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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
http://lilab.stanford.edu/SNPiR/
Software for reliable Identification of Genomic Variants Using RNA-seq Data.
Proper citation: SNPiR (RRID:SCR_000557) Copy
http://paleogenomics.irmacs.sfu.ca/FPSAC/
Sogftware for fast Phylogenetic Scaffolding of Ancient Contigs.
Proper citation: FPSAC (RRID:SCR_000555) Copy
http://bbc.mdc-berlin.de/software
Multi-purpose SNV calling software enhanced by probabilistic integration of quality scores.
Proper citation: ACCUSA2 (RRID:SCR_000558) Copy
https://code.google.com/p/dysc/
Software for Greedy Clustering of 16S rRNA Reads which uses a dynamic seeding strategy.
Proper citation: DySC (RRID:SCR_000553) Copy
https://sourceforge.net/projects/popbam/
A tool to perform evolutionary or population-based analyses of next-generation sequencing data. POPBAM takes a BAM file as its input and can compute many widely used evolutionary genetics measures in sliding windows across a genome.
Proper citation: POPBAM (RRID:SCR_000464) Copy
http://drfast.sourceforge.net/
A software which maps di-base reads (SOLiD color space reads) to reference genome assemblies in a fast and memory-efficient manner.
Proper citation: drFAST (RRID:SCR_000586) Copy
http://genome.crg.es/software/gfftools/GFF2PS.html
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software program for visualizing annotations of genomic sequences. The program has features such as the ability to create comprehensive plots, customizable parameters, and flexibility in file format.
Proper citation: Genome BioInformatics Research Lab - gff2ps (RRID:SCR_000462) Copy
http://bioinfo2.ugr.es/NGSmethPipe/
A software tool which generates high-quality methylation maps.
Proper citation: NGSmethPipe (RRID:SCR_000583) Copy
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
https://github.com/holtjma/msbwt
A software package for creating, merging, and querying multi-string BWTs.
Proper citation: msbwt (RRID:SCR_000458) Copy
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
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
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
A division of the Stanford University Libraries, which produces the online versions of journals and other scholarly content.
Proper citation: HighWire Press (RRID:SCR_000761) Copy
http://trace.ddbj.nig.ac.jp/dor/index_e.html
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6,2023. Archival database of functional genomics data generated by microarray and highly parallel new generation sequencers. Data are exchanged between ArrayExpress at EBI and DOR in common MAGE-TAB format. Supports MIAME and MINSEQE-compliant data submissions. DOR issues accession numbers, E-DORD-n to experiment and A-DORD-n to array design. DOR exchanges public data with the EBI ArrayExpress in common MAGE-TAB format. Note: At present, DOR does not accept submissions. DDBJ will announce launch of DOR when it is ready. (2013/01/31) The data can be kept private until your paper is published. You can set the hold date for a maximum of 1 year and can change it. Registered records are released according to the Data Release Policy.
Proper citation: DDBJ Omics Archive (RRID:SCR_000597) Copy
http://www.broadinstitute.org/cancer/cga/contest
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 8,2025. A software tool (and method) for estimating the amount of cross-sample contamination in next generation sequencing data.
Proper citation: ContEst (RRID:SCR_000595) Copy
http://www.helsinki.fi/bsg/software/BEBaC/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software for Bayesian estimation of bacterial communities.
Proper citation: BEBaC (RRID:SCR_000621) Copy
http://bioconductor.org/packages/release/bioc/html/flipflop.html
Software that discovers which isoforms of a gene are expressed in a given sample together with their abundances, based on RNA-Seq read data.
Proper citation: FlipFlop (RRID:SCR_000625) Copy
A wiki where users of the Gene Ontology can contribute and view notes about how specific GO terms are used. GONUTS can also be used as a GO term browser, or to search for GO annotations of specific genes from included organisms. The rationale for this wiki is based on helping new users of the gene ontology understand and use it. The GONUTS wiki is not an official product of the the Gene Ontology consortium. The GO consortium has a public wiki at their website, http://wiki.geneontology.org/. Maintaining the ontology involves many decisions to carefully choose terms and relationships. These decisions are currently made at GO meetings and via online discussion using the GO mailing lists and the Sourceforge curator request tracker. However, it is difficult for someone starting to use GO to understand these decisions. Some insight can be obtained by mining the tracker, the listservs and the minutes of GO meetings, but this is difficult, as these discussions are often dispersed and sometimes don't contain the GO accessions in the relevant messages. Wikis provide a way to create collaboratively written documentation for each GO term to explain how it should be used, how to satisfy the true path requirement, and whether an annotation should be placed at a different level. In addition, the wiki pages provide a discussion space, where users can post questions and discuss possible changes to the ontology. GONUTS is currently set up so anyone can view or search, but only registered users can edit or add pages. Currently registered users can create new users, and we are working to add at least one registered user for each participating database (So far we have registered users at EcoliHub, EcoCyc, GOA, BeeBase, SGD, dictyBase, FlyBase, WormBase, TAIR, Rat Genome Database, ZFIN, MGI, UCL and AgBase...
Proper citation: GONUTS (RRID:SCR_000653) Copy
https://bitbucket.org/dkessner/forqs
Software for forward-in-time population genetics simulation that tracks individual haplotype chunks as they recombine each generation. It also also models quantitative traits and selection on those traits.
Proper citation: forqs (RRID:SCR_000643) Copy
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