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https://github.com/atlab/TwoPhoton
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6,2023. Code used for analysis of TwoPhoton data.
Proper citation: TwoPhoton (RRID:SCR_003596) Copy
http://www.broad.mit.edu/mpr/lung
Data set of a molecular taxonomy of lung carcinoma, the leading cause of cancer death in the United States and worldwide. Using oligonucleotide microarrays, researchers analyzed mRNA expression levels corresponding to 12,600 transcript sequences in 186 lung tumor samples, including 139 adenocarcinomas resected from the lung. Hierarchical and probabilistic clustering of expression data defined distinct sub-classes of lung adenocarcinoma. Among these were tumors with high relative expression of neuroendocrine genes and of type II pneumocyte genes, respectively. Retrospective analysis revealed a less favorable outcome for the adenocarcinomas with neuroendocrine gene expression. The diagnostic potential of expression profiling is emphasized by its ability to discriminate primary lung adenocarcinomas from metastases of extra-pulmonary origin. These results suggest that integration of expression profile data with clinical parameters could aid in diagnosis of lung cancer patients.
Proper citation: Classification of Human Lung Carcinomas by mRNA Expression Profiling Reveals Distinct Adenocarcinoma Sub-classes (RRID:SCR_003010) Copy
http://mrtools.mgh.harvard.edu/index.php/TBR
A tool for functional connectivity analysis of fcMRI data that maps functional data from individual sessions onto a priori spatial components from group level parcellations.
Proper citation: Template Based Rotation (RRID:SCR_012157) Copy
https://compumedicsneuroscan.com/products/by-name/curry/
Processing software for multimodal neuroimaging centered on combining functional data such as EEG and MEG with imaging data from MRI and CT to optimize source reconstruction. They are now combining Curry's strength with the acquisition and signal processing features of the SCAN software for a comprehensive EEG acquisition, data analysis, source localization and source imaging package.
Proper citation: CURRY (RRID:SCR_009546) Copy
http://openbabel.org/wiki/Main_Page
Software toolbox that is used to convert, analyze, or store data from molecular modeling, chemistry, biochemistry and other related areas. This software is used to read, write, and convert into over 110 chemical file formats.
Proper citation: Open Babel (RRID:SCR_014920) Copy
https://www.keyence.co.jp/products/microscope/fluorescence-microscope/bz-x700/models/bz-h3a/
Software tool as analysis application BZ-H3A by Keyence, Osaka, Japan for fluorescence microscope BZ-X series.
Proper citation: BZ-H3A analyzer software (RRID:SCR_017375) Copy
Center for Computational Biology as a joint research center in the McKusick-Nathans Institute of Genetic Medicine, spanning the School of Medicine, the Whiting School of Engineering, the Bloomberg School of Public Health, and the Krieger School of Arts & Sciences. Multidisciplinary center dedicated to research on genomics, genetics, DNA sequencing technology, and computational methods for DNA and RNA sequence analysis.
Proper citation: Center for Computational Biology at JHU (RRID:SCR_016680) Copy
http://www.reproducibleimaging.org
Center to help neuroimaging researchers to find and share data in FAIR fashion, to describe their data and analysis workflows in replicable fashion, to manage their computational resource options so that outcomes of neuroimaging research are more reproducible.
Proper citation: ReproNim: A Center for Reproducible Neuroimaging Computation (RRID:SCR_016001) Copy
Software designed for analysis of microscopy data. It performs sub-pixel precision detection, quantification of cells and fluorescence signals, as well as other image analysis functions.
Proper citation: Oufti (RRID:SCR_016244) Copy
https://www.silkscientific.com/gel-analysis.htm
Software package for densitometry measurements of electrophoresis gels by Silk Scientific Inc. Gel analysis software. Turns scanner into gel densitometer. Works with most image formats (TIFF, JPG, BMP, GIF, etc.) from any scanner, digital camera, or other image source. Can quantify Western blots, Agarose gels, PCR gels, TLC.
Proper citation: UN-SCAN-IT Gel Analysis Software (RRID:SCR_017291) Copy
https://github.com/YuanXue1993/SegAN
Image analysis software for medical image segmentation. The software is fueled by an end-to-end adversarial neural network that generates segmentation label maps.
Proper citation: SegAN (RRID:SCR_016215) Copy
https://www.essenbioscience.com/en/products/software/incucyte-chemotaxis-software/
IncuCyte™ Chemotaxis Cell Migration Software by Essen Bioscience. Add on software module for IncuCyte ZOOM® live cell analysis system. To analyze label free and fluorescently labeled chemotactic cell migration images acquired using ClearView Chemotaxis Plate.
Proper citation: IncuCyte® Chemotaxis Software (RRID:SCR_017316) Copy
Software integrated platform used for obtaining 3D structural information from single particle cryo-EM data. Enables automated, high quality and high-throughput structure discovery of proteins, viruses and molecular complexes for research and drug discovery.
Proper citation: cryoSPARC (RRID:SCR_016501) Copy
Platform for reproducible research. Code base for publishing data. For merging science and cyberinfrastructure pathways. Data Infrastructure Building Block (DIBBS) initiative to build scalable, open source, web-based, multi-user platform for reproducible research enabling creation, publication, and execution of tales – executable research objects that capture data, code, and complete software environment used to produce research findings. To enable researchers to define and create computational environment to manage complete conduct of computational experiments and expose them for analysis and reproducibility.
Proper citation: Whole Tale (RRID:SCR_017537) Copy
https://github.com/fritzsedlazeck/Sniffles
Software tool as structural variation caller using third generation sequencing (PacBio or Oxford Nanopore). It detects all types of SVs (10bp+) using evidence from split-read alignments, high-mismatch regions, and coverage analysis. Used to avoid single molecule long read sequencing high error rates.
Proper citation: Sniffles (RRID:SCR_017619) Copy
https://app.terra.bio/#workspaces/pathogen-genomic-surveillance/COVID-19
Broad Terra cloud workspace for best practices with COVID-19 genomics data. Raw COVID-19 sequencing data from NCBI Sequence Read Archive. Workflows for genome assembly, quality control, metagenomic classification, and aggregate statistics.
Proper citation: Broad Terra cloud commons for pathogen surveillance (RRID:SCR_018278) Copy
Software tool for image analysis by Cytiva. Automated image analysis software for general purpose electrophoresis gel, blot, arrays and colony counting.
Proper citation: Image Quant TL (RRID:SCR_018374) Copy
https://www.mbfbioscience.com/stereo-investigator-whole-slide-edition
Software tool for quantitative analysis using stereology on whole slide images. Used to analyze whole slide image data. Includes number, length, area and volume analyses.
Proper citation: Stereo Investigator - Whole Slide Edition (RRID:SCR_017667) Copy
https://www.indicalab.com/halo/
Software image analysis platform for quantitative tissue analysis in digital pathology by Indica Labs. Used for high-throughput, quantitative tissue analysis in oncology, neuroscience, metabolism, toxicology.
Proper citation: HALO (RRID:SCR_018350) Copy
Open source Java based image processing software program designed for scientific multidimensional images. ImageJ has been transformed to ImageJ2 application to improve data engine to be sufficient to analyze modern datasets.
Proper citation: ImageJ (RRID:SCR_003070) Copy
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