Search Results for "alignment" - Page 12
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Showing 522 open source projects for "alignment"
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SUPERmerge
ChIP-seq coverage island analysis algorithm for broad histone marks
SUPERmerge is a ChIP-seq read pileup analysis and annotation algorithm for investigating alignment (BAM) files of diffuse histone modification ChIP-seq datasets with broad chromatin domains at a single base pair resolution level. SUPERmerge allows flexible regulation of a variety of read pileup parameters, thereby revealing how read islands aggregate into areas of coverage across the genome and what annotation features they map to within individual biological replicates. -
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AKtoolbox
Matlab Toolbox for coevolution analysis of multiple sequence alignment
AK Toolbox is a Matlab Toolbox for co-evolution analysis for protein Multiple Sequence Alignment (MSA) distributed under Simplified BSD License. The aim of AK toolbox is to provide a set of Matlab functions, which are independent of Matlab Bioinforamtics Toolbox, for coevolution anaylsis for MSA. At present, co-evolution methods available in this package are Statistical Coupling Analysis (SCA), Explicit Likelihood of Subset Covariance (ELSC), Mutual Information (MI), Observed Minus Expected Square method (OMES), McLanhlan Based Substitution Correlation (MCBASC), Direct-coupling analysis (DCA) and logR. ... -
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RNAseq Tutorial
Informatics for RNA-seq: A web resource for analysis on the cloud
rnaseq_tutorial is a tutorial and educational resource created by the Griffith Lab that guides users through the steps of RNA-seq data analysis. It includes working pipelines for alignment, differential expression, alternative splicing, visualization, and interpretation. It is designed to run in the cloud or local environments, providing introductory material on file formats, reference genomes / annotation, QC, mapping, quantifying expression, visualizing results, etc. The version in that repo is deprecated, but still maintains content for those wishing to follow the original published workflow. ... -
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SW#
smith waterman, gpu, cuda, alignment
SW# (swsharp) is a library for sequence alignment based on CUDA enabled GPUs. It utilizes Hirschbergs and Ukkonens algorithm for memory efficiency and additional speed up. The library is scalable for use with multiple GPUs. Some parts of the library utilize MPI for CUDA enabled clusters. This work has been supported in part by Croatian Science Foundation under the project UIP-11-2013-7353. -
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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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SPANDx
Comparative analysis of haploid next-generation genome sequence data
SPANDx is your one-stop tool for identifying SNP and indel variants in haploid genomes using NGS data. SPANDx performs alignment of raw NGS reads against your chosen reference genome or pan-genome, followed by accurate variant calling and annotation, and locus presence/absence determination. SPANDx produces SNP and indel matrices for downstream phylogenetic analyses. Annotated, genome-wide SNPs and indels can also be identified if specified, and are output in human readable format. ... -
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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. -
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MITP
MITP - conserve & novel miRNA identification & target prediction tool
miRNA is a widely known small non-coding RNA which can mediate gene regulation of most important biological processes in plants and animals. Therefore, identification conserve and novel miRNA and their target genes in model and new sequenced species are inevitable. MITP is designed to identify miRNA easily and faster based on sequence mapping result from any mapping software which producing SAM format output result, blast result (default output result) or blat result (default output result).... -
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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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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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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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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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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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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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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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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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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
