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http://bioinfo2.ugr.es/NGSmethPipe/

A software tool which generates high-quality methylation maps.

Proper citation: NGSmethPipe (RRID:SCR_000583) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/src/contrib/Archive/sybil/

A Systems Biology Library for R, implementing algorithms for constraint based analyses of metabolic networks (e.g. flux-balance analysis (FBA), minimization of metabolic adjustment (MOMA), regulatory on/off minimization (ROOM), robustness analysis and flux variability analysis). This is an implementation of COBRA toolbox in R language.

Proper citation: sybil - Efficient Constrained Based Modelling in R (RRID:SCR_000457) Copy   

•   Source: SciCrunch Registry

https://github.com/holtjma/msbwt

A software package for creating, merging, and querying multi-string BWTs.

Proper citation: msbwt (RRID:SCR_000458) Copy   

•   Source: SciCrunch Registry

http://www.stanford.edu/~cpatton/maxc.html

A series of programs for determining the free metal concentration in the presence of chelators or total metal given a desired free concentration.

Proper citation: MAXCHELATOR (RRID:SCR_000459) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/release/bioc/html/Rdisop.html

Software for identification of metabolites using high precision mass spectrometry. MS Peaks are used to derive a ranked list of sum formulae, alternatively for a given sum formula the theoretical isotope distribution can be calculated to search in MS peak lists.

Proper citation: Rdisop (RRID:SCR_000453) Copy   

•   Source: SciCrunch Registry

http://bsec.ornl.gov/AdaptiveCrawler.shtml

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 9,2022. A web crawler that can intelligently acquire social media content on the Internet to meet the specific online data source acquisition needs of cancer researchers.

Proper citation: AdaptiveCrawler (RRID:SCR_000573) Copy   

•   Source: SciCrunch Registry

https://github.com/PacificBiosciences/stsPlots

Software to plot primary analysis quality control metrics to assess potential SMRTcell loading problems.

Proper citation: stsPlots (RRID:SCR_000449) Copy   

•   Source: SciCrunch Registry

https://sites.google.com/site/jingyijli/SLIDE.zip

Software package that takes exon boundaries and RNA-Seq data as input to discern the set of mRNA isoforms that are most likely to present in an RNA-Seq sample. It is based on a linear model with a design matrix that models the sampling probability of RNA-Seq reads from different mRNA isoforms. To tackle the model unidentifiability issue, SLIDE uses a modified Lasso procedure for parameter estimation. Compared with deterministic isoform assembly algorithms (e.g., Cufflinks), SLIDE considers the stochastic aspects of RNA-Seq reads in exons from different isoforms and thus has increased power in detecting more novel isoforms. Another advantage of SLIDE is its flexibility of incorporating other transcriptomic data such as RACE, CAGE, and EST into its model to further increase isoform discovery accuracy. SLIDE can also work downstream of other RNA-Seq assembly algorithms to integrate newly discovered genes and exons. Besides isoform discovery, SLIDE sequentially uses the same linear model to estimate the abundance of discovered isoforms.

Proper citation: SLIDE (RRID:SCR_005137) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/viralfusionseq/

A versatile high-throughput sequencing (HTS) tool for discovering viral integration events and reconstruct fusion transcripts at single-base resolution. It 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.

Proper citation: VFS (RRID:SCR_005138) Copy   

•   Source: SciCrunch Registry

https://github.com/tk2/RetroSeq

A tool for discovery and genotyping of transposable element variants (TEVs) (also known as mobile element insertions) from next-gen sequencing reads aligned to a reference genome in BAM format. The goal is to call TEVs that are not present in the reference genome but present in the sample that has been sequenced. It should be noted that RetroSeq can be used to locate any class of viral insertion in any species where whole-genome sequencing data with a suitable reference genome is available. RetroSeq is a two phase process, the first being the read pair discovery phase where discorandant mate pairs are detected and assigned to a TE class (Alu, SINE, LINE, etc.) by using either the annotated TE elements in the reference and/or aligned with Exonerate to the supplied library of viral sequences.

Proper citation: RetroSeq (RRID:SCR_005133) Copy   

•   Source: SciCrunch Registry

https://github.com/cwhelan/cloudbreak

Software providing a Hadoop-based genomic structural variation (SV) caller for Illumina paired-end DNA sequencing data. It contains a full pipeline for aligning data in the form of FASTQ files using alignment pipelines that generate many possible mappings for every read, in the Hadoop framework. It then contains Hadoop jobs for computing genomic features from the alignments, and for calling insertion and deletion variants from those features.

Proper citation: Cloudbreak (RRID:SCR_005097) Copy   

•   Source: SciCrunch Registry

http://yost.genetics.utah.edu/software.php

A software analysis pipeline for mapping mutations using RNA-seq that works without parental strain information, without the requirement of a pre-existing snp map of the organism, and without erroneous assumptions that recombination occurs at the same frequency across the genome. In addition, it compensates for the considerable amount of noise in RNA-seq datasets and simultaneously identifies the region where the mutation lies and generates a list of putative coding region mutations in the linked genomic segment. MMAPPR can utilize RNA-seq datasets from isolated tissues or whole organisms that are often generated for phenotypic analysis and gene network analysis in novel mutants.

Proper citation: MMAPPR (RRID:SCR_005092) Copy   

•   Source: SciCrunch Registry

http://www.murdock-trust.org/

The M. J. Murdock Charitable Trust seeks to enrich the quality of life in the Pacific Northwest by providing grants and enrichment programs to non-profit organizations that seek to strengthen the region''s educational, spiritual, and cultural base in creative and sustainable ways. In addition to a special interest in education and scientific research, the Trust partners with a wide variety of organizations that serve the arts, public affairs, health and medicine, human services, leadership development, and persons with disabilities. Eligibility for scientific research grants is limited. Select public research universities and medical institutes located within the five-state region (Pacific Northwest: Alaska, Washington, Oregon, Idaho, Montana) are typically considered for funding. The Trust prefers requests for projects in the natural sciences where the main objective is the acquisition of new knowledge. However, requests for research in engineering and medicine are also eligible. Training students in conducting research is an important consideration.

Proper citation: MJ Murdock Charitable Trust (RRID:SCR_005122) Copy   

•   Source: SciCrunch Registry

http://www.nasonline.org/news-and-multimedia/podcasts/

Subscribe to the National Academy of Sciences podcasts to learn more about scientists and their work, the latest in research, and key findings of National Research Council reports. * InterViews: InterViews provides first-person accounts of the lives and work of National Academy of Sciences members. In this series of one-on-one conversations, scientists talk about what inspired them to pursue the careers they chose and describe some of the most fascinating aspects of their research. * Science Sessions: The Proceedings of the National Academy of Sciences offers brief, 5-minute, nontechnical conversations with cutting-edge researchers, including members of the National Academy of Sciences, and policymakers as they discuss topics relevant to today''s scientific community. Learn the behind-the-scenes story of work published in PNAS, plus a broad range of scientific news about discoveries that affect the world around us. * News from the National Academies: Listen to the latest news conferences and public briefings on National Research Council and Institute of Medicine reports. * Sounds of Science: This informative and entertaining series puts a spotlight on the high-impact work of the National Research Council. Focusing on a wide range of critical issues in science, engineering, and medicine, these short episodes are a quick and easy way to tune in our key findings and important recommendations. * Cultural Programs: The Cultural Programs of the National Academy of Sciences presents public exhibitions, lectures, and other programs exploring the intersections of art, science, and culture. The podcast features audio recordings of past lectures and other events. * Engineering Innovation: This weekly podcast from the National Academy of Engineering highlights exciting developments in engineering and provides technical context to stories in the news. The 40-second episodes demonstrate how engineers are making an impactin energy, health, the environment, sports, and more.

Proper citation: National Academy of Sciences Podcasts (RRID:SCR_005124) Copy   

•   Source: SciCrunch Registry

http://www.dcc.ac.uk/

The Digital Curation Centre (DCC) is a world-leading centre of expertise in digital information curation with a focus on building capacity, capability and skills for research data management across the UK''s higher education research community. The Digital Curation Centre provides expert advice and practical help to anyone in UK higher education and research wanting to store, manage, protect and share digital research data. The DCC provides access to a range of resources including our popular How-to Guides, case studies and online services. Our training programmes aim to equip researchers and data custodians with the skills they need to manage and share date effectively. We also provide consultancy and support with issues such as policy development and data management planning.

Proper citation: Digital Curation Centre (RRID:SCR_005087) Copy   

•   Source: SciCrunch Registry

http://www.omicsoft.com/fusionmap/

An efficient fusion aligner which aligns reads spanning fusion junctions directly to the genome without prior knowledge of potential fusion regions. It detects and characterizes fusion junctions at base-pair resolution. FusionMap can be applied to detect fusion junctions in both single- and paired-end dataset from either gDNA-Seq or RNA-Seq studies. FusionMap runs under both Windows and Linux (requiring MONO) environments. Although it can run on 32 bit machine, it is recommended to run on 64-bit machine with 8GB RAM or more. If you have an ArrayStudio License, you can run the fusion detection easily through its GUI.

Proper citation: FusionMap (RRID:SCR_005242) Copy   

•   Source: SciCrunch Registry

http://www.cs.helsinki.fi/en/gsa/traph/

A software tool for transcript identification and quantification with RNA-Seq. The method has a two-fold advantage: on the one hand, it translates the problem as an established one in the field of network flows, which can be solved in polynomial time, with different existing solvers; on the other hand, it is general enough to encompass many of the previous proposals under the least sum of squares model.

Proper citation: Traph (RRID:SCR_005119) Copy   

•   Source: SciCrunch Registry

http://jobs.newscientist.com/

At New Scientist Jobs you can search our database for hundreds of Science and Technology jobs from across the globe. Registration is free and you can upload your resume, set up email job alerts, subscribe to RSS feeds and apply for Science and Technology jobs online. Employers can post jobs. We also work in partnership with the science and academic community to help them recruit the right Science and Technology candidates for their vacancies online.

Proper citation: New Scientist Jobs (RRID:SCR_005155) Copy   

•   Source: SciCrunch Registry

http://www.raetschlab.org/suppl/rquant

Software for quantitative detection of alternative transcripts with RNA-Seq data. The method, based on quadratic programming, estimates biases introduced by experimental settings and is thus a powerful tool to reveal and quantify novel (alternative) transcripts.

Proper citation: rQuant (RRID:SCR_005150) Copy   

•   Source: SciCrunch Registry

http://www.uku.fi/english/

University of Eastern Finland was formed through merger of two formerly independent universities, the University of Joensuu and the University of Kuopio.Public University of Eastern Finland Kuopio Campus is located in the Savilahti area.

Proper citation: University of Eastern Finland at Kuopio; Kuopio; Finland (RRID:SCR_005214) Copy   

•   Source: SciCrunch Registry