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https://github.com/caleblareau/mgatk
Software python-based command line interface for processing .bam files with mitochondrial reads and generating high-quality heteroplasmy estimation from sequencing data. This package places a special emphasis on mitochondrial genotypes generated from single-cell genomics data, primarily mtscATAC-seq, but is generally applicable across other assays.
Proper citation: mgatk (RRID:SCR_021159) Copy
Commercial provider of innovative DNA extraction technologies and products for life science research. Reagents for preparation of DNA from mouse tails, ear pieces, yolk sac, and culture cells, DNA extracts, DNA markers.
Proper citation: Viagen Biotech (RRID:SCR_017106) Copy
https://sils.fnwi.uva.nl/bcb/Object-Image/object-image.html
Image analysis software package that allows non-destructive image marking, input for further image processing, and marking the results of automatic measurements. Object-Image integrates measurements, macros, graphical objects and image names in a closed unit called 'object file' so that it reduces file clutter.
Proper citation: Object-Image (RRID:SCR_015720) Copy
Center that is part of the NIH Library of Integrated Network-based Cellular Signatures (LINCS) Program. Its goals are to collect and disseminate data and analytical tools needed to understand how human cells respond to perturbation by drugs, the environment, and mutation.
Proper citation: HMS LINCS Center (RRID:SCR_016370) Copy
Portal of NCATS (the National Center for Advancing Translational Sciences) for drug development information including:US approved drugs, marketed drugs, investigational drugs. Provides manually curated data supplied by the FDA and private companies. Provides drugs marketing and regulatory status, drug ingredient definitions, biological activity and clinical use.
Proper citation: Inxight (RRID:SCR_016490) Copy
https://github.com/MikkelSchubert/paleomix
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software toolkit for the processing of ancient and modern HTS data. PALEOMIX also aids in metagenomic analysis of the extracts from the HTS processing.
Proper citation: PALEOMIX (RRID:SCR_015057) Copy
Web portal for the administration of Norwegian e-Infrastructure for Life Sciences. Enables Norwegian life scientists and their international collaborators to store, share, archive, and analyse their genomics scale data. NeLS is one of the packages of the ELIXIR.NO project.
Proper citation: NeLS (RRID:SCR_016301) Copy
https://www.ars-grin.gov/npgs/
Cooperative effort by U.S. state and federal government and private organizations to preserve the genetic diversity of plants. The NPGS aids scientists and the need for genetic diversity by acquiring, preserving, evaluating, documenting and distributing crop germplasm. The NPGS is managed by the Agricultural Research Service (ARS), the in-house research agency of the United States Department of Agriculture (USDA). Funding for the NPGS comes primarily through appropriations from the U.S. Congress.
Proper citation: National Plant Germplasm System (NPGS) (RRID:SCR_016785) Copy
Open community of researchers, educators, and professionals with goal of improving way we develop, share, use, and re-use agent based and computational models for study of social and ecological systems. Develops and maintains CoMSES Model Library, digital repository that supports discovery and good practices for software citation, digital preservation, reproducibility, and reuse.
Proper citation: CoMSES Net (RRID:SCR_017598) Copy
http://www.vilber.de/en/products/analysis-software/capt-software/
Software for molecular weight, quantification of bands, colony counting and distance calculation in Vilber Lourmat gel documentation imaging systems. Used in molecular biology laboratories.
Proper citation: CAPT (RRID:SCR_016305) Copy
Library with storage capacity of over million compounds possessing diversified structures. Coupled with this library will be advanced sample handling, information management and quality control systems. As important material and information resource, CNCL will work with both domestic and international stakeholders to promote sustained development of Chinese pharmaceutical industry.
Proper citation: Chinese National Compound Library (RRID:SCR_018723) Copy
https://www.southernbiotech.com/
Commercial antibody company that focuses on the development, production, purification, conjugation, and commercialization of antibodies.
Proper citation: SouthernBiotech (RRID:SCR_019250) Copy
A manufacturer of early discovery research products including antibodies, recombinant proteins, ELISA kits, second step reagents and other life sciences products.
Proper citation: Leinco Technologies (RRID:SCR_019252) Copy
https://www.med.upenn.edu/cbica/captk/
Software platform for analysis of radiographic cancer images. Used as quantitative imaging analytics for precision diagnostics and predictive modeling of clinical outcome.
Proper citation: Cancer Imaging Phenomics Toolkit (RRID:SCR_017323) Copy
Open Source software package for digital pathology image analysis. Used for whole slide image analysis and digital pathology. Provides researchers with batch processing and scripting functionality, and extensible platform with which to develop and share new algorithms to analyze complex tissue images.
Proper citation: QuPath (RRID:SCR_018257) Copy
Software toolbox for quantitative MRI in neuroscience and clinical research. Open source and flexible tool for qMRI data handling and processing. Allows estimation of high quality multi parameter qMRI maps followed by spatial registration in common space for statistical analysis.
Proper citation: hMRI-toolbox (RRID:SCR_017682) Copy
https://chlorobox.mpimp-golm.mpg.de/geseq.html
Software tool for rapid and accurate annotation of organelle genomes, in particular chloroplast genomes.
Proper citation: GeSeq (RRID:SCR_017336) Copy
http://www.gelifesciences.co.kr/wp-content/uploads/2016/08/IN-Cell-Developer-Toolbox-v1.9.pdf
Image analysis software for developing new cellular assay analysis routines. This software provides a selection of advanced segmentation, pre-processing and post-postprocessing tools.
Proper citation: INCell Developer Toolbox (RRID:SCR_015790) Copy
https://www.nest-initiative.org
Incorporated as non-profit member based organization promoting scientfic collaboration in computational neuroscience.Advances computational neuroscience by pushing limits of large scale simulations of biologically realistic neuronal networks.
Proper citation: NEST Initiative (RRID:SCR_020978) Copy
https://github.com/berenslab/mini-atlas
Phenotypic variation of transcriptomic cell types in mouse motor cortex.Repository contains analysis code and preprocessed data.Data includes exonic and intronic gene counts, extracted electrophysiological features, extracted morphological features and z-profiles. Datasets with recorded at room temperature and recorded at physiological temperature.
Proper citation: BarensLab Mini-Atlas (RRID:SCR_021115) Copy
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