Search Results for "alignment" - Page 12
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Showing 492 open source projects for "alignment"
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PeaksAndValleys
Peaks and Valley detection using NGS data
...However, a variety of experimental and sequencing-induced biases can preclude robust detection of novel regulatory elements: variations in copy number and somy, errors in sequencing and alignment, and biases introduced by nuclease -
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This is where AAF originally published. For the most recent updates, please go to its Homepage indicated below. It is on GitHub thus easier to report bugs. Thanks for choosing AAF and leave me a comment on its Github page if you have any question or problem.
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The Maltcms - Modular Application Toolkit for Chromatography Mass-Spectrometry is a JAVA API for preprocessing, alignment, analysis and visualization of data stored in open file formats used in Proteomics and Metabolomics research.
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FOCUS
A model to identify organisms present in metagenomes in seconds
...Availability and implementation: The code implemented in Python can be found here and a web-sever at http://edwards.sdsu.edu/FOCUS. Dependencies: Jellyfish, Numpy, and Scipy. Cite FOCUS Silva, G. G. Z., D. A. Cuevas, B. E. Dutilh, and R. A. Edwards, 2014: FOCUS: an alignment-free model to identify organisms in metagenomes using non-negative least squares. PeerJ, 2, e425,doi:10.7717/peerj.425. -
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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Reflexbox
Responsive React Flexbox Grid System
Reflexbox is a React utility library that provides a set of flexible layout components built on top of the CSS Flexbox specification, enabling developers to create responsive layouts with minimal effort. It introduces components such as Box and Flex that abstract common layout patterns into reusable primitives, allowing developers to apply spacing, alignment, and sizing through props rather than writing custom CSS. The library integrates seamlessly with styled-system, enabling theme-based design and consistent spacing scales across applications. Reflexbox is designed to be highly composable, allowing developers to build complex layouts by combining simple components. It emphasizes responsiveness by supporting array-based props that adapt styles across breakpoints. ... -
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CoverageAnalyzer
RNA modification detection by RT signatures in deep sequencing data
Combination of reverse transcription (RT) and deep sequencing has emerged as a powerful instrument for detection of RNA modifications, a field that has seen a recent surge in activity because of its importance in gene regulation. Recent studies yielded high-resolution RT signatures relying on both, sequence dependent mismatch patterns and RT arrests. Common alignment viewers lack in specialized functionality, such as filtering, tailored visualization, differential analysis and export. Consequently, the community will profit from a platform seamlessly connecting detailed visual inspection of RT signatures and automated screening for modification candidates. CoverageAnalyzer was developed in response to the demand for a powerful inspection tool, running on all 3 OSes. ... -
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AstroTortilla
Astrophotography assistant
AstroTortilla is a wrapper around common astrophotography tools intended to automate basic tasks such as polar alignment and goto correction. Not in active development presently. -
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Tabular
Vim script for text filtering and alignment
Tabular is a Vim plugin for aligning text into neat columns using pattern-driven rules. Instead of manually spacing content, you define an alignment target—such as : in dictionaries, = in assignments, or | in Markdown tables—and the plugin rearranges whitespace to produce straight columns. It supports regular expressions, so you can craft smart alignment that respects context or ignores edge cases. The workflow fits naturally into Vim: you visually select lines (or operate on a motion), run a command, and instantly get well-formatted blocks. ... -
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Zika-RNAseq-Pipeline
An open RNA-Seq data analysis pipeline tutorial
...However, open and standard pipelines to perform RNA-seq analysis by non-experts remain challenging due to the large size of the raw data files and the hardware requirements for running the alignment step. Here we introduce a reproducible open source RNA-seq pipeline delivered as an IPython notebook and a Docker image. The pipeline uses state-of-the-art tools and can run on various platforms with minimal configuration overhead. The pipeline enables the extraction of knowledge from typical RNA-seq studies by generating interactive principal component analysis (PCA) and hierarchical clustering (HC) plots, performing enrichment analyses against over 90 gene set libraries, and obtaining lists of small molecules that are predicted to either mimic or reverse the observed changes in mRNA expression. -
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converts a SAM file to fasta file. SAM file is a file output from bwa alignment software. It outputs aligned fasta file.
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Faligner
Faligner: a Local Sequence Alignment Ubuntu Package
A package based on 3 local alignment tools i.e., Bowtie, Bowtie2 and BWA. Package covers single-end, paired-end alignments. Moreover, the package also demonstrates overlap alignment and colorspace alignment features. The package also includes graphical user interface to make it interactive. -
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pPGallery
Free Joomla! plugin to create a simple image gallery.
** minor bug fix to work with J! 3.6.x, current version: 4.316x ** /03.Aug.16 Free Joomla! content-plugin to create a simple image gallery based on 'prettyPhoto' display engine (a jQuery lightbox clone: http://www.no-margin-for-errors.com/projects/prettyPhoto-jquery-lightbox-clone). Images from folders or directly inserted into the content/article can be processed with automatic thumbnail generation. For tutorials and more detailed information refer to the Wiki: ... -
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MSAProbs: Multiple Sequence Alignment
One of the most accurate multiple protein sequence aligners
MSAProbs is an open-source protein multiple sequence ailgnment algorithm, achieving the stastistically highest alignment accuracy on popular benchmarks: BALIBASE, PREFAB, SABMARK, OXBENCH, compared to ClustalW, MAFFT, MUSCLE, ProbCons and Probalign. -
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Pathoscope
Predicts strains of genomes in Nextgen seq alignment file (sam/bl8)
...Please visit github for the latest version of the software: https://github.com/pathoscope PathoScope takes next-generation sequencing reads from a mixture sample and predicts which genomes are present. We use a Bayesian framework combined with an initial reference-based alignment to assign reads to the correct genome of origin. Pathoscope 2.0: Wiki: http://sourceforge.net/p/pathoscope/wiki/Home/ Tutorial: http://sourceforge.net/projects/pathoscope/files/pathoscope2.0_v0.02_tutorial.pdf Clinical Pathoscope version: http://sourceforge.net/p/pathoscope/wiki/clinical_pathoscope/ PathoQC download: http://sourceforge.net/projects/pathoscope/files/pathoqc_v0.1.4.tar.gz/download Publications: http://www.microbiomejournal.com/content/2/1/33 http://www.biomedcentral.com/1471-2105/15/262 http://genome.cshlp.org/content/23/10/1721 Support: PS: Please send an email to mani2012 at bu dot edu if you have any questions. -
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CATO Clone Alignment Tool
Identifies clone sequences corresponding to set of reference sequences
Specialized sequence alignment software that helps associate the most likely matches of clone sequences to a set of reference sequences. Both sets of sequences are assumed to be nucleotides. -
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geneslider
Gene Slider for Alignment Visualisation
Gene Slider can be used to visualize conservation and entropy of aligned DNA and protein sequences by presenting them as one long sequence logo. The presented sequence logo can be zoomed in and out. It can also display motifs in alignments. A built-in search function can be used to find motifs. Gene Slider is available online on the Bio-Analytic Resource and for download here. -
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SPRITE
Parallel SNP detection pipeline
SPRITE is an open-source software package providing a parallel implementation of the Single Nucleotide Polymorphisms (SNP) detection genomic data analysis workflow. It consists of three tools: PRUNE for read alignment, SAMPA for intermediate file processing, and PARSNIP for parallel SNP calling. -
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logmap-matcher
LogMap: An Ontology Alignment and Alignment Repair System
LogMap is a highly scalable ontology matching system with ‘built-in’ reasoning and inconsistency repair capabilities. LogMap extract mappings between classes, properties and instances. To the best of our knowledge, LogMap is one of the few matching systems that: 1. can efficiently match semantically rich ontologies containing tens (and even hundreds) of thousands of classes, 2. incorporates sophisticated reasoning and repair techniques to minimise the number of logical... -
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RAFTS3
Rapid Alignment Free Tool for Sequences Similarity Search
RAFTS3 can perform high-speed protein search comparisons locally using a desktop computer or laptop. RAFTS3 performed searches many times faster than those with BLASTp against large protein databases such as NR and Pfam, with a small loss of sensitivity depending on the similarity degree of the sequences. RAFTS3 is a new alternative for fast comparison of protein sequences, genome annotation and biological data mining. Preprint: http://dx.doi.org/10.1101/055269 Precomputed databases... -
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CytoscapeAlignmentDrawerPlugin
a Cytoscape plugin for visualizing SANA alignment
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erne
ERNE - Extended Randomized Numerical alignEr
We present ERNE (Extended Randomized Numerical alignEr), a short string alignment package whose goal is to provide an all-inclusive set of tools to handle short (NGS-like) reads. ERNE comprises ERNE-FILTER (read trimming and continamination filtering), ERNE-MAP (core alignment tool/algorithm), ERNE-BS5 (bisulfite treated reads aligner), and ERNE-PMAP/ERNE-PBS5 (distributed versions of the aligners), -
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PolyRec
Unistroke gesture recognizer
...More technical details on PolyRec can be found in the following scientific paper: V Fuccella, G. Costagliola; Unistroke Gesture Recognition Through Polyline Approximation and Alignment; in Proceedings of CHI 2015; pp. 3351-3354 http://dl.acm.org/citation.cfm?id=2702 -
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Phylomark
Identification of phylogenetic markers from whole genome alignments
Phylomark is a python script used to identify phylogenetic markers from whole genome alignments. Accurate phylogenetic markers are chosen based on low Robinson-Foulds distance to a phylogeny inferred from the whole genome alignment. -
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MeSeq is a package providing ease in installing some popular Multiple Sequence Alignment Tools. It also provides a GUI interface for the tools.
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To speed up the alignment of DNA reads or assembled contigs against a protein database has been a challenge up to now. The recent tool DIAMOND has signi cantly improved the speed of BLASTX and RAPSearch, with a similar degree of sensitivity. Yet for applications like metagenomics, where a large amount of data is involved, DIAMOND still takes too much time.