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https://github.com/vinguyenle/k-FLBPCM-method

Software tool as novel k-FLBPCM method for detecting morphologically similar crops and weeds based on combination of contour masks and Local Binary Pattern operators.

Proper citation: k-FLBPCM method (RRID:SCR_017973) Copy   

•   Source: SciCrunch Registry

http://www.fruitfly.org

Database on the sequence of the euchromatic genome of Drosophila melanogaster In addition to genomic sequencing, the BDGP is 1) producing gene disruptions using P element-mediated mutagenesis on a scale unprecedented in metazoans; 2) characterizing the sequence and expression of cDNAs; and 3) developing informatics tools that support the experimental process, identify features of DNA sequence, and allow us to present up-to-date information about the annotated sequence to the research community. Resources * Universal Proteomics Resource: Search for clones for expression and tissue culture * Materials: Request genomic or cDNA clones, library filters or fly stocks * Download Sequence data sets and annotations in fasta or xml format by http or ftp * Publications: Browse or download BDGP papers * Methods: BDGP laboratory protocols and vector maps * Analysis Tools: Search sequences for CRMs, promoters, splice sites, and gene predictions * Apollo: Genome annotation viewer and editor September 15, 2009 Illumina RNA-Seq data from 30 developmental time points of D. melanogaster has been submitted to the Short Read Archive at NCBI as part of the modENCODE project. The data set currently contains 2.2 billion single-end and paired reads and over 201 billion base pairs.

Proper citation: Berkeley Drosophila Genome Project (RRID:SCR_013094) Copy   

•   Source: SciCrunch Registry

https://www.cellosaurus.org/

Database of all cell lines used in biomedical research which include immortalized cell lines, naturally immortal cell lines (stem cells), widely used and distributed finite life cell lines, vertebrate cell lines (majority being human, mouse, and rat), and invertebrate (insects and ticks) cell lines, as well as cell line synonyms. Each cell line is provided with the following information: the recommended name (the name which appears in the original publication), a list of synonyms, a unique accession number, comments on a number of topics including misspellings and gene transfection, information on the tissue/organ origin with the UBERON code, the NCI Thesaurus or Orphanet ORDO code for the disease(s) the individual suffered from (for cancer and human genetic disease lines only), the species of origin, the parent cell line, cross-references of sister cell lines, the sex of the individual, the category in which the cell line belongs (Adult stem cell; Cancer cell line; Embryonic stem cell; Factor-dependent cell line; Finite cell line; Hybrid cell line; Hybridoma; Induced pluripotent stem cell; Spontaneously immortalized cell line; Stromal cell line; Telomerase immortalized cell line; Transformed cell line; Undefined cell line type), web links, publication references, and/or cross-references to cell line catalogs/collections, ontologies, cell lines databases/resources, and to databases that list cell lines as samples.

Proper citation: Cellosaurus (RRID:SCR_013869) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/sfmproject/

Structure from motion algorithms repository. Common interface for various sfm algorithms.

Proper citation: SFMProject (RRID:SCR_014166) Copy   

•   Source: SciCrunch Registry

http://mloss.org/software/

A software repository which provides open source software for machine learning. Software entries include information such as author, license, data format, and programming language. The ultimate goal of mloss.org is to create a comprehensive open source machine learning environment where open source machine learning software can compete with comercial closed source solutions.

Proper citation: machine learning open source software (RRID:SCR_013990) Copy   

•   Source: SciCrunch Registry

http://www.cancer.gov/researchandfunding

Federal government agency for cancer research and training established in 1937. National Cancer Program is responsibility of NCI to coordinate, conduct and support research, training, health information dissemination with respect to cause, diagnosis, prevention, and treatment of cancer, rehabilitation from cancer, and continuing care of cancer patients and families of cancer patients. Supports construction of laboratories, clinics, and related facilities necessary for cancer research through award of grants.

Proper citation: National Cancer Institute (RRID:SCR_011176) Copy   

•   Source: SciCrunch Registry

https://github.com/ChristophRau/wMICA

Weighted implementation of Maximal Information Component Analysis, a co-expression network analysis algorithm for analysis of large interconnected networks and the identification of modules of similarly-acting nodes within the larger network.

Proper citation: wMICA (RRID:SCR_015490) Copy   

•   Source: SciCrunch Registry

http://www.dbemt.bioinfo-minzhao.org/

Database to establish comprehnsive gene resource for epithelial-mesenchymal transition.

Proper citation: dbEMT 2 (RRID:SCR_024692) Copy   

•   Source: SciCrunch Registry

https://github.com/yhoogstrate/dr-disco

Software tool fo detecting genomic breakpoints of fusion transcripts in random hexamer RNA-seq data. Used for detection of exonic, intronic and intergenic fusion transcripts and their genomic breakpoints in poly(A)+ and rRNA-minus RNA sequencing data.

Proper citation: Dr. Disco (RRID:SCR_021739) Copy   

•   Source: SciCrunch Registry

http://carbonyldb.missouri.edu/CarbonylDB/index.php/

Curated data resource of protein carbonylation sites.Manually curated data resource of experimentally confirmed carbonylated proteins and sites.Provides information on other related resources such as list of other oxidative protein modification databases, list of protein oxidation and carbonylation prediction tools.

Proper citation: CarbonylDB (RRID:SCR_023924) Copy   

•   Source: SciCrunch Registry

https://rockd.org/

Map database allows to record your geological observations and uses your location to provide spatially informed suggestions for nearby geologic units, time intervals, and fossils.

Proper citation: rockd (RRID:SCR_024431) Copy   

•   Source: SciCrunch Registry

https://github.com/ZhenjiangFan/DAG-deepVASE

Software tool for identifying nonlinear causal relations and estimating their effect size help to understand complex disease pathobiology.

Proper citation: DAG-deepVASE (RRID:SCR_023612) Copy   

•   Source: SciCrunch Registry

https://github.com/lapphe/raspberry_rat

Software Python platform for recording, converting, and uploading videos to cloud and for performing scheduled video recordings. Repository also includes wiki section with comprehensive guide to setting up Raspberry Pis for this purpose. Raspberry Pis are often cheaper than camcorder and can produce HD video. They are also equipped with infrared camera, making them ideal for recordings of animals that are active in low light conditions.

Proper citation: Rasberry rat (RRID:SCR_023467) Copy   

•   Source: SciCrunch Registry

https://github.com/PIEFoundry/Microfabrication/wiki/Parylene-MEA-Fabrication

Parylene MEA Fabrication is related to SPARC. Repository for standard fabrication procedure for Parylene C microelectrode arrays and similar devices.

Proper citation: HORNET CENTER FOR AUTONOMIC NERVE RECORDING AND STIMULATION SYSTEMS (RRID:SCR_023681) Copy   

•   Source: SciCrunch Registry

https://pypi.org/

Software repository for Python programming language.Used to find and install software developed and shared by Python community.

Proper citation: PyPI (RRID:SCR_023145) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/FilterFFPE/

Software R package to find and filter artificial chimeric reads specifically generated in next generation sequencing process of formalin fixed paraffin embedded tissues. These artificial chimeric reads can lead to large number of false positive structural variant calls. Artifact chimeric read filter to improve SV detection in FFPE samples.

Proper citation: FilterFFPE (RRID:SCR_021086) Copy   

•   Source: SciCrunch Registry

https://sparrow-data.org/

Software for managing geochemical data created by individual geochronology laboratory. Designed for flexibility and extensibility, so that it can be tailored to the needs of individual analytical labs that manage wide variety of data. Database set up for metadata tracking.

Proper citation: Sparrow-data (RRID:SCR_024432) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/DrugSim2DR/

Software R package to predict drug functional similarity to drug repurposing.

Proper citation: DrugSim2DR (RRID:SCR_024564) Copy   

•   Source: SciCrunch Registry

https://github.com/bioinfo-center-pasteur-fr/toppred

Software tool for membrane protein structure prediction.Transmembrane topology prediction.Used for predicting topology of bacterial inner membrane proteins.

Proper citation: toppred (RRID:SCR_024385) Copy   

•   Source: SciCrunch Registry

https://github.com/paulgeeleher/pRRophetic

Software R package for prediction of clinical chemotherapeutic response from tumor gene expression levels. Used to predict phenotypes from gene expression microarray data, gene expression microarray data,

Proper citation: pRRophetic (RRID:SCR_024417) Copy   

•   Source: SciCrunch Registry