease-associated gene network identification
MSIGNET integrates disease-specific gene expression data and human protein-protein interactions in a Bayesian network, and identifies interactions of genes significantly expressed under the disease condition. -
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PPIXpress
specific protein interaction networks from transcript expression
Although protein-protein interaction networks are an ubiquitous component of modern systems biology, comparatively few efforts have been made to tailor their topology to the actual cellular condition under study. Since a simple reduction of the networks to the subset of expressed genes only scratches the surface of higher organisms’ regulatory capabilities, we propose the advanced method PPIXpress that allows to exploit expression data at the transcript-level and is thus able to also reveal... -
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MetaPA is a de Bruijn graph algorithm to obtain complete protein coding genes by assembling metagenomic and metatranscriptomic short reads. Jiemeng Liu*, Qichao Lian*, Yamao Chen, Ji Qi. (2019) Amino acid based de Bruijn graph algorithm for identifying complete coding genes from metagenomic and metatranscriptomic short reads. Nucleic Acids Research.
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GLUVAB
Genomic Lineages of Uncultured Viruses of Archaea and Bacteria
Perl script that automates the analyses to establish GL-UVAB (Genomic Lineages of Uncultured Viruses of Archaea and Bacteria). These include: 1) Identification of protein encoding genes with Prodigal. 2) All-versus-all protein search with Diamond. 3) Calculating Dice distances. 4) Building Dice tree using R 5) Identifying lineages based on the user defined criteria. -
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svdetect.sh is a shell script to run SVDetect to detect SV in exome-seq and Shatterproof to detect chromothripsis. ***Update*** The output files of SVDetect can be annotated by genes with multi-threading.
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rRNAFinder
Fast ribosomal RNA detector and annotator
rRNAFinder is a small perl software package, which can be used to automatically predict and classify the ribosome RNA genes using the assembled genome/metagenome contigs as input. The software were only tested on the Linux operating system. "rRNAFinder.pl" program included in the package uses nhmmer program searching against the arc.hmm, bac.hmm, and euk.hmm databases to identify rRNA genes from the input contigs. The predicated rRNA genes include 16S, 18S, 23S, 28S, 5S, and 5.8S rRNA genes... -
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RWRMTN
Predicting disease-associated miRNAs on a miRNA-target gene network
The misregulations of microRNA have been shown the contribution to diseases. Recently, we have proposed a computational method based on a random walk framework on a microRNA-target gene network to predict disease-associated microRNAs. This was shown superior when compared to existing state-of-the-art network- and machine learning-based methods since it well exploits mutual regulation between miRNAs and their target genes in microRNA-target gene networks. To facilitate the use of this method... -
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BCAW Tool
Bio Codon Analysis Workflow Tool
BCAWT was developed using python 3.7 with build in and third-party modules. The usage of BCAWT is made to be very easy where users have only to input a fasta format file containing genes to be analyzed, and a bunch of analysis will be performed with 23 different output files -
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OncoBase
A platform for decoding regulatory somatic mutations in human cancers
Whole-exome and whole-genome sequencing have revealed millions of somatic mutations associated with different human cancers. The vast majority of identified somatic mutations are located outside of coding sequences, making it challenging to directly interpret their functional effects. With the rapid advances in high-throughput chromosome conformation capture (3C)-based technologies, genome-scale long-range chromatin interactions were detected, and distal target genes of regulatory elements were... -
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selectseq
Get specific sequences from a FASTA or FASTQ file.
A command-line utility to manipulate biological sequences from a FASTA or FASTQ file. It can, given a list of identifiers, get only a subset of the sequences (or their complement, i.e., sequences NOT in the list). Can also get sequence number N only. Compressed sequences files are supported if readable by zcat. -
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This is a Python-based efficient implementation of several semantic similarity measures. The target is to enable fast and easy calculation of similarity between proteins and genes using the Gene Ontology (GO).
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Epi-Gene
EASY HANDLING OF MICROBIAL GENOMES
Epi Gene can cluster the whole genomes into 3 categories of core, accessory and unique genes. It can build two types of panmatrixes (i) Binary Panmatrix based on absence and presence of genes. (ii) Panmatrix based on the identity of the sequences. Binary pan-matrix will be used to build a UPMGA tree and heatmap to further describe an evolutionary relationship. While the pan-matrix based on sequence identity can be used for further quantitative analyses. This package can only works on WINDOWS...