Search Results for "together"
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Showing 27 open source projects for "together"
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kSNP
kSNP4 does SNP discovery and SNP annotation from whole genomes
...kSNP4 can analyze both complete (finished) genomes and unfinished genomes in assembled contigs or raw, unassembled reads. Finished and unfinished genomes can be analyzed together, and kSNP can automatically download Genbank files of the finished genomes and incorporate the information in those files into the SNP annotation. No programming skills are required to use kSNP4 Gardner, S.N. and Hall, B.G. 2013. . PLoS ONE, 8(12):e81760.doi:10.1371/journal.pone.0081760 Gardner, S.N., T. Slezak, and B.G. Hall. 2015 Bioinformatics 31: 2877-2878 doi: 10.1093/bioinformatics/btv271 -
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misc genomics tools
Various scripts used in sequencing, annotation and RNAseq analysis
...Also, please be aware that these were very much developed with expediency in mind - that is, the process was expected to be performed in its final form once; little care was given to optimising runtime or chaining scripts together, and sometimes external resources are accessed manually. -
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MetaErg
Metagenome Annotation Pipeline
MetaErg is a stand-alone and fully automated metagenome and metaproteome annotation pipeline published at: https://www.frontiersin.org/articles/10.3389/fgene.2019.00999/full. If you are using this pipeline for your work, please cite: Dong X and Strous M (2019) An Integrated Pipeline for Annotation and Visualization of Metagenomic Contigs. Front. Genet. 10:999. doi: 10.3389/fgene.2019.00999 The instructions on configuring and running the MetaErg pipeline is available at GitHub... -
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Peak List 2 MSP
Simple peak list to MSP file converter
...It: takes lists from the clipboard (or drag and drop), sorts them by mass, normalises intensities, rejects below a cut off (that you define), adds MSP headers, puts the result back in the clipboard (or a file), has a command line interface so you can pass files in programmatically, has an api so you can call it in your own code (should you feel the urge). You: put a peak list in the clipboard from your favourite mass spec viewing software, append another list if you want (then you can merge lists together), copy-out or save the MSP that appears in the right hand box. Command line arguments: /? displays help information - Start from here. There are a few of them. And if this doesn't mean anything to you then this probably isn't the app for you Happy MSPing -
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Collaborative Computing Project for NMR
Collaborative Computing Project for NMR (CCPN)
...CCPN also has a leading role in the development of a NMR data-sharing standard and coordination of NMR instrumentation proposals for RCUK and BIS. The 28 partners of CCPN jointly cover all aspects of biomolecular NMR and together they promote excellence in science in their respective fields. -
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...RUbioSeq+ is free and includes all the core functionalities implemented in the original release of RUbioSeq (v3.2.1) but, also, outperforms and expands RUbioSeq capabilities supporting the parallelized analysis of full genomes in computing farms. RUbioSeq+ also incorporates a new GUI designed for interdisciplinary research groups where bioinformaticians and biomedical researchers work together.
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ISVASE
identification of sequence variant associated with splicing event
To generate correct mature mRNAs, the exons must be identified and joined together precisely and efficiently by RNA splicing mechanism. It is to be noted that about one third or a half of all disease-causing mutations effect RNA splicing. However, there is little bioinformatics tools to directly identify sequence variants associated with splicing events (SVASE) based on RNA-seq data. We developed ISVASE, a simple and convenient tool for identifying SVASE directly using RNA-seq data. ... -
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iCAS - An Illumina Clone Assembly System
An Illumina clone assembly system using SOAPdenovo and ABySS
...With iCAS the data filtering process is based on a novel kmer frequency algorithm, resulting in near perfect pre-assembly reads. Contigs are generated using different assembly algorithms and then merged together to achieve longer continuity. 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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riboFR-seq
A novel approach to linking 16S rRNA amplicon profiles to metagenomes
16S rRNA amplicon analysis and shotgun metagenome sequencing are two main culture-independent strategies to explore the genetic landscape of various microbial communities. Recently, numerous studies have employed these two approaches together, but downstream data analyses were performed separately, which always generated incongruent or conflict signals on both taxonomic and functional classifications. Here we propose a novel approach, RiboFR-Seq (Ribosomal RNA gene Flanking Region Sequencing), for capturing both ribosomal RNA variable regions and their flanking protein-coding genes simultaneously. ... -
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ChIP-RNA-seqPRO
ChIP-RNA-sequencing-processing (ChIP-RNA-seqPRO)
ChIP-RNA-seqPRO: A strategy for identifying regions of epigenetic deregulation associated with aberrant transcript splicing and RNA-editing sites. Runnable python scripts packaged together with customized annotation libraries, demo data input and README guide. 9/26 : v1.1 Updated MAIN_IV to debug error thrown by python pandas no longer supporting 'subset'. This code will no longer be actively maintained/updated here. A cloud-based resource for comparative analysis of epigenetic, sequence variation, and expression datasets is now available. ... -
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Lab Storage
Rediscover the Simplicity http://www.atgclabs.com/
Help us to improve Freezer Web Access. We want to hear your feedback! Request new Freezer Web Access feature or module and receive a free Single User version with new feature. https://www.atgclabs.com/products/fw Freezer Web Access is a user friendly program designed to assist researchers with establishing an efficient system for storing frozen biological samples. FWA can track all of your research, development and process scale-up data in a single data storage platform, providing a... -
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Sample Tracking
Rediscover the Simplicity http://www.atgclabs.com/
Help us to improve Freezer Web Access. We want to hear your feedback! Request new Freezer Web Access feature or module and receive a free Single User version with new feature. https://www.atgclabs.com/products/fw Freezer Web Access is a user friendly program designed to assist researchers with establishing an efficient system for storing frozen biological samples. FWA can track all of your research, development and process scale-up data in a single data storage platform, providing a... -
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This is the reference library for ICS (Image Cytometry Standard), an open standard for writing images of any dimensionality and data type to file, together with associated information regarding the recording equipment or recorded subject.
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SplitMEM
Graphical pan-genome analysis with suffix skips
With the rise of improved sequencing technologies, genomics is expanding from a single reference per species paradigm into a more comprehensive pan-genome approach with multiple individuals represented and analyzed together. Here we introduce a novel O(n log n) time and space algorithm called splitMEM, that directly constructs the compressed de Bruijn graph for a pan-genome of total length n. To achieve this time complexity, we augment the suffix tree with suffix skips, a new construct that allows us to traverse several suffix links in constant time, and use them to efficiently decompose maximal exact matches (MEMs) during a suffix tree traversal. -
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mrCaNaVaR is a more user friendly and faster re-implementation of our previously published algorithm together with the mrFAST/mrsFAST/drFAST read mapping programs to discover large segmental duplications and deletions and predicts absolute copy numbers.
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cosmos-fp7
COordination of Standards in MetabOlomicS
COSMOS (Coordination of Standards in Metabolomics) brings together European data providers to set and promote community standards that will make it easier to disseminate metabolomics data through life science e-infrastructures. The sf.net project is home for tools and data which don't have another upstream. -
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Linking Yabi with RDA
This software system enables publication of YABI workflows to the RDA.
Modern life science research requires bringing together Biology and Information technology. To help make this process easier, the CCG has developed YABI, an Internet based workflow application that is aimed at biologists who wish to conduct bioinformatics analysis. YABI integrates bioinformatics tools and data via an intuitive workflow creation and management environment. YABI can be used to access the NCI-SF in Bioinformatics and the tools available through the Embl Australia EBI mirror hosted at the University of Queensland. ... -
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A set of command-line utilities for annotating and manipulating DNA sequences in FASTA format. Generate restriction fragments, ORF's, translations, reverse complement, etc. . - and tie it all together with Unix pipes for complete virtual cloning.
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These classes are useful for signal processing in Matlab or C++. They bring together tools and methods which may be used interchangeably for Matlab and C++. Their initial use is in conjunction with work towards my degree at UC Berkeley.
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LAITOR is a text mining software developed to find co-occurrence of biological entities (gene/protein terms) together with biointeractions and concepts term from customized dictionaries.
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This software uses data gathered from published biodiversity inventories, together with physical and vegetational maps, to build a biodiversity map (darkening geographical landscape according with the richness/diversity of species).
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A Python library bringing together utilities I've written over the years for work in bioinformatics and biostatistics, which should be generally applicable outside these fields as well. Focuses on string processing, DBI, and math.
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ChemCpp is a C++ toolbox for chemoinformatics focusing on the computation of kernel functions between chemical compounds. Together with Support Vector Machines, these kernel functions find natural applications for virtual screening of molecules.
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MetaPepSeq is metaserver for protein identification in Mass Spectrometry Experiments. It helps joining the power of Mascot and de novo sequencing algorithms by merging together into one tool.
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The set of tools for biopolymer sequence analysis together with GUI to work with biopolymer sequence databases. The tools include pairwise and multiple alignment, philogenetic tree construction and other.