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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.
Project to determine the gene expression profiles of normal, precancer, and cancer cells, whose generated resources are available to the cancer community. Interconnected modules provide access to all CGAP data, bioinformatic analysis tools, and biological resources allowing the user to find in silico answers to biological questions in a fraction of the time it once took in the laboratory. * Genes * Tissues * Pathways * RNAi * Chromosomes * SAGE Genie * Tools
Proper citation: Cancer Genome Anatomy Project (RRID:SCR_003072) Copy
https://github.com/WorkflowConversion/CTDopts
Software gives your command-line tools a CTD-compatible interface. Module for enabling tools with CTD reading/writing, argument parsing, validating and manipulating capabilities.
Proper citation: CTDopts (RRID:SCR_023997) Copy
https://github.com/jkbonfield/htscodecs/
Software repository implements the custom CRAM codecs used for "EXTERNAL" block types.Custom compression for CRAM custom algorithm written to compress the BAM file format for DNA sequencing data.
Proper citation: Htscodecs (RRID:SCR_024034) Copy
https://github.com/conda/conda-package-handling
Software to create and extract conda packages of various formats.
Proper citation: conda-package-handling (RRID:SCR_023991) Copy
http://www.cbcb.umd.edu/software/ELPH/index.shtml
Software tool as general purpose Gibbs sampler for finding motifs in set of DNA or protein sequences.Takes as input a set containing sequences, and searches through them for the most common motif, assuming that each sequence contains one copy of the motif. Used to find patterns such as ribosome binding sites (RBSs) and exon splicing enhancers (ESEs).
Proper citation: ELPH (RRID:SCR_024011) Copy
https://github.com/PacificBiosciences/unanimity
Software to generate highly accurate single molecule consensus reads.
Proper citation: CCS (RRID:SCR_024379) Copy
https://github.com/cancerit/alleleCount
Software package to prevent code duplication. Support code for NGS copy number algorithms. Generates count of coverage of each allele ACGT at that location given any filter settings.
Proper citation: alleleCount (RRID:SCR_023961) Copy
https://github.com/mateidavid/fast5
Software C++ library for accessing Oxford Nanopore Technologies sequencing data.
Proper citation: Fast5 Library (RRID:SCR_024023) Copy
Software provides command line interface and Python API for working with Biological Observation Matrix files.
Proper citation: python-biom-format (RRID:SCR_024193) Copy
http://www.well.ox.ac.uk/happy/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software package for Multipoint QTL Mapping in Genetically Heterogeneous Animals (entry from Genetic Analysis Software) The method is implemented in a C-program and there is now an R version of HAPPY. You can run HAPPY remotely from their web server using your own data (or try it out on the data provided for download).
Proper citation: Happy (RRID:SCR_001395) Copy
Software toolkit for gray scale medical image analysis. Provides combination of command line tools, plug-ins, and libraries that make it possible to run image processing tasks interactively in command shell and prototype algorithms as shell scripts. MIA is build around a plug-in structure that makes it easy to add functionality without compromising the original code base, and it makes use of wide variety of external libraries that provide additional functionality.
Proper citation: MIA (RRID:SCR_024081) Copy
http://code.google.com/p/pbsim/
Software that simulates PacBio reads by using either a model-based or sampling-based simulation.
Proper citation: PBSIM (RRID:SCR_002512) Copy
https://www.hgmd.cf.ac.uk/ac/introduction.php?lang=english
Curated database of known (published) gene lesions responsible for human inherited disease.
Proper citation: Human Gene Mutation Database (RRID:SCR_001621) Copy
A system providing resolvable persistent Uniform Resource Identifiers (URIs) used to identify data for the scientific community, with a current focus on the Life Sciences domain. The provision of resolvable identifiers (URLs) fits well with the Semantic Web vision, and the Linked Data initiative. It provides direct access to the identified data using one chosen physical location (or resource). If more than one physical locations providing the data are recorded in the Registry, then you can access them via the top banner or by using a profile.
Proper citation: Identifiers.org (RRID:SCR_003735) Copy
https://github.com/smajidian/phaseme
Software tool set to assess quality of per read phasing information and help to reduce errors during this process.
Proper citation: PhaseME (RRID:SCR_018739) Copy
https://github.com/bionitio-team/bionitio
Open source software tool to provide template for command line bioinformatics tools in various programming languages. Program reads one or more input FASTA files, computes variety of statistics on each file, and prints tabulated output. Used as basis for learning and as foundation for starting new projects.
Proper citation: Bionitio (RRID:SCR_017259) Copy
http://sourceforge.net/projects/ipig/
Standalone software tool for the integration of peptide identifications from mass spectrometry experiments into existing genome browser visualizations.
Proper citation: iPiG (RRID:SCR_016164) Copy
https://github.com/smithlabcode/riborex
Software R package for identification of differential translation from Ribo-seq data. Computational tool for mapping genome wide differences in translation efficiency.
Proper citation: riborex (RRID:SCR_019104) Copy
https://github.com/anuprulez/galaxy_tool_recommendation
Software developed by analyzing workflows composed by researchers on European Galaxy server, using deep learning approach. Used to recommend tools in Galaxy. Gated recurrent units neural network.
Proper citation: Tool recommender system in Galaxy (RRID:SCR_018491) Copy
https://github.com/DReichLab/AdmixTools
Software package that supports formal tests of whether admixture occurred, and makes it possible to infer admixture proportions and dates.
Proper citation: ADMIXTOOLS (RRID:SCR_018495) Copy
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