Search Results for "quality"
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Showing 49 open source projects for "quality"
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Build Securely on AWS with Proven FrameworksMoving to the cloud brings new challenges. How can you manage a larger attack surface while ensuring great network performance? Turn to Fortinet’s Tested Reference Architectures, blueprints for designing and securing cloud environments built by cybersecurity experts. Learn more and explore use cases in this white paper.
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MongoDB Atlas runs apps anywhereMongoDB Atlas gives you the freedom to build and run modern applications anywhere—across AWS, Azure, and Google Cloud. With global availability in over 115 regions, Atlas lets you deploy close to your users, meet compliance needs, and scale with confidence across any geography.
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CTK
CLIP Tool Kit (CTK)
CTK (CLIP Tool Kit) is a computational biology toolkit implemented in Perl, designed for analyzing CLIP sequencing data. It offers a streamlined pipeline from raw reads through peak calling and motif discovery. -
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DkIT Bridge Designer
Dundalk Institute of Technology Virtual Bridge Design Competition
The DkIT Bridge Designer will provide you with a realistic introduction to engineering through an authentic, hands-on design experience. This software provides you with the tools to model, test, and optimize a steel highway bridge, based on realistic specifications, constraints, and performance criteria. Supported by Dundalk Insititute of Technology and All-Island Funds, this is a virtual bridge designer that allows kids of all ages learn about engineering and compete with their classmates! -
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EvidentialGene
Evidence Directed Gene Construction for Eukaryotes
EvidentialGene is a genome informatics project, "Evidence Directed Gene Construction for Eukaryotes", to construct high quality, accurate gene sets for animals and plants, developed by Don Gilbert at Indiana University, see http://arthropods.eugenes.org/EvidentialGene/ Construction refers to the combination of classical gene prediction, and more recent gene assembly (de-novo and genome-assisted) methods. The basic Evigene methods involve using available best-of-breed gene prediction and assembly software, combining all evidence for genes, from expressed sequences, genome assembly sequences, related species protein sequences, and any other, to annotate and score gene constructions. ... -
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Design PCR primers from DNA sequence. Widely used (190k Google hits for "primer3"). From mispriming libraries to sequence quality data to the generation of internal oligos, primer3 does it. C&perl. Developers/testers/documenters needed.
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Build Agents and Models on One PlatformGemini Enterprise Agent Platform is Google Cloud's comprehensive platform for developers to build, scale, govern, and optimize agents and models. Choose from Google's most advanced models and third-party models like Anthropic's Claude Model Family.
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hr ("High Resolution") is a small command-line utility to calculate possible elemental compositions for a given mass. It allows to run calculations interactively, in batch mode, via the command line, or (using a webserver) via a web interface.
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Microarray assosiated motif analyzer
Cis-element prediction tool from microarray data
...Simulation of gene expression was performed using a support vector machine and based on the presence of predicted motifs and motif pairs. The accuracy of simulated gene expression was used to evaluate the quality of prediction and to optimize the parameters used in this method. After optimization, MAMA accurately simulated more than 87% of gene expression. See Kakei Y, Ogo Y, Itai RN, et al. (2013) Development of a novel prediction method of cis-elements to hypothesize collaborative functions of cis-element pairs in iron-deficient. Rice 6(1): 22. -
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Bridge Designer and Contest
A national virtual bridge engineering contest for kids of all ages.
*** Bridge Designer has been replaced with the web app ASCE Bridge Designer, Cloud Edition (Google this term to find the app)! Binaries posted here will go away on 1 July 2026. The source repo will remain. The contest is no longer active. *** A national virtual bridge engineering contest with prizes for middle and high school kids, grades 6 to 12, but anyone can enter for fun. Based on the award-wining Bridge Designer client software, now open source through this project. Web site... -
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bspipe
An End-to-End Analysis Pipeline for BS-seq
BSpipe is a comprehensive pipeline from sequence quality control and mapping to functional analysis of differentially methylated regions: (1) sequencing quality assessment, (2) sequence cleaning, (3) sequence read mapping, (4) methylation quantification, (4) sample comparisons based on methylation profile, (5) identification of DMRs (differentially methylated regions), (6) annotation of DMRs, (7) functional analysis of differentially methylated genes, (8) generation of input files for visualization, and (9) support for advanced sequencing technologies such as TAB-seq, OxBS-seq, MAP-it, and NOMe-seq. -
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CRISPR-offinder-v1-2
A CRISPR tool for user-defined protospacer adjacent motif
CRISPR/Cas system undoubtedly holds great potential for genome editing. Target site cleavage by CRISPR technology requires a protospacer adjacent motif (PAM) immediately downstream or upstream of the protospacer element to which the sgRNA binds. However, Cas9 from different types of bacteria or variant recognizes different PAM sequences. To meet the needs of different CRISPR system with specific and efficient sgRNA design, CRISPR-offinder was developed. Given an input FASTA file of the... -
Stop Cyber Threats with VM-Series Next-Gen Firewall on AzureGain integrated visibility across all traffic in a single pass. Deploy Palo Alto Networks VM-Series to determine application identity and content while automating security policy updates via rich APIs.
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MOIRAI
Simple Scientific Workflow System for CAGE Analysis
...MOIRAI is a compact yet flexible workflow system designed to carry out the main steps in data processing and analysis of CAGE data. MOIRAI has a graphical interface allowing wet-lab researchers to create, modify and run analysis workflows. Embedded within the workflows are graphical quality control indicators allowing users assess data quality and to quickly spot potential problems. MOIRAI package comes with three main workflows allowing users to map, annotate and perform an expression analysis over multiple samples. -
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ViralFusionSeq [VFS]
Accurately discover viral integration events and fusion transcripts
...VFS combines soft-clipping information, read-pair analysis, and targeted de novo assembly to discover and annotate viral-human fusion events. A simple yet effective empirical statistical model is used to evaluate the quality of fusion breakpoints. Minimal user defined parameters are required. Source code with user manual and installation guide of VFS is available at sourceforge's "Files" section. Citation: http://www.ncbi.nlm.nih.gov/pubmed/ -
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iCAS - An Illumina Clone Assembly System
An Illumina clone assembly system using SOAPdenovo and ABySS
...Re-aligning all the reads back to the draft contigs and recalibrating each sequence base achieves a final consensus. Using finished clones for QC, the pipeline is able to obtain assemblies with clone coverage of 99.7% and consensus base quality of Q39. Developed at the Wellcome Trust Sanger Institute. -
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gladTeX
GladTeX -- embed LaTeX-quality images in HTML
GladTeX is a preprocessor that enables the use of LaTeX maths within HTML code. The maths, embedded in <eq>..</eq> tags, as if within $$..$$ in LaTeX, is fed through latex and replaced by images. Additionally, alt-tags are auto-generated which display the LaTeX-equations when the HTML is viewed e.g. with a text mode browser or by someone with vision loss. The project home has moved, please visit https://humenda.github.io/GladTeX -
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CNVision
CNV prediction from Illumina genotyping data
CNVision is a Perl script that runs Illumina genotyping data (all chips from 300k to latest Omni) through PennCNV, QuantiSNPv2.3 and GNOSIS (an in-built algorithm). It merges the results and assesses the quality of the raw data. CNVision can also identify de novo CNVs in family-based data using a highly accurate algorithm that considers the possibility of CNVs in either parent based on the raw genotyping data. The script is optimized to work in a UNIX-based environment; it should work in Windows, however running the PennCNV component gives errors with the newer versions of PennCNV. ... -
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MethylExtract
High-Quality methylation maps and SNV calling from BS-Seq experiments
MethylExtract is a user friendly tool to generate i) high quality, whole genome methylation maps and ii) to detect sequence variation within the same sample preparation. The program is implemented into a single script and takes into account all major error sources: sequencing errors, bisulfite failure, clonal reads and single nucleotide variants. MethylExtract detects variation (SNVs – Single Nucleotide Variation) in a similar way than VarScan, a very sensitive method extensively used in SNP and genotype calling based on non-bisulfite treated reads. -
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Just_Annotate_My_Genome
Comprehensively annotate your non-model species genome.
Uses an existing exonerate output or just predicted proteins (e.g. from Transdecoder or just a FASTA file) to prepare gene prediction inputs for Augustus, SNAP and geneid. Exonerate is run (enabled via AAT) if it is not provided. GTF file is produced to judge quality of annotation. Sorts out high quality alignments from those that don't meet the criteria. -
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QUASI is a toolkit to rapidly assess the quality of shRNA-Seq based data and call differential abundance using common statistical inference methods (DESeq, edgeR, baySeq).
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HBSAnalyzer
Aligner and methylation caller for hairpin bisulfite sequencing data
HBS Analyzer is a methylation calling tool for hairpin-bisulfite sequencing data. HBS Analyzer can accept raw hairpin-bisulfite sequencing data in FASTA or FASTQ format, align the paired end reads to the reference genome and call methylation. Given the double stranded nature of the data that is used, HBS analyzer can identify errors caused by PCR and sequencing along with identifying hemi-methylated sites. This error information is also considered while making the methylation call and hence... -
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HBSAnalyzer
Aligner and methylation caller for hairpin bisulfite sequencing data
HBS Analyzer is a methylation calling tool for hairpin-bisulfite sequencing data. HBS Analyzer can accept raw hairpin-bisulfite sequencing data in FASTA or FASTQ format, align the paired end reads to the reference genome and call methylation. Given the double stranded nature of the data that is used, HBS analyzer can identify errors caused by PCR and sequencing along with identifying hemi-methylated sites. This error information is also considered while making the methylation call and hence... -
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PlaTypUS
Plasmodium Typing Utility Software
The goal of PlaTypUS is to establish a unified Plasmodium whole genome analysis tool, that aligns short read sequences in an agreed upon manner, with many quality control steps, and calls both SNVs and CNVs in a community agreed standard way. We also seek to provide this analysis in a stand-alone graphic user interface so that labs around the world can analyze their own whole genome sequencing data, rather than relying on outside institutes. -
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CAPE RNA
Classification based Analysis of Paired Expression data of RNA
CAPE RNA is package of command-line tools for integrated analysis of miRNA-mRNA expression data. miRNA-mRNA interaction states are assigned for each sample independent of a priori known experimental groups. Using these interaction classifications Jaccard-indexes are calculated to evaluate the quality of a predicted interaction based on the distribution of assigned interaction states compared to experimental groups. In addition, negative correlation between miRNA and mRNA expression can be analyzed. -
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CSEA
Correcting Structural Errors After Genome Assembly
CSEA is a suite of programs for correcting structural errors after assembly without reference, improve the quality of genome assembly. The program is specially designed for second-generation sequencing reads. It also can do denovo assembly and correct errors. Contact: jbtangcn@gmail.com -
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easyPAC
easy Primer prediction from Alignments and Consensus sequences
Primer prediction from alignments and consensus sequences. easyPAC applies all standard quality tests to degenerate primer and primer pairs and optionally maps all primer candidates to an arbitrary number of reference files like repeat databases or genomes to ensure target specifity. -
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MID Adjust
Prepare reads with no MIDs or variable length MIDs for analysis
...When you have no MIDs, or variable-length MIDs, MID Adjust appends new MIDs or extends existing ones to satisfy Pyrotagger requirements. New features include the ability to generate fake quality scores and to parse and generate QIIME mapping files. -
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An integrated bioinformatics toolkit for analysis of ChIPseq data from the Illumina DNA sequencing platform. Includes filtering, quality control, simulation, peakfinding, visualization, and comparison of samples.
