Search Results for "data quality"
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18 projects for "data quality" with 2 filters applied:
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Ship Agents FasterGemini Enterprise Agent Platform lets you rapidly build, scale, govern and optimize production-ready agents grounded in your organization's data. The platform enables developers to build custom or pre-built agents for virtually any use case. New customers get $300 in free credits.
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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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VarScan
Variant detection in next-generation sequencing data
Variant detection in massively parallel sequencing. For one sample, calls SNPs, indels, and consensus genotypes. For tumor-normal pairs, further classifies each variant as Germline, Somatic, or LOH, and also detects somatic copy number changes. THE LATEST VERSION IS AVAILABLE ON GITHUB -
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HTQC
Quality control and filtration for illumina sequencing data
A toolkit including statistics tool for illumina high-throughput sequencing data, and filtration tools for sequence quality, length, tail quality, etc.. -
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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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xPyder PyMOL Plugin
Analyze and visualize coupled residues and their networks in proteins
xPyder is a PyMOL plugin to analyze and visualize on the 3D structure dynamical cross-correlation matrices (DCCM), linear mutual information (LMI), communication propensities (CP), intra- and inter-molecular interactions (e.g. PSN), and more, to produce highly customizable publication-quality images. xPyder identifies networks (using concepts from graph theory, such as hubs and shortest path searching), compares matrices and focuses the analysis on relevant information by filtering the data using a modular, user-expandable plugin system that takes advantage of structural and dynamical information, contributing to bridge the gap between dynamical and mechanical properties at the molecular level. -
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CoDeCZ
Derive copy number status from targeted sequencing data
CoDeCZ derives copy number state from targeted sequencing data on gene or exon level. Results are NOT true copy number however, but they are semi-quantitative: It uses the modified z-score to calculate deviation in normalized coverage per specified region. The higher the Z-score, the higher the copy number. The final z-score depends on the quality of the data and the makeup of the reference pool. -
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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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Musket - short read error corrector
a parallel short-read error corrector for Illumina sequencing
Musket is an efficient multistage k-mer based corrector for Illumina short read data. This corrector employs the k-mer spectrum approach and introduces three correction techniques in a multistage workflow. Our performance evaluation results, in terms of correction quality and de novo genome assembly measures, reveal that Musket is consistently one of the top performing substitution-error-based correctors. In addition, Musket is multi-threaded using a master-slave model and demonstrates superior parallel scalability compared to all other evaluated correctors as well as a highly competitive overall execution time. -
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noise-free-cnv
program for analyzing and manipulating DNA microarray data
CNV calling software may produce false-positive calls due to imperfect source material. Direct inspection of the microarray data with the noise-free-cnv software helps to appreciate the quality of the data and to identify artificial calls. With noise-free-cnv it is possible to visualize individual datasets, to compare different datasets and to perform simple transformations. The visualization and the suppression of genomic waves, the comparison of two datasets by subtraction and the simultaneous inspection of LRR and BAF values are amongst the most frequent applications of this software. ... -
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rnasimulase
Simulation of allele-specific RNA-seq data
Simulation of allele-specific RNA-seq data -
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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.
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QUASR
Cross-platform NGS processing and analysis pipeline in Python
QUASR is a lightweight pipeline written to process and analyse next-generation sequencing (NGS) data from Illumina, 454, and Ion Torrent platforms. Although originally written for viral data, it is generic enough to work on any NGS dataset. Functions include: duplicate removal demultiplexing primer-removal quality-assurance (QA) graphing quality control (QC) consensus-generation minority-variant determination minority-variant graphing The main current version is 6.X, which is written in Python3. 7.X is my rewrite in Java, but is still work in progress. ... -
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This is a MATLAB toolbox for the quality control and scoring of EMAP and SGA genetic interaction data. It includes a graphical user interface and some automatic plot-generating tools.
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CNV Workshop is a web-enabled platform for analyzing genome variation such as copy number variation (CNV). Learn about CNV Workshop in our associated BMC Bioinformatics manuscript: http://www.biomedcentral.com/1471-2105/11/74
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MASQOT-GUI is an open-source, platform-independent application for two-channel microarray spot quality control. Included is a set of tools for gridding, segmentation, quantification, multivariate spot quality assessment and data visualization.
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UMD Overlapper takes a set of reads and quality data and determines which read pairs plausibly overlap; that is, it determines the pairs of reads containing subsequences that are similar enough that they may have come from overlapping parts of the genome.
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Multilayered feed-forward neural network software written in C++. Backpropagation and RPROP are available as training algorithms. Design goals: speed of execution when calculating the output to new data, and quality of training (preprocessing: PCA).
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