Search Results for "genes" - Page 8
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Showing 268 open source projects for "genes"
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SKUDONET ADC, operates at the application layer, efficiently distributing network load and application load across multiple servers. This not only enhances the performance of your application but also ensures that your web servers can handle more traffic seamlessly.
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HubSpot is an AI-powered customer platform with all the software, integrations, and resources you need to connect your marketing, sales, and customer service. HubSpot's connected platform enables you to grow your business faster by focusing on what matters most: your customers.
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locusvu
Tool for genomics;automates data retrieval from db;enables workflows
LocusVu is a novel Java based software tool that accepts a list of genomic loci (positions on the chromosome) as input and automates fetching of related information (cytogenetic band, gene name, OMIM data etc.) from public databases such as the UCSC genome browser database. It then enables multiple workflows on the retrieved results, like comparing multiple datasets (comparative genomics), viewing neighboring genes for a loci from within the tool itself, or graphically representing... -
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ScreenSifter
ScreenSifter is a unique tool for RNAi Screen analysis and management
ScreenSifter can help you in managing all your RNAi screens related projects in organized fashion. ScreenSifter, to perform the sequential, user friendly, guided, and advanced statistical analyses of RNAi screening results. User can upload their raw signal intensities and will avail complete quality control of screen, hit selection, plotting of hit genes with gene ontology, comparing of replicates or comparing of channels. In addition, ScreenSifter has visualization tools to plot specific genes... -
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MMAD
Microarray Microdissection with Analysis of Differences (MMAD)
We have developed a new computational tool called MMAD, which is capable of performing robust tissue micro-dissection in silico, and which can improve the detection of differentially expressed genes. MMAD software is implemented in MATLAB. The MMAD.zip file contains a brief user guide and MATLAB source code for implementation of MMAD. Developers: David A Liebner, MD Kun Huang, PhD Jeffrey D Parvin, MD, PhD -
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Webapp
A web interface to the SnowyOwl gene prediction pipeline
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Over two-thirds of people reuse passwords across sites, resulting in an increasingly insecure e-commerce ecosystem. Learn how passwordless can not only mitigate these issues but make the authentication experience delightful. Implement Auth0 in any application in just five minutes
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Transpositions are large-scale mutational events that occur when a block of genes moves from a region of a chromosome to another region within the same chromosome. The transposition distance problem is the minimum number of transpositions required to transform one genome into another. Recently, Bulteau, Fertin and Rusu proved that finding the transposition distance is a NP-Hard problem. Some approximation algorithm for this problem have been presented to date. Here we focus on developing...
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BIRF
A Balanced Iterative Random Forest For Gene Selection From Microarray
A balanced iterative random forest algorithm is proposed to select the most relevant genes to the disease and can be used in the classification and prediction process. Balanced iterative random forest is an embedded feature selector that follows a backward elimination approach. The base learning algorithm is random forest which is involved in the process of determining which features are removed at each step. The algorithm starts with the entire set of features in the dataset. At every... -
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DAWGPAWS is a suite of command line programs written in Perl that accelerates annotation of genes and transposable elements in plant genomes by automating the process of running annotation programs and facilitating combined evidence annotation curation.
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DJDarwin
A Genetic algorithm approach to creating beats.
... (including inactive genes, changing instruments, and more) occur randomly (or at the user's control), and the user can add her own beats to the population. The program was written by Nir Rosenfeld and Assaf Michaely. -
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AMBIENT
Find active modules in metabolic networks using high-throughput data
... consistent characteristic. AMBIENT does not require predefined pathways and gives highly specific predictions of affected areas of metabolism. For example, scores for reactions based on transcriptional data of their annotated encoding genes can be used in the network and modules of coordinated expression changes can be found. This provides an alternative to pathway/gene set enrichment analyses which is simultaneously more flexible and more specific. -
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GenOO-HTS
A Modern Perl Framework for High Throughput Sequencing analysis
GenOO-HTS [jee-noo] is an open-source; object-oriented Perl framework specifically developed for the design of High Throughput Sequencing (HTS) analysis tools. The primary aim of GenOO-HTS is to make simple HTS analyses easy and complicated analyses possible. GenOO-HTS models biological entities into Perl objects and provides relevant attributes and methods that allow for the manipulation of high throughput sequencing data. Using GenOO-HTS as a core development module reduces the overhead... -
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HPeak
A HMM-based algorithm for defining enriched regions from ChIP-seq data
HPeak is a hidden Markov model-based approach that can accurately pinpoint regions to where significantly more sequence reads map. Testing on real data shows that these regions are indeed highly enriched by the right protein binding sites. Command (single-end): perl /compbio/software/HPeak3/HPeak.pl -sp HUMAN/MOUSE -format BED -t TREATMENT.inp -c CONTROL.inp -n OUTPUTPREFIX -fmin 100 -fmax 300 -r 36 -ann -wig -seq -interfiles Command (pair-end): perl /compbio/software/HPeak3/HPeak.pl -sp... -
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COVA
Comparison of variants and functional annotation
It’s a variant annotation and comparison tool for next-generation sequencing. It annotates the effects of variants on genes and compares those among multiple samples, which helps to pinpoint causal variation(s) relating to phenotype. -
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DHC-MEGE
DNase Hypersensitivity Connectivity Motif Enrichment in GeneExpression
What does it do? DHC-MEGE is a program designed for the identification of functional long-range cis elements such as enhancers from gene expression data. How does it work? DHC-MEGE takes a list of up- and down-regulated genes and extracts regions from a chromatin connectivity map which are predicted to physically associate with those genes. It then searches for over-represented sequence motifs and then reports instances of those motifs throughout the genome. What is the input? You need a list... -
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CORECLUST
CORECLUST (COnservative REgulatory CLUster STructure)
CORECLUST uses an HMM-based technique to predict cis-regulatory modules (CRMs) given known motifs for a set of system-specific transcription factors (TFs). Given regulatory regions of orthologous and/or co-regulated genes, CORECLUST constructs a model describing conserved rules of relative location of TF binding sites (CRM structure). The constructed model may be used for the CRM prediction, as well as for the investigation of the regulatory grammar of the system of interest. -
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GEO Profiles Search Engine
GEO Profiles Search Engine for Housekeeping Genes
JavaEE backend with AJAX frontend to analyze and display a statistical analysis of Housekeeping genes using GEO Profiles. -
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CUO
Codon Usage Optimizer
CUO is a GUI-based multiplatform software written in Java. It is open source and built with a user/developer-friendly structure. The main function of the software at the current development stage is to optimize genes to be transformed into the Chlamydomonas reinhardtii chloroplast genome although it can be used to optimize genes into other hosts as well. The main tool in CUO, Moptimizer, introduces a semi-automatic way of gene optimization which provides more flexibility and accuracy during... -
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SeqHunter2
a stand-alone bioinformatics software for querying genome sequences
SeqHunter2 is a stand-alone software with graphical user interface, running on Microsoft windows system. It is programmed with the following functions: 1) collect and manage local sequence databases; 2) run blast search by using a batch of sequences and with abundant output formats; 3) extract sequences by a set of IDs or coordinates; 4) generate sequences alignment; 5) edit sequence and translate nucleotide to proteins; 6) browse genome and search genes; 7) collect resource items and link... -
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genedne
To identify cancer-related genes
To identify cancer-related genes -
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CoNIFER
Homepage for CoNIFER (Copy Number Inference From Exome Reads)
CoNIFER uses exome sequencing data to find copy number variants (CNVs) and genotype the copy-number of duplicated genes. -
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gn2d
To recognize the cancer genes
To recognize the cancer genes -
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GeneExploration
To identify the cancer-related genes
This project is designed to explore cancer-related genes from gene expression data set -
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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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FASTApple
AppleScript Utilities for Working Quickly with the FASTA File
Written in Applescript, FASTApple is a suite of utilities for the average computational biologist that make working with FASTA files fast and easy. A basic and straightforward GUI makes choosing files a cinch. Currently three utilities are included: FASTA Concatenater combines multiple FASTA files into a single FASTA file. FASTA Gene Concatenater strings the DNA sequences of each taxon in a set of pre-aligned FASTA files with identical taxa. Specifically designed to prepare RAxML... -
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Translate VCF
Determine functional consequences of mutations in a vcf file
Takes vcf file input and determines functional consequence of mutations with regard to UCSC known genes, refseq genes or ensembl genes. Will use UCSC known gene annotation by default. A correctly formatted CDS file must be used containing CDS sequences and gene table info (i.e. info from knownGene.txt for UCSC genes, refGene.txt for RefSeq or ensGene.txt for ensembl as downloaded from the UCSC downloads page [http://hgdownload.cse.ucsc.edu/downloads.html or ftp://hgdownload.cse.ucsc.edu...